@article{chaudhary_breeding_2026,
	title = {Breeding for climate adaptation: genetic variation and genomic selection for drought response in {Scots} pine},
	volume = {27},
	issn = {1471-2164},
	shorttitle = {Breeding for climate adaptation},
	url = {https://doi.org/10.1186/s12864-026-12849-x},
	doi = {10.1186/s12864-026-12849-x},
	abstract = {Drought intensity and frequency are increasing under global warming in the boreal forests, and breeding for drought resistance will facilitate adaptation of new planting material to changing climate conditions. We used a tree-ring dataset of 559 individuals to study Scots pine genetic variation and the efficiency of genomic selection of drought-response traits (drought resistance, recovery and resilience), for the first time. From genotyping-by-sequencing (GBS), 31,101 SNPs were generated and used for the study.},
	language = {en},
	number = {1},
	urldate = {2026-04-30},
	journal = {BMC Genomics},
	author = {Chaudhary, Rajiv and Estravis Barcala, Maximiliano and Fundova, Irena and Funda, Tomas and Chen, Zhi-qiang and Wu, Harry X.},
	month = apr,
	year = {2026},
	keywords = {Climate adaptation, Dendroecology, Drought, GBS, Genomic selection, Scots pine},
	pages = {416},
}

Drought intensity and frequency are increasing under global warming in the boreal forests, and breeding for drought resistance will facilitate adaptation of new planting material to changing climate conditions. We used a tree-ring dataset of 559 individuals to study Scots pine genetic variation and the efficiency of genomic selection of drought-response traits (drought resistance, recovery and resilience), for the first time. From genotyping-by-sequencing (GBS), 31,101 SNPs were generated and used for the study.

@article{carlsson_cross-generational_2026,
	title = {Cross-generational decline in genomic selection accuracy in {Norway} spruce ({Picea} abies ({L}.) {H}. {Karst}) and strategies to mitigate it},
	volume = {37},
	issn = {1993-0607},
	url = {https://doi.org/10.1007/s11676-026-02108-w},
	doi = {10.1007/s11676-026-02108-w},
	abstract = {Genomic selection (GS) could be used to reduce the long cycle time for tree breeding. This assumes that marker-based predictions are sufficiently accurate without phenotypes. We evaluated GS across two linked generations of Norway spruce (Picea abies (L.) H. Karst), the first consisting of 954 plus-trees (G0) and the second of 956 progeny trees representing 34 full-sib families (G1), using 16 clonal field trials across mid- and southern Sweden. Both generations were measured for height and genotyped using a 50 K SNP chip array. Cross-validations within and across generations were compared. GS efficiency was evaluated using global prediction accuracy and within-family predictive ability, using GBLUP with phenotypes for independent validation. We used computer simulations to emulate the experimental data and repeat the same analysis under different assumptions of effective population size. Additional simulations were performed to investigate the cross-generation GS accuracy in future generations. Simulations assuming a historical effective population size of 1000 or 5000, together with experimental results, indicate that prediction accuracy decreased by 49–76\% for global prediction and by 15–65\% for within-family prediction when G1 was predicted from G0, compared with cross-validation within the G1 generation. Increasing the relatedness at the expense of training set size increased global accuracy but decreased within-family accuracy. Simulations of advanced generations showed that training on multiple generations increases GS accuracy, both for global and within-family prediction. Access to multiple generations for training and/or a higher density of markers may be recommended to increase accuracy for cross-generation and within-family GS in conifers.},
	language = {en},
	number = {1},
	urldate = {2026-08-10},
	journal = {Journal of Forestry Research},
	author = {Carlsson, Edward A. and Hallingbäck, Henrik R. and Ahlinder, Jon and Suontama, Mari and Wu, Harry X.},
	month = aug,
	year = {2026},
	keywords = {AlphaSimR, Cross-generation, Genomic selection (GS), Norway spruce, Within-family prediction},
	pages = {172},
}

Genomic selection (GS) could be used to reduce the long cycle time for tree breeding. This assumes that marker-based predictions are sufficiently accurate without phenotypes. We evaluated GS across two linked generations of Norway spruce (Picea abies (L.) H. Karst), the first consisting of 954 plus-trees (G0) and the second of 956 progeny trees representing 34 full-sib families (G1), using 16 clonal field trials across mid- and southern Sweden. Both generations were measured for height and genotyped using a 50 K SNP chip array. Cross-validations within and across generations were compared. GS efficiency was evaluated using global prediction accuracy and within-family predictive ability, using GBLUP with phenotypes for independent validation. We used computer simulations to emulate the experimental data and repeat the same analysis under different assumptions of effective population size. Additional simulations were performed to investigate the cross-generation GS accuracy in future generations. Simulations assuming a historical effective population size of 1000 or 5000, together with experimental results, indicate that prediction accuracy decreased by 49–76% for global prediction and by 15–65% for within-family prediction when G1 was predicted from G0, compared with cross-validation within the G1 generation. Increasing the relatedness at the expense of training set size increased global accuracy but decreased within-family accuracy. Simulations of advanced generations showed that training on multiple generations increases GS accuracy, both for global and within-family prediction. Access to multiple generations for training and/or a higher density of markers may be recommended to increase accuracy for cross-generation and within-family GS in conifers.

@article{feng_development_2026,
	title = {Development of a 50 {K} liquid-phased array for {Chinese} fir and its application in genomic selection},
	volume = {249},
	issn = {0926-6690},
	url = {https://www.sciencedirect.com/science/article/pii/S0926669026011581},
	doi = {10.1016/j.indcrop.2026.123771},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species for artificial plantations in China and has been subject to genetic improvement since the 1950s. Conventional breeding programs for this species are constrained by long generation cycles, therefore low genetic improvement per year. Genomic selection (GS) offers a novel and effective strategy for the genetic improvement of Chinese fir. However, the large size and complex genomic structure of Chinese fir make whole-genome resequencing (WGRS) costly for large breeding populations. Therefore, there is an urgent need to develop a cost-effective, efficient, and stable genotyping platform to facilitate genomic improvement in this species. In this study, the CunLa50K SNP array was developed based on WGRS data from 548 Chinese fir individuals spanning the species range. The array comprises 49,861 high-quality, uniformly distributed SNPs and 715 functional SNPs that are significantly associated with growth, wood properties, and bioclimatic traits. Performance evaluation showed an average coverage rate of 98.14\%, an average sequencing depth of 93.16 × , and a technical replicate concordance rate of 99.24\%. The array accurately identified kinship relationships and mismatched samples during pedigree verification. The genomic based best linear unbiased prediction (GBLUP) model achieved 100\% and 94.5\% of the prediction accuracy demonstrated by the conventional ABLUP model for the traits of diameter at breast height (DBH) and wood density (WD), respectively. This study provides a key technological tool for high-throughput genotyping and establishes a foundation for a GS breeding system in Chinese fir, facilitating a paradigm shift in its breeding strategy from phenotypic-based selection towards DNA-based selection.},
	urldate = {2026-07-24},
	journal = {Industrial Crops and Products},
	author = {Feng, Qihang and Li, Xueyu and Wu, Jinzhang and Niu, Diewei and Su, Shunde and Wu, Harry X. and Bian, Liming and Chen, Zhi-Qiang},
	month = jul,
	year = {2026},
	keywords = {Chinese fir, Genomic selection, Liquid-phased array, SNP},
	pages = {123771},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species for artificial plantations in China and has been subject to genetic improvement since the 1950s. Conventional breeding programs for this species are constrained by long generation cycles, therefore low genetic improvement per year. Genomic selection (GS) offers a novel and effective strategy for the genetic improvement of Chinese fir. However, the large size and complex genomic structure of Chinese fir make whole-genome resequencing (WGRS) costly for large breeding populations. Therefore, there is an urgent need to develop a cost-effective, efficient, and stable genotyping platform to facilitate genomic improvement in this species. In this study, the CunLa50K SNP array was developed based on WGRS data from 548 Chinese fir individuals spanning the species range. The array comprises 49,861 high-quality, uniformly distributed SNPs and 715 functional SNPs that are significantly associated with growth, wood properties, and bioclimatic traits. Performance evaluation showed an average coverage rate of 98.14%, an average sequencing depth of 93.16 × , and a technical replicate concordance rate of 99.24%. The array accurately identified kinship relationships and mismatched samples during pedigree verification. The genomic based best linear unbiased prediction (GBLUP) model achieved 100% and 94.5% of the prediction accuracy demonstrated by the conventional ABLUP model for the traits of diameter at breast height (DBH) and wood density (WD), respectively. This study provides a key technological tool for high-throughput genotyping and establishes a foundation for a GS breeding system in Chinese fir, facilitating a paradigm shift in its breeding strategy from phenotypic-based selection towards DNA-based selection.

@article{feng_genetic_2026,
	title = {Genetic structure and diversity of four {Chinese} fir breeding populations over 60 years},
	volume = {22},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-026-01750-z},
	doi = {10.1007/s11295-026-01750-z},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species in southern China. Since 2015, the Fujian Province has launched its fourth cycle of genetic improvement, yet the impact of intensive artificial selection for growth and wood quality traits on the genetic diversity of advanced-cycle populations remains unclear. In this study, genotyping-by-sequencing (GBS) was used to genotype 310 individuals sampled from four consecutive breeding populations (first to fourth cycle). Across cycles, diversity indices remained relatively stable, with the fourth-cycle population showing slightly higher values (Ho = 0.325, He = 0.272). The broadening of breeding objectives to include wood quality and resistance traits, together with the introduction of external elite germplasm from the second cycle onward, may have contributed to this balance. Consequently, genetic differentiation among the populations from different breeding cycles was minimal (Fst {\textless} 0.01). Comparison of the genomic and pedigree-based relationship matrices revealed discrepancies for some pairs, indicating that genomic estimates provide complementary information for characterizing relatedness. Overall, genetic diversity was maintained across the four breeding cycles. These results provide a genomic basis for managing genetic diversity and relatedness in advanced-cycle Chinese fir breeding.},
	language = {en},
	number = {5},
	urldate = {2026-09-02},
	journal = {Tree Genetics \& Genomes},
	author = {Feng, Qihang and Chen, Zhi-Qiang and Zhao, Benwen and Zhang, Long and Su, Shunde and Zhang, Xie and Chen, Yu and El-Kassaby, Yousry A. and Wu, Harry X. and Bian, Liming},
	month = aug,
	year = {2026},
	keywords = {Breeding population, Chinese fir, Genetic diversity, Genomic kinship},
	pages = {29},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most commercially important conifer species in southern China. Since 2015, the Fujian Province has launched its fourth cycle of genetic improvement, yet the impact of intensive artificial selection for growth and wood quality traits on the genetic diversity of advanced-cycle populations remains unclear. In this study, genotyping-by-sequencing (GBS) was used to genotype 310 individuals sampled from four consecutive breeding populations (first to fourth cycle). Across cycles, diversity indices remained relatively stable, with the fourth-cycle population showing slightly higher values (Ho = 0.325, He = 0.272). The broadening of breeding objectives to include wood quality and resistance traits, together with the introduction of external elite germplasm from the second cycle onward, may have contributed to this balance. Consequently, genetic differentiation among the populations from different breeding cycles was minimal (Fst \textless 0.01). Comparison of the genomic and pedigree-based relationship matrices revealed discrepancies for some pairs, indicating that genomic estimates provide complementary information for characterizing relatedness. Overall, genetic diversity was maintained across the four breeding cycles. These results provide a genomic basis for managing genetic diversity and relatedness in advanced-cycle Chinese fir breeding.

@article{wu_integrating_2026,
	title = {Integrating {GWAS}-guided markers preselection with genomic selection enhances prediction of pulpwood-related traits in slash pine ({Pinus} elliottii {Englem}.)},
	volume = {26},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-09114-4},
	doi = {10.1186/s12870-026-09114-4},
	abstract = {This study aimed to enhance the efficiency of genomic prediction for pulpwood-related traits in slash pine (Pinus elliottii Engelm. var. elliottii) by integrating genome-wide association study (GWAS) information with genomic selection (GS). We evaluated 12 traits related to growth, fiber, and wood chemical composition in a population of 340 individuals genotyped with 319,286 high-quality SNPs, comparing the performance of six GS models, including GBLUP and Bayesian methods, under varying training population sizes and marker densities. The results showed that while both GBLUP and Bayesian Lasso performed well, Bayesian Lasso slightly outperformed GBLUP for fiber traits. Predictive ability (PA) plateaued at approximately 100 K SNPs for fiber traits, 60 K for DBH, and 10 K for wood chemical composition traits in all models. Using 100 K random SNPs, PA ranged from 0.05 to 0.23, which expanded to 0.09–0.35 with GWAS-guided SNP preselection (maximum improvement of 16.26\%) and further broadened to 0.01–0.38 by incorporating large-effect QTLs (greatest improvement of 23.54\%). Overall, integrating GWAS information into GS frameworks significantly improved prediction accuracy as assessed by t-test, offering a cost-effective strategy to accelerate genetic improvement. These findings provide practical guidance for enhancing breeding efficiency in slash pine and other conifer breeding programs.},
	language = {en},
	number = {1},
	urldate = {2026-08-17},
	journal = {BMC Plant Biology},
	author = {Wu, Yadi and Ding, Xianyin and Diao, Shu and Huang, Qinyun and Shang, Guiqi and Tan, Zifeng and Wu, Shaoze and Hua, Xiahui and He, Chengbo and Luan, Qifu and Chen, Zhi-Qiang and Wu, Harry X.},
	month = may,
	year = {2026},
	keywords = {Bayesian Lasso, Genomic selection, Pulpwood properties, SNP preselection, Slash pine},
	pages = {1271},
}

This study aimed to enhance the efficiency of genomic prediction for pulpwood-related traits in slash pine (Pinus elliottii Engelm. var. elliottii) by integrating genome-wide association study (GWAS) information with genomic selection (GS). We evaluated 12 traits related to growth, fiber, and wood chemical composition in a population of 340 individuals genotyped with 319,286 high-quality SNPs, comparing the performance of six GS models, including GBLUP and Bayesian methods, under varying training population sizes and marker densities. The results showed that while both GBLUP and Bayesian Lasso performed well, Bayesian Lasso slightly outperformed GBLUP for fiber traits. Predictive ability (PA) plateaued at approximately 100 K SNPs for fiber traits, 60 K for DBH, and 10 K for wood chemical composition traits in all models. Using 100 K random SNPs, PA ranged from 0.05 to 0.23, which expanded to 0.09–0.35 with GWAS-guided SNP preselection (maximum improvement of 16.26%) and further broadened to 0.01–0.38 by incorporating large-effect QTLs (greatest improvement of 23.54%). Overall, integrating GWAS information into GS frameworks significantly improved prediction accuracy as assessed by t-test, offering a cost-effective strategy to accelerate genetic improvement. These findings provide practical guidance for enhancing breeding efficiency in slash pine and other conifer breeding programs.

@article{zhu_mmgs_2026,
	title = {{MMGS}: a novel genomic prediction framework to integrate genotype, environment and their interactions for multi-environment breeding trials},
	volume = {13},
	issn = {2662-6810},
	shorttitle = {{MMGS}},
	url = {https://doi.org/10.1093/hr/uhag035},
	doi = {10.1093/hr/uhag035},
	abstract = {Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-environments genomic selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.},
	number = {5},
	urldate = {2026-05-15},
	journal = {Horticulture Research},
	author = {Zhu, Mingjia and Zheng, Zeyu and Liu, Wei and Han, Yu and Mou, Wenjie and Yin, Tongming and Dai, Xiaogang and Wu, Huaitong and Yang, Yongzhi and Zan, Yanjun and Liu, Jianquan},
	month = may,
	year = {2026},
	pages = {uhag035},
}

Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-environments genomic selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.

@article{soro_minimum_2026,
	title = {Minimum marker densities for accurate genomic predictions and heritability estimates in three major {North} {American} and {European} spruce species},
	volume = {135},
	copyright = {2026 His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources and the Authors},
	issn = {1365-2540},
	url = {https://www.nature.com/articles/s41437-026-00836-7},
	doi = {10.1038/s41437-026-00836-7},
	abstract = {Genomic selection (GS) is being increasingly used in tree breeding with the aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by resampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 and 8000 SNPs for a spruce genome size of around 2000 centimorgans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such minimum marker densities should be financially affordable for most spruce breeding programs, striking a balance between the need for maximizing GS accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes.},
	language = {en},
	number = {5},
	urldate = {2026-05-29},
	journal = {Heredity},
	publisher = {Nature Publishing Group},
	author = {Soro, André and Lenz, Patrick and Beaulieu, Jean and Laverdière, Jean-Philippe and Nadeau, Simon and Gagnon, France and Ogut, Funda and Wu, Harry X. and Perron, Martin and Bousquet, Jean},
	month = may,
	year = {2026},
	keywords = {Comparative genomics, Ecological genetics, Forestry},
	pages = {342--357},
}

Genomic selection (GS) is being increasingly used in tree breeding with the aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by resampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 and 8000 SNPs for a spruce genome size of around 2000 centimorgans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such minimum marker densities should be financially affordable for most spruce breeding programs, striking a balance between the need for maximizing GS accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes.

@article{yang_natural_2026,
	title = {Natural selection and recombination interact to structure genome-wide variation in pines},
	volume = {126},
	copyright = {© 2026 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.70866},
	doi = {10.1111/tpj.70866},
	abstract = {Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions—genomic valleys—remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species—Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.},
	language = {en},
	number = {1},
	urldate = {2026-04-24},
	journal = {The Plant Journal},
	author = {Yang, Chen-Jui and Funda, Tomas and Chaudhary, Rajiv and Chen, Zhi-Qiang and Barcala, Maximiliano Estravis and Wu, Harry},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.70866},
	keywords = {Pinus, comparative genomics, conifer genome, genomic landscapes, long gene, natural selection, recombination},
	pages = {e70866},
}

Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions—genomic valleys—remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species—Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.

@article{liu_genome_2025,
	title = {Genome and transcriptome analysis provide insights into the genetics and breeding of {Salix} suchowensis growth traits},
	volume = {56},
	issn = {1573-5095},
	url = {https://doi.org/10.1007/s11056-025-10132-7},
	doi = {10.1007/s11056-025-10132-7},
	abstract = {Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.},
	language = {en},
	number = {6},
	urldate = {2025-11-07},
	journal = {New Forests},
	author = {Liu, Wei and Gu, Shaobo and Zhu, Mingjia and Han, Yu and Dai, Xiaogang and Wu, Huaitong and Yin, Tongming and Guo, Linjie and Feng, Landi and Zan, Yanjun and Liu, Jianquan},
	month = oct,
	year = {2025},
	keywords = {Breeding prediction, Ground diameter, Plant height, QTL, QTL-by-environment interactions, Salix suchowensis},
	pages = {63},
}

Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.

@article{ding_insights_2025,
	title = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis: {Integrating} high-throughput phenotyping, {GWAS}, and transgenic studies},
	volume = {300},
	issn = {0141-8130},
	shorttitle = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis},
	url = {https://www.sciencedirect.com/science/article/pii/S0141813025002776},
	doi = {10.1016/j.ijbiomac.2025.139728},
	abstract = {Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph\_c0), PeGLYCOSYLTRANSFERASE (c160167.graph\_c0), PeASIL2 (c324347.graph\_c0), and PeERF168 (c311225.graph\_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.},
	urldate = {2025-01-31},
	journal = {International Journal of Biological Macromolecules},
	author = {Ding, Xianyin and Diao, Shu and Zhang, Yini and Luan, Qifu and Li, Yanjie and Jiang, Jingmin and Wu, Harry X.},
	month = apr,
	year = {2025},
	keywords = {GWAS, High-throughput phenotyping, Slash pine, Terpene biosynthesis, eQTL mapping},
	pages = {139728},
}

Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph_c0), PeGLYCOSYLTRANSFERASE (c160167.graph_c0), PeASIL2 (c324347.graph_c0), and PeERF168 (c311225.graph_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.

@article{aro_multivariate_2025,
	title = {Multivariate models improve accuracy of genomic prediction for spring frost tolerance in {Norway} spruce},
	volume = {18},
	copyright = {© 2025 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.},
	issn = {1940-3372},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/tpg2.70151},
	doi = {10.1002/tpg2.70151},
	abstract = {Warming spring temperatures increase the risk of frost damage to emerging Norway spruce (Picea abies) buds by advancing their spring phenology and increasing the frost event frequency. We present a field-based electrolyte leakage assay to assess basal frost tolerance in newly emerging buds. Using this assay, we estimated genetic parameters and tested the effectiveness of multivariate genomic selection (GS) models integrating frost tolerance, bud burst phenology, and height growth. Multivariate models significantly improved frost tolerance prediction accuracy, particularly when incorporating bud burst data, due to a strong genetic correlation between traits (r ≈ –0.63) and high heritability of bud burst (h2 ≈ 0.60). The observed genetic correlations suggest that early-flushing genotypes exhibit higher tolerance to spring frost. Our findings underscore the importance of basal frost tolerance as a complementary trait to traditional phenological frost-avoidance strategies. Additionally, we emphasize that early-stage bud burst assessments in controlled environments can accelerate genomic predictions, overcoming the limitations imposed by long growth cycles. Integrating multi-trait genomic prediction models optimized with bud burst as an assisting trait and optimized model parameters enhances prediction accuracy of spring frost tolerance and supports the development of climate-resilient breeding strategies in Norway spruce.},
	language = {en},
	number = {4},
	urldate = {2025-11-28},
	journal = {The Plant Genome},
	author = {Aro, Tuuli and Tan, Biyue and Chen, Zhi-Qiang and Hallingbäck, Henrik and Suontama, Mari and Westin, Johan and Wu, Harry and Hurry, Vaughan},
	year = {2025},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.1002/tpg2.70151},
	pages = {e70151},
}

Warming spring temperatures increase the risk of frost damage to emerging Norway spruce (Picea abies) buds by advancing their spring phenology and increasing the frost event frequency. We present a field-based electrolyte leakage assay to assess basal frost tolerance in newly emerging buds. Using this assay, we estimated genetic parameters and tested the effectiveness of multivariate genomic selection (GS) models integrating frost tolerance, bud burst phenology, and height growth. Multivariate models significantly improved frost tolerance prediction accuracy, particularly when incorporating bud burst data, due to a strong genetic correlation between traits (r ≈ –0.63) and high heritability of bud burst (h2 ≈ 0.60). The observed genetic correlations suggest that early-flushing genotypes exhibit higher tolerance to spring frost. Our findings underscore the importance of basal frost tolerance as a complementary trait to traditional phenological frost-avoidance strategies. Additionally, we emphasize that early-stage bud burst assessments in controlled environments can accelerate genomic predictions, overcoming the limitations imposed by long growth cycles. Integrating multi-trait genomic prediction models optimized with bud burst as an assisting trait and optimized model parameters enhances prediction accuracy of spring frost tolerance and supports the development of climate-resilient breeding strategies in Norway spruce.

@article{diao_development_2024,
	title = {Development of 51 {K} liquid-phased probe array for {Loblolly} and {Slash} pines and its application to {GWAS} of {Slash} pine breeding population},
	volume = {216},
	issn = {0926-6690},
	doi = {10.1016/j.indcrop.2024.118777},
	abstract = {Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26\% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers. © 2024 Elsevier B.V.},
	language = {English},
	journal = {Industrial Crops and Products},
	author = {Diao, S. and Ding, X. and Luan, Q. and Chen, Z.-Q. and Wu, H.X. and Li, X. and Zhang, Y. and Sun, J. and Wu, Y. and Zou, L.-H. and Jiang, J.},
	month = sep,
	year = {2024},
	keywords = {Candidate gene, Genetic variation, Genotyping by target sequencing, In-solution probe, SNPs},
}

Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers. © 2024 Elsevier B.V.

@article{hayatgheibi_implications_2024,
	title = {Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in {Norway} spruce},
	volume = {25},
	issn = {2730-6844},
	url = {https://doi.org/10.1186/s12863-024-01241-x},
	doi = {10.1186/s12863-024-01241-x},
	abstract = {Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).},
	number = {1},
	urldate = {2024-07-01},
	journal = {BMC Genomic Data},
	author = {Hayatgheibi, Haleh and Hallingbäck, Henrik R. and Lundqvist, Sven-Olof and Grahn, Thomas and Scheepers, Gerhard and Nordström, Peter and Chen, Zhi-Qiang and Kärkkäinen, Katri and Wu, Harry X. and García-Gil, M. Rosario},
	month = jun,
	year = {2024},
	keywords = {Cross-validation, Norway spruce, Population structure, Prediction accuracy, Wood properties},
	pages = {60},
}

Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).

@article{climent_trade-offs_2024,
	title = {Trade-offs and {Trait} {Integration} in {Tree} {Phenotypes}: {Consequences} for the {Sustainable} {Use} of {Genetic} {Resources}},
	issn = {2198-6436},
	shorttitle = {Trade-offs and {Trait} {Integration} in {Tree} {Phenotypes}},
	url = {https://doi.org/10.1007/s40725-024-00217-5},
	doi = {10.1007/s40725-024-00217-5},
	abstract = {In this review, we synthesise current knowledge on trade-offs among traits in key fitness dimensions and identify major research gaps with the intention of laying the groundwork for a rapid advance in tree breeding for multiple objectives as a key contribution to the sustainability of planted forests in the future.},
	language = {en},
	urldate = {2024-04-02},
	journal = {Current Forestry Reports},
	author = {Climent, Jose and Alía, Ricardo and Karkkainen, Katri and Bastien, Catherine and Benito-Garzon, Marta and Bouffier, Laurent and De Dato, Giovanbattista and Delzon, Sylvain and Dowkiw, Arnaud and Elvira-Recuenco, Margarita and Grivet, Delphine and González-Martínez, Santiago C. and Hayatgheibi, Haleh and Kujala, Sonja and Leplé, Jean-Charles and Martín-Sanz, Ruth C. and de Miguel, Marina and Monteverdi, M. Cristina and Mutke, Sven and Plomion, Christophe and Ramírez-Valiente, José Alberto and Sanchez, Leopoldo and Solé-Medina, Aida and Soularue, Jean-Paul and Steffenrem, Arne and Teani, Angela and Westin, Johan and Whittet, Richard and Wu, Harry and Zas, Rafael and Cavers, Stephen},
	month = mar,
	year = {2024},
	keywords = {Breeding, Forest trees, Global change, Phenotypic integration, Resilience, Trade-offs},
}

In this review, we synthesise current knowledge on trade-offs among traits in key fitness dimensions and identify major research gaps with the intention of laying the groundwork for a rapid advance in tree breeding for multiple objectives as a key contribution to the sustainability of planted forests in the future.

@article{estravis_barcala_whole-genome_2024,
	title = {Whole-genome resequencing facilitates the development of a {50K} single nucleotide polymorphism genotyping array for {Scots} pine ({Pinus} sylvestris {L}.) and its transferability to other pine species},
	volume = {117},
	copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535},
	doi = {10.1111/tpj.16535},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84\%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.},
	language = {en},
	number = {3},
	urldate = {2024-02-02},
	journal = {The Plant Journal},
	author = {Estravis Barcala, Maximiliano and van der Valk, Tom and Chen, Zhiqiang and Funda, Tomas and Chaudhary, Rajiv and Klingberg, Adam and Fundova, Irena and Suontama, Mari and Hallingbäck, Henrik and Bernhardsson, Carolina and Nystedt, Björn and Ingvarsson, Pär K. and Sherwood, Ellen and Street, Nathaniel and Gyllensten, Ulf and Nilsson, Ove and Wu, Harry X.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535},
	keywords = {Pinus sylvestris, SNP array, genome resequencing, genome-wide association studies, genomic selection, pines},
	pages = {944--955},
}

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

@article{zhao_development_2023,
	title = {Development of an {Advanced}-{Generation} {Multi}-{Objective} {Breeding} {Population} for the 4th {Cycle} of {Chinese} {Fir} ({Cunninghamia} lanceolata ({Lamb}.) {Hook}.)},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/14/8/1658},
	doi = {10.3390/f14081658},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is an important timber species native to southern China. While the single, unstructured breeding strategy was employed in the past three cycles of breeding, it is no longer adequate for managing a more advanced breeding population. In this study, we utilized restriction-site-associated DNA-sequencing (RAD-seq) to estimate the genetic diversity of breeding populations and phenotypic values or breeding values to estimate the genetic gain of hundred-grain weight, diameter at breast height, and wood basic density. To achieve a balance between genetic gain and genetic diversity, we combined the multiple populations and core-main populations methods to construct the fourth cycle breeding population. Finally, the fourth cycle breeding population was made up of a core population of 50 individuals with an inbreeding coefficient of {\textasciitilde}0, and an additional main population of 183 individuals, with an effective population size of 108. Crossings made within and/or between different trait-targeted subpopulations could facilitate bidirectional gene flow between the core and main populations, depending on the breeding objectives. This structured breeding population of Chinese fir could aim for both short- and long-term genetic gains and has the potential to support the preservation of germplasm resources for future climate change.},
	language = {en},
	number = {8},
	urldate = {2023-09-06},
	journal = {Forests},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Zhao, Benwen and Bian, Liming and Feng, Qihang and Wu, Jinzhang and Zhang, Xuefeng and Zheng, Renhua and Zheng, Xueyan and Yang, Zhiyuan and Chen, Zhiqiang and Wu, Harry X. and Shi, Jisen},
	month = aug,
	year = {2023},
	note = {Number: 8},
	keywords = {Chinese fir, SNP, breeding population, genetic diversity, genetic gain},
	pages = {1658},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is an important timber species native to southern China. While the single, unstructured breeding strategy was employed in the past three cycles of breeding, it is no longer adequate for managing a more advanced breeding population. In this study, we utilized restriction-site-associated DNA-sequencing (RAD-seq) to estimate the genetic diversity of breeding populations and phenotypic values or breeding values to estimate the genetic gain of hundred-grain weight, diameter at breast height, and wood basic density. To achieve a balance between genetic gain and genetic diversity, we combined the multiple populations and core-main populations methods to construct the fourth cycle breeding population. Finally, the fourth cycle breeding population was made up of a core population of 50 individuals with an inbreeding coefficient of ~0, and an additional main population of 183 individuals, with an effective population size of 108. Crossings made within and/or between different trait-targeted subpopulations could facilitate bidirectional gene flow between the core and main populations, depending on the breeding objectives. This structured breeding population of Chinese fir could aim for both short- and long-term genetic gains and has the potential to support the preservation of germplasm resources for future climate change.

@article{xiao_natural_2023,
	title = {Natural variation in the prolyl 4-hydroxylase gene {PtoP4H9} contributes to perennial stem growth in {Populus}},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad212},
	doi = {10.1093/plcell/koad212},
	abstract = {Perennial trees must maintain stem growth throughout their entire lifespan to progressively increase in size as they age. The overarching question of the molecular mechanisms that govern stem perennial growth in trees remains largely unanswered. Here we deciphered the genetic architecture that underlies perennial growth trajectories using genome-wide association studies (GWAS) for measures of growth traits across years in a natural population of Populus tomentosa. By analyzing the stem growth trajectory, we identified PtoP4H9, encoding prolyl 4-hydroxylase 9, which is responsible for the natural variation in the growth rate of diameter at breast height (DBH) across years. Quantifying the dynamic genetic contribution of PtoP4H9 loci to stem growth showed that PtoP4H9 played a pivotal role in stem growth regulation. Spatiotemporal expression analysis showed that PtoP4H9 was highly expressed in cambium tissues of poplars of various ages. Overexpression and knockdown of PtoP4H9 revealed that it altered cell expansion to regulate cell wall modification and mechanical characteristics, thereby promoting stem growth in Populus. We showed that natural variation in PtoP4H9 occurred in a BASIC PENTACYSTEINE transcription factor PtoBPC1-binding promoter element controlling PtoP4H9 expression. The geographic distribution of PtoP4H9 allelic variation was consistent with the modes of selection among populations. Altogether, our study provides important genetic insights into dynamic stem growth in Populus, and we confirmed PtoP4H9 as a potential useful marker for breeding or genetic engineering of poplars.},
	number = {11},
	urldate = {2023-11-10},
	journal = {The Plant Cell},
	author = {Xiao, Liang and Fang, Yuanyuan and Zhang, He and Quan, Mingyang and Zhou, Jiaxuan and Li, Peng and Wang, Dan and Ji, Li and Ingvarsson, Pär K and Wu, Harry X and El-Kassaby, Yousry A and Du, Qingzhang and Zhang, Deqiang},
	month = nov,
	year = {2023},
	pages = {4046--4065},
}

Perennial trees must maintain stem growth throughout their entire lifespan to progressively increase in size as they age. The overarching question of the molecular mechanisms that govern stem perennial growth in trees remains largely unanswered. Here we deciphered the genetic architecture that underlies perennial growth trajectories using genome-wide association studies (GWAS) for measures of growth traits across years in a natural population of Populus tomentosa. By analyzing the stem growth trajectory, we identified PtoP4H9, encoding prolyl 4-hydroxylase 9, which is responsible for the natural variation in the growth rate of diameter at breast height (DBH) across years. Quantifying the dynamic genetic contribution of PtoP4H9 loci to stem growth showed that PtoP4H9 played a pivotal role in stem growth regulation. Spatiotemporal expression analysis showed that PtoP4H9 was highly expressed in cambium tissues of poplars of various ages. Overexpression and knockdown of PtoP4H9 revealed that it altered cell expansion to regulate cell wall modification and mechanical characteristics, thereby promoting stem growth in Populus. We showed that natural variation in PtoP4H9 occurred in a BASIC PENTACYSTEINE transcription factor PtoBPC1-binding promoter element controlling PtoP4H9 expression. The geographic distribution of PtoP4H9 allelic variation was consistent with the modes of selection among populations. Altogether, our study provides important genetic insights into dynamic stem growth in Populus, and we confirmed PtoP4H9 as a potential useful marker for breeding or genetic engineering of poplars.

@article{chen_preselection_2023,
	title = {Preselection of {QTL} markers enhances accuracy of genomic selection in {Norway} spruce},
	volume = {24},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-023-09250-3},
	doi = {10.1186/s12864-023-09250-3},
	abstract = {Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1\% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 – 13 associations were observed and the PVE of the strongest effects ranged from 1.2\% to 2.0\%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000–4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5\%.},
	number = {1},
	urldate = {2023-04-11},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Klingberg, Adam and Hallingbäck, Henrik R. and Wu, Harry X.},
	month = mar,
	year = {2023},
	keywords = {GWAS, Genomic prediction, Marker preselection, Picea abies},
	pages = {147},
}

Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 – 13 associations were observed and the PVE of the strongest effects ranged from 1.2% to 2.0%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000–4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5%.

@article{li_methylation_2023,
	title = {The methylation landscape of giga-genome and the epigenetic timer of age in {Chinese} pine},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-37684-6},
	doi = {10.1038/s41467-023-37684-6},
	abstract = {DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.},
	language = {en},
	number = {1},
	urldate = {2023-04-21},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Li, Jiang and Han, Fangxu and Yuan, Tongqi and Li, Wei and Li, Yue and Wu, Harry X. and Wei, Hairong and Niu, Shihui},
	month = apr,
	year = {2023},
	note = {Number: 1},
	keywords = {Agricultural genetics, DNA methylation, Plant development, Plant genetics},
	pages = {1--11},
}

DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.

@article{kang_pan-genome_2023,
	title = {The pan-genome and local adaptation of {Arabidopsis} thaliana},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-42029-4},
	doi = {10.1038/s41467-023-42029-4},
	abstract = {Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.},
	language = {en},
	number = {1},
	urldate = {2026-05-19},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Kang, Minghui and Wu, Haolin and Liu, Huanhuan and Liu, Wenyu and Zhu, Mingjia and Han, Yu and Liu, Wei and Chen, Chunlin and Song, Yan and Tan, Luna and Yin, Kangqun and Zhao, Yusen and Yan, Zhen and Lou, Shangling and Zan, Yanjun and Liu, Jianquan},
	month = oct,
	year = {2023},
	keywords = {Evolutionary biology, Natural variation in plants, Plant evolution, Structural variation},
	pages = {6259},
}

Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.

@article{wu_threatened_2023,
	title = {Threatened forests},
	volume = {24},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.15252/embr.202357106},
	doi = {10.15252/embr.202357106},
	abstract = {Climate change is having dramatic effects on forest health and growth ? tree genomics provides tools for understanding and mitigating these effects.},
	number = {5},
	urldate = {2023-05-12},
	journal = {EMBO reports},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Wu, Harry and Nilsson, Ove},
	month = may,
	year = {2023},
	pages = {e57106},
}

Climate change is having dramatic effects on forest health and growth ? tree genomics provides tools for understanding and mitigating these effects.

@article{ding_transcriptome-based_2022,
	title = {A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population},
	volume = {18},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010017},
	doi = {10/gpn67c},
	abstract = {Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3\% to 21.8\% and from 10.6\% to 16.7\%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.},
	language = {en},
	number = {2},
	urldate = {2022-03-03},
	journal = {PLOS Genetics},
	author = {Ding, Xianyin and Diao, Shu and Luan, Qifu and Wu, Harry X. and Zhang, Yini and Jiang, Jingmin},
	month = feb,
	year = {2022},
	keywords = {Gene expression, Genetics, Genome-wide association studies, Phenotypes, Phylogenetic analysis, Pines, Single nucleotide polymorphisms, Transcriptome analysis},
	pages = {e1010017},
}

Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.

@article{chen_genetic_2022,
	title = {Genetic architecture behind developmental and seasonal control of tree growth and wood properties in {Norway} spruce},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.927673/full},
	doi = {10.3389/fpls.2022.927673},
	abstract = {Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multitrait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1303 Norway spruce individuals using exome capture to cover {\textasciitilde}130K single nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a population of the mother trees. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1 which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.},
	language = {English},
	urldate = {2026-04-10},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Zhou, Linghua and Karlsson, Bo and Tuominen, Hannele and García-Gil, Maria Rosario and Wu, Harry X.},
	month = aug,
	year = {2022},
	keywords = {Developmental Stage, Norway spruce, Seasonal variation, Wood properties, genome-wide association, ⛔ No DOI found},
}

Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multitrait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1303 Norway spruce individuals using exome capture to cover ~130K single nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a population of the mother trees. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1 which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.

@article{nie_genome-wide_2022,
	title = {Genome-wide {TCP} transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in {Pinus} tabuliformis},
	volume = {22},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-022-03554-4},
	doi = {10.1186/s12870-022-03554-4},
	abstract = {Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood.},
	number = {1},
	urldate = {2022-04-08},
	journal = {BMC Plant Biology},
	author = {Nie, Yu-meng and Han, Fang-xu and Ma, Jing-jing and Chen, Xi and Song, Yi-tong and Niu, Shi-Hui and Wu, Harry X.},
	month = apr,
	year = {2022},
	keywords = {Diurnal, Gene family, Oscillation, Pinus tabuliformis, Seasonal, TCP},
	pages = {167},
}

Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood.

@article{chen_lncrna_2022,
	title = {{LncRNA} {PMAT}–{PtoMYB46} module represses {PtoMATE} and {PtoARF2} promoting {Pb2}+ uptake and plant growth in poplar},
	volume = {433},
	issn = {0304-3894},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389422005581},
	doi = {10.1016/j.jhazmat.2022.128769},
	abstract = {Lead (Pb2+) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb2+ uptake in woody plants remains unclear. Here, we identified 226 Pb2+-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb2+-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb2+ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT–PtoMYB46–PtoMATE–PtoARF2 regulatory module control Pb2+ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb2+ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.},
	language = {en},
	urldate = {2022-04-22},
	journal = {Journal of Hazardous Materials},
	author = {Chen, Panfei and Song, Yuepeng and Liu, Xin and Xiao, Liang and Bu, Chenhao and Liu, Peng and Zhao, Lei and Ingvarsson, Pär K. and Wu, Harry X. and El-Kassaby, Yousry A. and Zhang, Deqiang},
	month = jul,
	year = {2022},
	keywords = {Association genetics, Lead, Long non-coding RNAs, Phytoremediation},
	pages = {128769},
}

Lead (Pb2+) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb2+ uptake in woody plants remains unclear. Here, we identified 226 Pb2+-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb2+-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb2+ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT–PtoMYB46–PtoMATE–PtoARF2 regulatory module control Pb2+ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb2+ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.

@article{pervaiz_microrna_2022,
	title = {{MicroRNA} and {cDNA}-{Microarray} as {Potential} {Targets} against {Abiotic} {Stress} {Response} in {Plants}: {Advances} and {Prospects}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4395},
	shorttitle = {{MicroRNA} and {cDNA}-{Microarray} as {Potential} {Targets} against {Abiotic} {Stress} {Response} in {Plants}},
	url = {https://www.mdpi.com/2073-4395/12/1/11},
	doi = {10/gpjfdp},
	abstract = {Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.},
	language = {en},
	number = {1},
	urldate = {2022-02-14},
	journal = {Agronomy},
	author = {Pervaiz, Tariq and Amjid, Muhammad Waqas and El-kereamy, Ashraf and Niu, Shi-Hui and Wu, Harry X.},
	month = jan,
	year = {2022},
	keywords = {abiotic stress tolerance, adaptation, cold stress, drought stress, miRNA target gene expression, salinity stress},
	pages = {11},
}

Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.

@article{li_teasing_2022,
	title = {Teasing apart the joint effect of demography and natural selection in the birth of a contact zone},
	volume = {236},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18480},
	doi = {10.1111/nph.18480},
	abstract = {Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.},
	language = {en},
	number = {5},
	urldate = {2022-11-10},
	journal = {New Phytologist},
	author = {Li, Lili and Milesi, Pascal and Tiret, Mathieu and Chen, Jun and Sendrowski, Janek and Baison, John and Chen, Zhi-qiang and Zhou, Linghua and Karlsson, Bo and Berlin, Mats and Westin, Johan and Garcia-Gil, Maria Rosario and Wu, Harry X. and Lascoux, Martin},
	month = dec,
	year = {2022},
	keywords = {Climate change, Contact zone, Demography, Last Glacial Maximum, Local adaptation, Natural selection, Picea abies, climate change, contact zone, demography, local adaptation, natural selection},
	pages = {1976--1987},
}

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.

@article{niu_chinese_2022,
	title = {The {Chinese} pine genome and methylome unveil key features of conifer evolution},
	volume = {185},
	issn = {0092-8674, 1097-4172},
	url = {https://www.cell.com/cell/abstract/S0092-8674(21)01428-8},
	doi = {10/gnw8q5},
	abstract = {Conifers dominate the world’s forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2\% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers’ adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.},
	language = {English},
	number = {1},
	urldate = {2022-02-04},
	journal = {Cell},
	author = {Niu, Shihui and Li, Jiang and Bo, Wenhao and Yang, Weifei and Zuccolo, Andrea and Giacomello, Stefania and Chen, Xi and Han, Fangxu and Yang, Junhe and Song, Yitong and Nie, Yumeng and Zhou, Biao and Wang, Peiyi and Zuo, Quan and Zhang, Hui and Ma, Jingjing and Wang, Jun and Wang, Lvji and Zhu, Qianya and Zhao, Huanhuan and Liu, Zhanmin and Zhang, Xuemei and Liu, Tao and Pei, Surui and Li, Zhimin and Hu, Yao and Yang, Yehui and Li, Wenzhao and Zan, Yanjun and Zhou, Linghua and Lin, Jinxing and Yuan, Tongqi and Li, Wei and Li, Yue and Wei, Hairong and Wu, Harry X.},
	month = jan,
	year = {2022},
	keywords = {Chinese pine, chromosome-level genome, climate adaptation, conifer evolution, conifer reproduction, gene expression, genome expansion, long intron, methylome},
	pages = {204--217.e14},
}

Conifers dominate the world’s forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers’ adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

@article{wu_balancing_2021,
	title = {Balancing {Breeding} for {Growth} and {Fecundity} in {Radiata} {Pine} (\textit{{Pinus} radiata} {D}. {Don}) {Breeding} {Programme}},
	volume = {14},
	issn = {1752-4571, 1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/eva.13164},
	doi = {10.1111/eva.13164},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Evolutionary Applications},
	author = {Wu, Harry X. and Ker, Richard and Chen, Zhiqiang and Ivkovic, Milos},
	month = mar,
	year = {2021},
	pages = {834--846},
}

@article{chen_determination_2021,
	title = {Determination of conifer age biomarker {DAL1} interactome using {Y2H}-seq},
	volume = {1},
	copyright = {2021 The Author(s)},
	issn = {2767-3812},
	url = {http://www.maxapress.com/rticle/doi/10.48130/FR-2021-0012},
	doi = {10/gnj3pg},
	abstract = {Age is a sophisticated physiological signal that ensures the sequence of different developmental stages in organisms. The regulation of ageing pathways appears to differ between gymnosperms and angiosperms. We previously identified \textit{DAL1} as a conserved conifer age biomarker that plays a crucial role in the transition from vegetative to reproductive life-history phases in pines. Therefore, elucidating the specific interaction events related to DAL1 is key to understanding how age drives conifer development. Large-scale yeast two-hybrid (Y2H) analysis followed by next-generation high-throughput sequencing (Y2H-seq) allowed us to identify 135 PtDAL1 interacting proteins in \textit{Pinus tabuliformis}. Our study found that PtDAL1 interacting proteins showed an ageing-related module, with sophisticated interacting networks composed of transcription factors (TFs), transcriptional regulators (TRs), and kinases. These interacting proteins are produced in response to a variety of phytohormones and environmental signals, and are likely involved in wood formation, needle development, oleoresin terpenoids biosynthesis, and reproductive development. In this study, we propose a novel regulation model of conifer ageing pathways whereby PtDAL1 coordinates different environmental stimuli and interacts with corresponding proteins to regulate appropriate development.},
	language = {en},
	number = {1},
	urldate = {2021-11-22},
	journal = {Forestry Research},
	author = {Chen, Xi and Zhu, Qianya and Nie, Yumeng and Han, Fangxu and Li, Yue and Wu, Harry X. and Niu, Shihui},
	month = jul,
	year = {2021},
	pages = {1--12},
}

Age is a sophisticated physiological signal that ensures the sequence of different developmental stages in organisms. The regulation of ageing pathways appears to differ between gymnosperms and angiosperms. We previously identified DAL1 as a conserved conifer age biomarker that plays a crucial role in the transition from vegetative to reproductive life-history phases in pines. Therefore, elucidating the specific interaction events related to DAL1 is key to understanding how age drives conifer development. Large-scale yeast two-hybrid (Y2H) analysis followed by next-generation high-throughput sequencing (Y2H-seq) allowed us to identify 135 PtDAL1 interacting proteins in Pinus tabuliformis. Our study found that PtDAL1 interacting proteins showed an ageing-related module, with sophisticated interacting networks composed of transcription factors (TFs), transcriptional regulators (TRs), and kinases. These interacting proteins are produced in response to a variety of phytohormones and environmental signals, and are likely involved in wood formation, needle development, oleoresin terpenoids biosynthesis, and reproductive development. In this study, we propose a novel regulation model of conifer ageing pathways whereby PtDAL1 coordinates different environmental stimuli and interacts with corresponding proteins to regulate appropriate development.

@article{bernhardsson_development_2021,
	title = {Development of a highly efficient {50K} single nucleotide polymorphism genotyping array for the large and complex genome of {Norway} spruce ( \textit{{Picea} abies} {L}. {Karst}) by whole genome resequencing and its transferability to other spruce species},
	volume = {21},
	issn = {1755-098X, 1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13292},
	doi = {10.1111/1755-0998.13292},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Molecular Ecology Resources},
	author = {Bernhardsson, Carolina and Zan, Yanjun and Chen, Zhiqiang and Ingvarsson, Pär K. and Wu, Harry X.},
	month = apr,
	year = {2021},
	pages = {880--896},
}

@article{nguyen_effect_2021,
	title = {Effect of additive, dominant and epistatic variances on breeding and deployment strategy in {Norway} spruce},
	issn = {0015-752X},
	url = {https://doi.org/10.1093/forestry/cpab052},
	doi = {10/gnzpmt},
	abstract = {Genetic variances are important parameters and have a great impact on the determination of optimal breeding strategies of tree species. A large clonal testing program was conducted to estimate additive, dominant and epistatic variances for the development of breeding and deployment strategies in Norway spruce (Picea abies (L.) Karst.). The analysis results of genetic variation for growth and wood properties in two clonal trials in central Sweden indicated that the important sources of total genetic variation were both additive and non-additive genetic variances. Additive genetic variation accounted for the majority of total genetic variation for diameter at breast height (DBH) and wood quality traits, whereas non-additive genetic variation was significant only for tree height at an early age. Predicted genetic gain was the highest for clonal deployment based on best tested (replicated) clones (4.7–65.3 per cent), followed by clonal deployment of the best individual trees from a full-sib family trial (3.5–57.7 per cent), and the deployment of seedlings generated by open-pollination (1.9–48.3 per cent).},
	urldate = {2022-01-05},
	journal = {Forestry: An International Journal of Forest Research},
	author = {Nguyen, Hong T H and Chen, Zhi-Qiang and Fries, Anders and Berlin, Mats and Hallingbäck, Henrik R and Wu, Harry X},
	month = dec,
	year = {2021},
	pages = {cpab052},
}

Genetic variances are important parameters and have a great impact on the determination of optimal breeding strategies of tree species. A large clonal testing program was conducted to estimate additive, dominant and epistatic variances for the development of breeding and deployment strategies in Norway spruce (Picea abies (L.) Karst.). The analysis results of genetic variation for growth and wood properties in two clonal trials in central Sweden indicated that the important sources of total genetic variation were both additive and non-additive genetic variances. Additive genetic variation accounted for the majority of total genetic variation for diameter at breast height (DBH) and wood quality traits, whereas non-additive genetic variation was significant only for tree height at an early age. Predicted genetic gain was the highest for clonal deployment based on best tested (replicated) clones (4.7–65.3 per cent), followed by clonal deployment of the best individual trees from a full-sib family trial (3.5–57.7 per cent), and the deployment of seedlings generated by open-pollination (1.9–48.3 per cent).

@article{calleja-rodriguez_genomic_2021,
	title = {Genomic {Predictions} {With} {Nonadditive} {Effects} {Improved} {Estimates} of {Additive} {Effects} and {Predictions} of {Total} {Genetic} {Values} in {Pinus} sylvestris},
	volume = {12},
	issn = {1664-462X},
	doi = {10/gmhq7h},
	abstract = {Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive × additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5\% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1\%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.},
	language = {eng},
	journal = {Frontiers in Plant Science},
	author = {Calleja-Rodriguez, Ainhoa and Chen, ZhiQiang and Suontama, Mari and Pan, Jin and Wu, Harry X.},
	year = {2021},
	keywords = {dominance, epistasis, genetic gain, genomic prediction, nonadditive effects, response to selection, scots pine (Pinus sylvestris L)},
	pages = {666820},
}

Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive × additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.

@article{capador-barreto_killing_2021,
	title = {Killing two enemies with one stone? {Genomics} of resistance to two sympatric pathogens in {Norway} spruce},
	volume = {30},
	issn = {1365-294X},
	shorttitle = {Killing two enemies with one stone?},
	doi = {10.1111/mec.16058},
	abstract = {Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.},
	language = {eng},
	number = {18},
	journal = {Molecular Ecology},
	author = {Capador-Barreto, Hernán D. and Bernhardsson, Carolina and Milesi, Pascal and Vos, Ingrid and Lundén, Karl and Wu, Harry X. and Karlsson, Bo and Ingvarsson, Pär K. and Stenlid, Jan and Elfstrand, Malin},
	month = sep,
	year = {2021},
	keywords = {Basidiomycota, Genome wide association study (GWAS), Genomics, Homicide, Norway, Picea, Picea abies, Plant Diseases, cline, disease resistance, genome-wide association study, pleiotropy, root-rot},
	pages = {4433--4447},
}

Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.

@article{chen_leveraging_2021,
	title = {Leveraging breeding programs and genomic data in {Norway} spruce ({Picea} abies {L}. {Karst}) for {GWAS} analysis},
	volume = {22},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-021-02392-1},
	doi = {10.1186/s13059-021-02392-1},
	abstract = {Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Genome Biology},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Milesi, Pascal and Zhou, Linghua and Chen, Jun and Li, Lili and Cui, BinBin and Niu, Shihui and Westin, Johan and Karlsson, Bo and García-Gil, Maria Rosario and Lascoux, Martin and Wu, Harry X.},
	month = jun,
	year = {2021},
	keywords = {Budburst stage, Frost damage, Genome-wide association study, MAP3K gene, Norway spruce, Wood quality},
	pages = {179},
}

Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

@article{ma_mads-box_2021,
	title = {{MADS}-box transcription factors {MADS11} and {DAL1} interact to mediate the vegetative-to-reproductive transition in pine},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab250},
	doi = {10.1093/plphys/kiab250},
	abstract = {The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.},
	number = {1},
	urldate = {2021-10-01},
	journal = {Plant Physiology},
	author = {Ma, Jing-Jing and Chen, Xi and Song, Yi-Tong and Zhang, Gui-Fang and Zhou, Xian-Qing and Que, Shu-Peng and Mao, Fei and Pervaiz, Tariq and Lin, Jin-Xing and Li, Yue and Li, Wei and Wu, Harry X. and Niu, Shi-Hui},
	month = sep,
	year = {2021},
	pages = {247--262},
}

The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.

@article{pervaiz_transcriptional_2021,
	title = {The {Transcriptional} {Landscape} and {Hub} {Genes} {Associated} with {Physiological} {Responses} to {Drought} {Stress} in {Pinus} tabuliformis},
	volume = {22},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1422-0067/22/17/9604},
	doi = {10.3390/ijms22179604},
	abstract = {Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70\% (6163) genes had a homologous in arabidopsis, out of which 52\% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.},
	language = {en},
	number = {17},
	urldate = {2021-11-04},
	journal = {International Journal of Molecular Sciences},
	author = {Pervaiz, Tariq and Liu, Shuang-Wei and Uddin, Saleem and Amjid, Muhammad Waqas and Niu, Shi-Hui and Wu, Harry X.},
	month = jan,
	year = {2021},
	keywords = {\textit{Pinus tabuliformis}, \textit{PtNCED3}, ABA signaling, RNA-Seq, drought stress, drought-recovery},
	pages = {9604},
}

Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.

@article{chen_advantage_2020,
	title = {Advantage of clonal deployment in {Norway} spruce ({Picea} abies ({L}.) {H}. {Karst})},
	volume = {77},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-020-0920-1},
	doi = {10.1007/s13595-020-0920-1},
	abstract = {Abstract
            
              
                
                  Key message
                
              
              
                There is considerable genetic gain of tree volume from clonal deployment in Norway spruce (
                
                  Picea abies
                
                (L.) H. Karst) and clonal deployment will have at least 50\% more or double genetic gain than the seedling deployment.
              
            
            
              
                
                  Context
                
              
              Genetic parameters and genetic gains for wood quality and growth traits were estimated in six large clonal progeny trials.
            
            
              
                
                  Aims
                
              
              Develop the optimal clonal deployment strategy of Norway spruce in Sweden.
            
            
              
                
                  Methods
                
              
              Wood quality and growth traits were measured in all clonal trials and additive and non-additive genetic variances are partitioned.
            
            
              
                
                  Results
                
              
              Additive and non-additive genetic variances were equally important for growth traits while non-additive variance was small or not significant for wood quality trait. The genetic gain predicted for clonal deployment was greater than any of the other four deployment strategies. Selecting the top 1\% of tested clones (clonal forestry) would have 48.4\% and 134.6\% more gain than the gain predicted for the seedling deployment of selected full-sib families and half-sib family (family forestry), respectively, at the same selection intensity.
            
            
              
                
                  Conclusion
                
              
              This study highlights that testing of 30–40 clones per family would maximize the realized genetic gain for different clonal selection scenarios, either selecting the best ten or 20 clones without any co-ancestry restrictions or selecting the best single clone from each of the best ten or 20 families (e.g., co-ancestry restriction). Clonal mean selection and vegetative deployment are the most effective.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Chen, Zhi-Qiang and Hai, Hong Nguyen Thi and Helmersson, Andreas and Liziniewicz, Mateusz and Hallingbäck, Henrik R. and Fries, Anders and Berlin, Mats and Wu, Harry X.},
	month = mar,
	year = {2020},
	pages = {14},
}

Abstract Key message There is considerable genetic gain of tree volume from clonal deployment in Norway spruce ( Picea abies (L.) H. Karst) and clonal deployment will have at least 50% more or double genetic gain than the seedling deployment. Context Genetic parameters and genetic gains for wood quality and growth traits were estimated in six large clonal progeny trials. Aims Develop the optimal clonal deployment strategy of Norway spruce in Sweden. Methods Wood quality and growth traits were measured in all clonal trials and additive and non-additive genetic variances are partitioned. Results Additive and non-additive genetic variances were equally important for growth traits while non-additive variance was small or not significant for wood quality trait. The genetic gain predicted for clonal deployment was greater than any of the other four deployment strategies. Selecting the top 1% of tested clones (clonal forestry) would have 48.4% and 134.6% more gain than the gain predicted for the seedling deployment of selected full-sib families and half-sib family (family forestry), respectively, at the same selection intensity. Conclusion This study highlights that testing of 30–40 clones per family would maximize the realized genetic gain for different clonal selection scenarios, either selecting the best ten or 20 clones without any co-ancestry restrictions or selecting the best single clone from each of the best ten or 20 families (e.g., co-ancestry restriction). Clonal mean selection and vegetative deployment are the most effective.

@article{elfstrand_association_2020,
	title = {Association genetics identifies a specifically regulated {Norway} spruce laccase gene, {\textless}span style="font-variant:small-caps;"{\textgreater} \textit{{PaLAC5}} {\textless}/span{\textgreater} , linked to \textit{{Heterobasidion} parviporum} resistance},
	volume = {43},
	issn = {0140-7791, 1365-3040},
	shorttitle = {Association genetics identifies a specifically regulated {Norway} spruce laccase gene, {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13768},
	doi = {10.1111/pce.13768},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Elfstrand, Malin and Baison, John and Lundén, Karl and Zhou, Linghua and Vos, Ingrid and Capador, Hernan Dario and Åslund, Matilda Stein and Chen, Zhiqiang and Chaudhary, Rajiv and Olson, Åke and Wu, Harry X. and Karlsson, Bo and Stenlid, Jan and García‐Gil, María Rosario},
	month = jul,
	year = {2020},
	pages = {1779--1791},
}

@article{zhou_effect_2020,
	title = {Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of {Norway} spruce},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6737-3},
	doi = {10.1186/s12864-020-6737-3},
	abstract = {Abstract
            
              Background
              
                Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce (
                Picea abies
                (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments.
              
            
            
              Results
              GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30\% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95\% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12.
            
            
              Conclusions
              This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90\% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Zhou, Linghua and Chen, Zhiqiang and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {323},
}

Abstract Background Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce ( Picea abies (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. Results GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12. Conclusions This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.

@article{calleja-rodriguez_evaluation_2020,
	title = {Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in {Scots} pine},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07188-4},
	doi = {10.1186/s12864-020-07188-4},
	abstract = {Abstract
            
              Background
              
                Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (
                Pinus sylvestris
                L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers.
              
            
            
              Results
              Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143\% higher than the traditional pedigree-based selection.
            
            
              Conclusions
              Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50\%.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Calleja-Rodriguez, Ainhoa and Pan, Jin and Funda, Tomas and Chen, Zhiqiang and Baison, John and Isik, Fikret and Abrahamsson, Sara and Wu, Harry X.},
	month = dec,
	year = {2020},
	pages = {796},
}

Abstract Background Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine ( Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers. Results Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection. Conclusions Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.

@article{fundova_genetic_2020,
	title = {Genetic {Improvement} of {Sawn}-{Board} {Stiffness} and {Strength} in {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {20},
	issn = {1424-8220},
	url = {https://www.mdpi.com/1424-8220/20/4/1129},
	doi = {10.3390/s20041129},
	abstract = {Given an overall aim of improving Scots pine structural wood quality by selective tree breeding, we investigated the potential of non-destructive acoustic sensing tools to accurately predict wood stiffness (modulus of elasticity, MOE) and strength (modulus of rupture, MOR) of sawn boards. Non-destructive measurements of wood density (DEN), acoustic velocity (VEL) and MOE were carried out at different stages of wood processing chain (standing trees, felled logs and sawn boards), whilst destructively measured stiffness and strength served as benchmark traits. All acoustic based MOE and VEL estimates proved to be good proxies (rA {\textgreater} 0.65) for sawn-board stiffness while MOETREE, VELHIT and resistograph wood density (DENRES) measured on standing trees and MOELOG and VELFAK measured on felled logs well reflected board strength. Individual-tree narrow-sense heritability (     h i 2     ) for VEL, MOE and MOR were weak (0.05–0.26) but were substantially stronger for wood density (0.34–0.40). Moreover, additive genetic coefficients of variation for MOE and MOR were in the range from 5.4\% to 9.1\%, offering potential targets for exploitation by selective breeding. Consequently, selective breeding based on MOETREE, DENRES or stem straightness (STR) could improve several structural wood traits simultaneously.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Sensors},
	author = {Fundova, Irena and Hallingbäck, Henrik R. and Jansson, Gunnar and Wu, Harry X.},
	month = feb,
	year = {2020},
	pages = {1129},
}

Given an overall aim of improving Scots pine structural wood quality by selective tree breeding, we investigated the potential of non-destructive acoustic sensing tools to accurately predict wood stiffness (modulus of elasticity, MOE) and strength (modulus of rupture, MOR) of sawn boards. Non-destructive measurements of wood density (DEN), acoustic velocity (VEL) and MOE were carried out at different stages of wood processing chain (standing trees, felled logs and sawn boards), whilst destructively measured stiffness and strength served as benchmark traits. All acoustic based MOE and VEL estimates proved to be good proxies (rA \textgreater 0.65) for sawn-board stiffness while MOETREE, VELHIT and resistograph wood density (DENRES) measured on standing trees and MOELOG and VELFAK measured on felled logs well reflected board strength. Individual-tree narrow-sense heritability ( h i 2 ) for VEL, MOE and MOR were weak (0.05–0.26) but were substantially stronger for wood density (0.34–0.40). Moreover, additive genetic coefficients of variation for MOE and MOR were in the range from 5.4% to 9.1%, offering potential targets for exploitation by selective breeding. Consequently, selective breeding based on MOETREE, DENRES or stem straightness (STR) could improve several structural wood traits simultaneously.

@article{baison_genetic_2020,
	title = {Genetic control of tracheid properties in {Norway} spruce wood},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-72586-3},
	doi = {10.1038/s41598-020-72586-3},
	abstract = {Abstract
            
              Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (
              Picea abies
              (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are:
              Picea abies BIG GRAIN 2
              (
              PabBG2)
              with a predicted function in auxin transport and sensitivity, and
              MA\_373300g0010
              encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Baison, J. and Zhou, Linghua and Forsberg, Nils and Mörling, Tommy and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry X. and Mellerowicz, Ewa J. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {18089},
}

Abstract Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce ( Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 ( PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

@article{fundova_genetic_2020,
	title = {Genetic improvement of sawn-board shape stability in {Scots} pine ({Pinus} sylvestris {L}.)},
	volume = {157},
	issn = {09266690},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0926669020308566},
	doi = {10/gjcw67},
	language = {en},
	urldate = {2021-06-07},
	journal = {Industrial Crops and Products},
	author = {Fundova, Irena and Hallingbäck, Henrik R. and Jansson, Gunnar and Wu, Harry X.},
	month = dec,
	year = {2020},
	pages = {112939},
}

@article{funda_genetic_2020,
	title = {Genetic improvement of the chemical composition of {Scots} pine ( \textit{{Pinus} sylvestris} {L}.) juvenile wood for bioenergy production},
	volume = {12},
	issn = {1757-1693, 1757-1707},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/gcbb.12723},
	doi = {10.1111/gcbb.12723},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {GCB Bioenergy},
	author = {Funda, Tomáš and Fundová, Irena and Fries, Anders and Wu, Harry X.},
	month = oct,
	year = {2020},
	pages = {848--863},
}

@article{elfstrand_genotypic_2020,
	title = {Genotypic variation in {Norway} spruce correlates to fungal communities in vegetative buds},
	volume = {29},
	issn = {0962-1083, 1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15314},
	doi = {10.1111/mec.15314},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Molecular Ecology},
	author = {Elfstrand, Malin and Zhou, Linghua and Baison, John and Olson, Åke and Lundén, Karl and Karlsson, Bo and Wu, Harry X. and Stenlid, Jan and García‐Gil, M. Rosario},
	month = jan,
	year = {2020},
	pages = {199--213},
}

@article{funda_predicting_2020,
	title = {Predicting the chemical composition of juvenile and mature woods in {Scots} pine ({Pinus} sylvestris {L}.) using {FTIR} spectroscopy},
	volume = {54},
	issn = {0043-7719, 1432-5225},
	url = {http://link.springer.com/10.1007/s00226-020-01159-4},
	doi = {10.1007/s00226-020-01159-4},
	abstract = {Abstract
            
              The chemical composition of wood is one of the key features that determine wood quality. The focus of this study was on identifying differences between juvenile and mature woods in Scots pine (
              Pinus sylvestris
              L.) and developing models for predicting the chemical composition of these two wood types. Chemical traits, determined by traditional wet chemistry techniques, included the proportion of lignin, polysaccharides and extractives. Partial least squares regression of Fourier transform infrared (FTIR) spectra was used for model building. The model performance was primarily evaluated by root mean squared error of predictions (RMSEP). High predictive power was attained for the content of lignin (RMSEP of 0.476 and 0.495 for juvenile and mature woods, respectively) and extractives (0.302 and 0.471), good predictive power for cellulose (0.715 and 0.696) and hemicelluloses in juvenile wood (0.719) and low predictive power for hemicelluloses in mature wood (0.823). A distinct band was observed at 1693 cm
              −1
              , and its intensity was strongly associated with the content of extractives (
              r
               = 0.968 and 0.861 in juvenile and mature woods, respectively). FTIR has proved suitable for the rapid, non-destructive, cost-efficient assessment of the chemical composition of juvenile and mature woods in Scots pine. The band at 1693 cm
              −1
              is to be further investigated to unravel its link with individual extractive components.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Wood Science and Technology},
	author = {Funda, Tomas and Fundova, Irena and Gorzsás, András and Fries, Anders and Wu, Harry X.},
	month = mar,
	year = {2020},
	pages = {289--311},
}

Abstract The chemical composition of wood is one of the key features that determine wood quality. The focus of this study was on identifying differences between juvenile and mature woods in Scots pine ( Pinus sylvestris L.) and developing models for predicting the chemical composition of these two wood types. Chemical traits, determined by traditional wet chemistry techniques, included the proportion of lignin, polysaccharides and extractives. Partial least squares regression of Fourier transform infrared (FTIR) spectra was used for model building. The model performance was primarily evaluated by root mean squared error of predictions (RMSEP). High predictive power was attained for the content of lignin (RMSEP of 0.476 and 0.495 for juvenile and mature woods, respectively) and extractives (0.302 and 0.471), good predictive power for cellulose (0.715 and 0.696) and hemicelluloses in juvenile wood (0.719) and low predictive power for hemicelluloses in mature wood (0.823). A distinct band was observed at 1693 cm −1 , and its intensity was strongly associated with the content of extractives ( r  = 0.968 and 0.861 in juvenile and mature woods, respectively). FTIR has proved suitable for the rapid, non-destructive, cost-efficient assessment of the chemical composition of juvenile and mature woods in Scots pine. The band at 1693 cm −1 is to be further investigated to unravel its link with individual extractive components.

@article{dong_spatial_2020,
	title = {Spatial and competition models increase the progeny testing efficiency of {Japanese} larch},
	volume = {50},
	issn = {0045-5067, 1208-6037},
	url = {https://cdnsciencepub.com/doi/10.1139/cjfr-2020-0007},
	doi = {10/gjcxch},
	abstract = {The main purpose of this study was to examine spatial and competition effects on estimates of genetic parameters, as well as on selection options for growth traits, including height (H), diameter at breast height (DBH), and volume (V), in a progeny test of Japanese larch (Larix kaempferi (Lam.) Carrière) at age 20 years. We compared performances among the individual-tree additive genetic base model (B) with design factors only, the spatial effect model (AR1), the competition model (C), and the combined competition and spatial model (CS). We found that spatial heterogeneity had significant effects on growth traits and that plot variance decreased by more than 80\% in the AR1 model relative to the B model. Competition had significant effects on DBH and V but a smaller effect on H. In the C model, direct additive genetic variances ([Formula: see text]) for DBH and V increased by 205\% and 93\%, respectively, whereas residual variances ([Formula: see text]) decreased by 8\% and 6\%, respectively. In the CS model, the correlations between direct and competitive genetic effects were 0.83, −0.97, and −0.98 for H, DBH, and V, respectively. Competition significantly affected the forward selection. The proportions of selected elite trees were only 39\% and 25\% common between the B and CS models for DBH and V, respectively, when selection intensity was 5\%. For breeding selection, depending on thinning regimes planned, trees of high additive breeding values but low competitive breeding values are preferable for plantation.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Dong, Leiming and Xie, Yunhui and Wu, Harry X. and Sun, Xiaomei},
	month = dec,
	year = {2020},
	pages = {1373--1382},
}

The main purpose of this study was to examine spatial and competition effects on estimates of genetic parameters, as well as on selection options for growth traits, including height (H), diameter at breast height (DBH), and volume (V), in a progeny test of Japanese larch (Larix kaempferi (Lam.) Carrière) at age 20 years. We compared performances among the individual-tree additive genetic base model (B) with design factors only, the spatial effect model (AR1), the competition model (C), and the combined competition and spatial model (CS). We found that spatial heterogeneity had significant effects on growth traits and that plot variance decreased by more than 80% in the AR1 model relative to the B model. Competition had significant effects on DBH and V but a smaller effect on H. In the C model, direct additive genetic variances ([Formula: see text]) for DBH and V increased by 205% and 93%, respectively, whereas residual variances ([Formula: see text]) decreased by 8% and 6%, respectively. In the CS model, the correlations between direct and competitive genetic effects were 0.83, −0.97, and −0.98 for H, DBH, and V, respectively. Competition significantly affected the forward selection. The proportions of selected elite trees were only 39% and 25% common between the B and CS models for DBH and V, respectively, when selection intensity was 5%. For breeding selection, depending on thinning regimes planned, trees of high additive breeding values but low competitive breeding values are preferable for plantation.

@article{calleja-rodriguez_analysis_2019,
	title = {Analysis of phenotypic- and {Estimated} {Breeding} {Values} ({EBV}) to dissect the genetic architecture of complex traits in a {Scots} pine three-generation pedigree design},
	volume = {462},
	issn = {00225193},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S002251931830554X},
	doi = {10.1016/j.jtbi.2018.11.007},
	language = {en},
	urldate = {2021-06-07},
	journal = {Journal of Theoretical Biology},
	author = {Calleja-Rodriguez, Ainhoa and Li, Zitong and Hallingbäck, Henrik R. and Sillanpää, Mikko J. and Wu, Harry X. and Abrahamsson, Sara and García-Gil, Maria Rosario},
	month = feb,
	year = {2019},
	pages = {283--292},
}

@article{wu_benefits_2019,
	title = {Benefits and risks of using clones in forestry – a review},
	volume = {34},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2018.1487579},
	doi = {10.1080/02827581.2018.1487579},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Wu, Harry X.},
	month = jul,
	year = {2019},
	pages = {352--359},
}

@article{hayatgheibi_estimation_2019,
	title = {Estimation of genetic parameters, provenance performances, and genotype by environment interactions for growth and stiffness in lodgepole pine ( \textit{{Pinus} contorta} )},
	volume = {34},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2018.1542025},
	doi = {10/gjcrjm},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Fries, Anders and Kroon, Johan and Wu, Harry X.},
	month = jan,
	year = {2019},
	pages = {1--11},
}

@article{hayatgheibi_genetic_2019,
	title = {Genetic analysis of fiber-dimension traits and combined selection for simultaneous improvement of growth and stiffness in lodgepole pine ( \textit{{Pinus} contorta} )},
	volume = {49},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0445},
	doi = {10/gg486q},
	abstract = {Quantitative genetic variation of fiber-dimension traits and their relationship with diameter at breast height (DBH) and solid-wood traits (i.e., density and modulus of elasticity (MOE)) was investigated in lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.). A total of 823 increment cores were sampled from 207 half-sib families at two independent progeny trials, aged 34–35 years, located in northern Sweden. High-resolution pith-to-bark profiles were obtained for radial fiber width (RFW), tangential fiber width (TFW), fiber wall thickness (FWT), and fiber coarseness (FC) using SilviScan. Heritabilities ranged from 0.29 to 0.74, and inheritance increased with cambial maturity. Estimated age–age genetic correlations indicate that early selection between ages 5 and 8 years is highly efficient. Our results indicate that selection for a 1\% increase in DBH or MOE incurs a negligible effect on fiber-dimension traits and maximum genetic gains are reached when DBH and MOE are considered jointly. Moreover, simultaneous improvement of growth and stiffness is achievable when a selection index with 7 to 10 economical weights for MOE relative to 1 for DBH is incorporated. However, the unfavorable relationship between solid-wood traits and pulp and paper related traits suggests that breeding strategies must be implemented to improve wood quality of lodgepole pine for multiple uses.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Fries, Anders and Kroon, Johan and Wu, Harry X.},
	month = may,
	year = {2019},
	pages = {500--509},
}

Quantitative genetic variation of fiber-dimension traits and their relationship with diameter at breast height (DBH) and solid-wood traits (i.e., density and modulus of elasticity (MOE)) was investigated in lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.). A total of 823 increment cores were sampled from 207 half-sib families at two independent progeny trials, aged 34–35 years, located in northern Sweden. High-resolution pith-to-bark profiles were obtained for radial fiber width (RFW), tangential fiber width (TFW), fiber wall thickness (FWT), and fiber coarseness (FC) using SilviScan. Heritabilities ranged from 0.29 to 0.74, and inheritance increased with cambial maturity. Estimated age–age genetic correlations indicate that early selection between ages 5 and 8 years is highly efficient. Our results indicate that selection for a 1% increase in DBH or MOE incurs a negligible effect on fiber-dimension traits and maximum genetic gains are reached when DBH and MOE are considered jointly. Moreover, simultaneous improvement of growth and stiffness is achievable when a selection index with 7 to 10 economical weights for MOE relative to 1 for DBH is incorporated. However, the unfavorable relationship between solid-wood traits and pulp and paper related traits suggests that breeding strategies must be implemented to improve wood quality of lodgepole pine for multiple uses.

@article{zhou_genetic_2019,
	title = {Genetic analysis of wood quality traits in {Norway} spruce open-pollinated progenies and their parent plus trees at clonal archives and the evaluation of phenotypic selection of plus trees},
	volume = {49},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0117},
	doi = {10/gjcjw5},
	abstract = {A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h
              2
              ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h
              2
              estimate, selection of the best clones from clonal archives would be an effective alternative.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Zhou, Linghua and Chen, Zhiqiang and Lundqvist, Sven-Olof and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {810--818},
}

A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h 2 ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h 2 estimate, selection of the best clones from clonal archives would be an effective alternative.

@article{nguyen_thi_hai_genetic_2019,
	title = {Genetic improvement for essential oil yield and quality in {Melaleuca} cajuputi},
	volume = {137},
	issn = {09266690},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S092666901930411X},
	doi = {10.1016/j.indcrop.2019.05.061},
	language = {en},
	urldate = {2021-06-07},
	journal = {Industrial Crops and Products},
	author = {Nguyen Thi Hai, Hong and Rimbawanto, Anto and {Prastyono} and Kartikawati, Noor K. and Wu, Harry},
	month = oct,
	year = {2019},
	pages = {681--686},
}

@article{nguyen_genetic_2019,
	title = {Genetic improvement for wood production in {Melaleuca} cajuputi},
	volume = {31},
	issn = {01281283, 25219847},
	url = {https://info.frim.gov.my/infocenter_applications/jtfsonline/jtfs/v31n2/230-239.pdf},
	doi = {10.1080/02827581.2018.1562565},
	number = {2},
	urldate = {2021-06-07},
	journal = {JOURNAL OF TROPICAL FOREST SCIENCE},
	author = {Nguyen, Thh and Konda, R and Kieu, Td and Tran, Tc and Phung, Vk and Tran, Th and Wu, Hx},
	month = may,
	year = {2019},
	pages = {230--239},
}

@article{baison_genomewide_2019,
	title = {Genome‐wide association study identified novel candidate loci affecting wood formation in {Norway} spruce},
	volume = {100},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14429},
	doi = {10/gjcj3d},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Baison, John and Vidalis, Amaryllis and Zhou, Linghua and Chen, Zhi‐Qiang and Li, Zitong and Sillanpää, Mikko J. and Bernhardsson, Carolina and Scofield, Douglas and Forsberg, Nils and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry and Ingvarsson, Pär K. and Lundqvist, Sven‐Olof and Niittylä, Totte and García‐Gil, M Rosario},
	month = oct,
	year = {2019},
	pages = {83--100},
}

@article{calleja-rodriguez_genotype-by-environment_2019,
	title = {Genotype-by-environment interactions and the dynamic relationship between tree vitality and height in northern {Pinus} sylvestris},
	volume = {15},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-019-1343-8},
	doi = {10/gjcrxs},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Calleja-Rodriguez, Ainhoa and Andersson Gull, Bengt and Wu, Harry X. and Mullin, Tim J. and Persson, Torgny},
	month = jun,
	year = {2019},
	pages = {36},
}

@article{chen_increased_2019,
	title = {Increased {Prediction} {Ability} in {Norway} {Spruce} {Trials} {Using} a {Marker} {X} {Environment} {Interaction} and {Non}-{Additive} {Genomic} {Selection} {Model}},
	volume = {110},
	issn = {0022-1503, 1465-7333},
	url = {https://academic.oup.com/jhered/article/110/7/830/5601174},
	doi = {10.1093/jhered/esz061},
	abstract = {Abstract
            A genomic selection study of growth and wood quality traits is reported based on control-pollinated Norway spruce families established in 2 Northern Swedish trials at 2 locations using exome capture as a genotyping platform. Nonadditive effects including dominance and first-order epistatic interactions (including additive-by-additive, dominance-by-dominance, and additive-by-dominance) and marker-by-environment interaction (M×E) effects were dissected in genomic and phenotypic selection models. Genomic selection models partitioned additive and nonadditive genetic variances more precisely than pedigree-based models. In addition, predictive ability in GS was substantially increased by including dominance and slightly increased by including M×E effects when these effects are significant. For velocity, response to genomic selection per year increased up to 78.9/80.8\%, 86.9/82.9\%, and 91.3/88.2\% compared with response to phenotypic selection per year when genomic selection was based on 1) main marker effects (M), 2) M + M×E effects (A), and 3) A + dominance effects (AD) for sites 1 and 2, respectively. This indicates that including M×E and dominance effects not only improves genetic parameter estimates but also when they are significant may improve the genetic gain. For tree height, Pilodyn, and modulus of elasticity (MOE), response to genomic selection per year improved up to 68.9\%, 91.3\%, and 92.6\% compared with response to phenotypic selection per year, respectively.Subject Area: Quantitative genetics and Mendelian inheritance},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Journal of Heredity},
	author = {Chen, Zhi-Qiang and Baison, John and Pan, Jin and Westin, Johan and Gil, Maria Rosario García and Wu, Harry X},
	editor = {Stommel, John R},
	month = dec,
	year = {2019},
	pages = {830--843},
}

Abstract A genomic selection study of growth and wood quality traits is reported based on control-pollinated Norway spruce families established in 2 Northern Swedish trials at 2 locations using exome capture as a genotyping platform. Nonadditive effects including dominance and first-order epistatic interactions (including additive-by-additive, dominance-by-dominance, and additive-by-dominance) and marker-by-environment interaction (M×E) effects were dissected in genomic and phenotypic selection models. Genomic selection models partitioned additive and nonadditive genetic variances more precisely than pedigree-based models. In addition, predictive ability in GS was substantially increased by including dominance and slightly increased by including M×E effects when these effects are significant. For velocity, response to genomic selection per year increased up to 78.9/80.8%, 86.9/82.9%, and 91.3/88.2% compared with response to phenotypic selection per year when genomic selection was based on 1) main marker effects (M), 2) M + M×E effects (A), and 3) A + dominance effects (AD) for sites 1 and 2, respectively. This indicates that including M×E and dominance effects not only improves genetic parameter estimates but also when they are significant may improve the genetic gain. For tree height, Pilodyn, and modulus of elasticity (MOE), response to genomic selection per year improved up to 68.9%, 91.3%, and 92.6% compared with response to phenotypic selection per year, respectively.Subject Area: Quantitative genetics and Mendelian inheritance

@article{fundova_non-destructive_2019,
	title = {Non-{Destructive} {Assessment} of {Wood} {Stiffness} in {Scots} {Pine} ({Pinus} sylvestris {L}.) and its {Use} in {Forest} {Tree} {Improvement}},
	volume = {10},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/10/6/491},
	doi = {10/gf68z9},
	abstract = {Wood stiffness is an important wood mechanical property that predetermines the suitability of sawn timber for construction purposes. Negative genetic correlations between wood stiffness and growth traits have, however, been reported for many conifer species including Scots pine. It is, therefore, important that breeding programs consider wood stiffness and growth traits simultaneously. The study aims to (1) evaluate different approaches of calculating the dynamic modulus of elasticity (MOE, non-destructively assessed stiffness) using data from X-ray analysis (SilviScan) as a benchmark, (2) estimate genetic parameters, and (3) apply index selection. In total, we non-destructively measured 622 standing trees from 175 full-sib families for acoustic velocity (VEL) using Hitman and for wood density (DEN) using Resistograph and Pilodyn. We combined VEL with different wood densities, raw (DENRES) and adjusted (DENRES.TB) Resistograph density, Pilodyn density measured with (DENPIL) and without bark (DENPIL.B), constant of 1000 kg·m−3 (DENCONST), and SilviScan density (DENSILV), to calculate MOEs and compare them with the benchmark SilviScan MOE (MOESILV). We also derived Smith–Hazel indices for simultaneous improvement of stem diameter (DBH) and wood stiffness. The highest additive genetic and phenotypic correlations of the benchmark MOESILV with the alternative MOE measures (tested) were attained by MOEDENSILV (0.95 and 0.75, respectively) and were closely followed by MOEDENRES.TB (0.91 and 0.70, respectively) and MOEDENCONST and VEL (0.91 and 0.65, respectively for both). Correlations with MOEDENPIL, MOEDENPIL.B, and MOEDENRES were lower. Narrow-sense heritabilities were moderate, ranging from 0.39 (MOESILV) to 0.46 (MOEDENSILV). All indices revealed an opportunity for joint improvement of DBH and MOE. Conclusions: MOEDENRES.TB appears to be the most efficient approach for indirect selection for wood stiffness in Scots pine, although VEL alone and MOEDENCONST have provided very good results too. An index combining DBH and MOEDENRES.TB seems to offer the best compromise for simultaneous improvement of growth, fiber, and wood quality traits.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Forests},
	author = {Fundova, Irena and Funda, Tomas and Wu, Harry X.},
	month = jun,
	year = {2019},
	pages = {491},
}

Wood stiffness is an important wood mechanical property that predetermines the suitability of sawn timber for construction purposes. Negative genetic correlations between wood stiffness and growth traits have, however, been reported for many conifer species including Scots pine. It is, therefore, important that breeding programs consider wood stiffness and growth traits simultaneously. The study aims to (1) evaluate different approaches of calculating the dynamic modulus of elasticity (MOE, non-destructively assessed stiffness) using data from X-ray analysis (SilviScan) as a benchmark, (2) estimate genetic parameters, and (3) apply index selection. In total, we non-destructively measured 622 standing trees from 175 full-sib families for acoustic velocity (VEL) using Hitman and for wood density (DEN) using Resistograph and Pilodyn. We combined VEL with different wood densities, raw (DENRES) and adjusted (DENRES.TB) Resistograph density, Pilodyn density measured with (DENPIL) and without bark (DENPIL.B), constant of 1000 kg·m−3 (DENCONST), and SilviScan density (DENSILV), to calculate MOEs and compare them with the benchmark SilviScan MOE (MOESILV). We also derived Smith–Hazel indices for simultaneous improvement of stem diameter (DBH) and wood stiffness. The highest additive genetic and phenotypic correlations of the benchmark MOESILV with the alternative MOE measures (tested) were attained by MOEDENSILV (0.95 and 0.75, respectively) and were closely followed by MOEDENRES.TB (0.91 and 0.70, respectively) and MOEDENCONST and VEL (0.91 and 0.65, respectively for both). Correlations with MOEDENPIL, MOEDENPIL.B, and MOEDENRES were lower. Narrow-sense heritabilities were moderate, ranging from 0.39 (MOESILV) to 0.46 (MOEDENSILV). All indices revealed an opportunity for joint improvement of DBH and MOE. Conclusions: MOEDENRES.TB appears to be the most efficient approach for indirect selection for wood stiffness in Scots pine, although VEL alone and MOEDENCONST have provided very good results too. An index combining DBH and MOEDENRES.TB seems to offer the best compromise for simultaneous improvement of growth, fiber, and wood quality traits.

@article{wu_review_2019,
	title = {Review of the book ‘{Domestication} of radiata pine’},
	volume = {82},
	issn = {0004-9158, 2325-6087},
	url = {https://www.tandfonline.com/doi/full/10.1080/00049158.2019.1578451},
	doi = {10/gkf56h},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Australian Forestry},
	author = {Wu, Harry X.},
	month = jan,
	year = {2019},
	pages = {48--51},
}

@article{rosvall_using_2019,
	title = {Using {Norway} spruce clones in {Swedish} forestry: implications of clones for management},
	volume = {34},
	issn = {0282-7581, 1651-1891},
	shorttitle = {Using {Norway} spruce clones in {Swedish} forestry},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2019.1590631},
	doi = {10/gjcr7k},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Rosvall, Ola and Bradshaw, Richard H. W. and Egertsdotter, Ulrika and Ingvarsson, Pär K. and Mullin, Tim J. and Wu, Harry},
	month = jul,
	year = {2019},
	pages = {390--404},
}

@article{rosvall_using_2019,
	title = {Using {Norway} spruce clones in {Swedish} forestry: introduction},
	volume = {34},
	issn = {0282-7581, 1651-1891},
	shorttitle = {Using {Norway} spruce clones in {Swedish} forestry},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2018.1562565},
	doi = {10/gjcr7h},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Rosvall, Ola and Bradshaw, Richard H.W. and Egertsdotter, Ulrika and Ingvarsson, Pär K. and Wu, Harry},
	month = jul,
	year = {2019},
	pages = {333--335},
}

@article{chen_accuracy_2018,
	title = {Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in {Norway} spruce},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5256-y},
	doi = {10/ghk9pc},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Baison, John and Pan, Jin and Karlsson, Bo and Andersson, Bengt and Westin, Johan and García-Gil, María Rosario and Wu, Harry X.},
	month = dec,
	year = {2018},
	pages = {946},
}

@article{chen_early_2018,
	title = {Early selection for resistance to {Heterobasidion} parviporum in {Norway} spruce is not likely to adversely affect growth and wood quality traits in late-age performance},
	volume = {137},
	issn = {1612-4669, 1612-4677},
	url = {http://link.springer.com/10.1007/s10342-018-1120-5},
	doi = {10/gdmzbk},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {European Journal of Forest Research},
	author = {Chen, Zhi-Qiang and Lundén, Karl and Karlsson, Bo and Vos, Ingrid and Olson, Åke and Lundqvist, Sven-Olof and Stenlid, Jan and Wu, Harry X. and García Gil, María Rosario and Elfstrand, Malin},
	month = aug,
	year = {2018},
	pages = {517--525},
}

@article{chen_efficiency_2018,
	title = {Efficiency of using spatial analysis for {Norway} spruce progeny tests in {Sweden}},
	volume = {75},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-017-0680-8},
	doi = {10/gdfmxt},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Chen, Zhiqiang and Helmersson, Andreas and Westin, Johan and Karlsson, Bo and Wu, Harry X.},
	month = mar,
	year = {2018},
	pages = {2},
}

@article{hayatgheibi_genetic_2018,
	title = {Genetic control of transition from juvenile to mature wood with respect to microfibril angle in {Norway} spruce ( \textit{{Picea} abies} ) and lodgepole pine ( \textit{{Pinus} contorta} )},
	volume = {48},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0140},
	doi = {10.1139/cjfr-2018-0140},
	abstract = {Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h
              2
              ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h
              2
              were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Forsberg, Nils Erik Gustaf and Lundqvist, Sven-Olof and Mörling, Tommy and Mellerowicz, Ewa J. and Karlsson, Bo and Wu, Harry X. and García-Gil, M. Rosario},
	month = nov,
	year = {2018},
	pages = {1358--1365},
}

Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h 2 ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h 2 were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.

@article{tan_genomic_2018,
	title = {Genomic relationships reveal significant dominance effects for growth in hybrid {Eucalyptus}},
	volume = {267},
	issn = {01689452},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168945217307847},
	doi = {10/gc3n47},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Science},
	author = {Tan, Biyue and Grattapaglia, Dario and Wu, Harry X. and Ingvarsson, Pär K.},
	month = feb,
	year = {2018},
	pages = {84--93},
}

@article{fundova_non-destructive_2018,
	title = {Non-destructive wood density assessment of {Scots} pine ({Pinus} sylvestris {L}.) using {Resistograph} and {Pilodyn}},
	volume = {13},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0204518},
	doi = {10.1371/journal.pone.0204518},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Fundova, Irena and Funda, Tomas and Wu, Harry X.},
	editor = {Gomory, Dusan},
	month = sep,
	year = {2018},
	pages = {e0204518},
}

@article{hayatgheibi_genetic_2017,
	title = {Genetic analysis of lodgepole pine ( \textit{{Pinus} contorta} ) solid-wood quality traits},
	volume = {47},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2017-0152},
	doi = {10/gcjb4x},
	abstract = {Potential improvement of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) solid-wood properties was examined by estimating age trends of inheritance, age–age genetic correlations, and the efficiency of early selection using 823 increment cores sampled from 207 half-sib families at two independent progeny trials, aged 34–35 years, located in northern Sweden. High-resolution radial variation of annual ring width, wood density, microfibril angle (MFA), and modulus of elasticity (clearwood stiffness; MOE
              S
              ) was measured using SilviScan. The dynamic stiffness (MOE
              tof
              ) of standing trees was also obtained using Hitman ST300. Heritabilities ranged from 0.10 to 0.64 for growth and earlywood, transition-wood, and latewood proportions, from 0.29 to 0.77 for density traits, and from 0.13 to 0.33 for MFA and stiffness traits. Genetic correlations between early age and the reference age (26 years) suggested that early selection is efficient at age 4 years for MFA and between ages 5 to 8 years for density and MOE
              S
              . Unfavorable diameter–stiffness genetic correlations and correlated responses indicate that breeding for a 1\% increase in diameter would confer 5.5\% and 2.3\% decreases in lodgepole pine MOE
              S
              and MOE
              tof
              , respectively. Index selection with appropriate economical weights for growth and wood stiffness is highly recommended for selective breeding.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Fries, Anders and Kroon, Johan and Wu, Harry X.},
	month = oct,
	year = {2017},
	pages = {1303--1313},
}

Potential improvement of lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) solid-wood properties was examined by estimating age trends of inheritance, age–age genetic correlations, and the efficiency of early selection using 823 increment cores sampled from 207 half-sib families at two independent progeny trials, aged 34–35 years, located in northern Sweden. High-resolution radial variation of annual ring width, wood density, microfibril angle (MFA), and modulus of elasticity (clearwood stiffness; MOE S ) was measured using SilviScan. The dynamic stiffness (MOE tof ) of standing trees was also obtained using Hitman ST300. Heritabilities ranged from 0.10 to 0.64 for growth and earlywood, transition-wood, and latewood proportions, from 0.29 to 0.77 for density traits, and from 0.13 to 0.33 for MFA and stiffness traits. Genetic correlations between early age and the reference age (26 years) suggested that early selection is efficient at age 4 years for MFA and between ages 5 to 8 years for density and MOE S . Unfavorable diameter–stiffness genetic correlations and correlated responses indicate that breeding for a 1% increase in diameter would confer 5.5% and 2.3% decreases in lodgepole pine MOE S and MOE tof , respectively. Index selection with appropriate economical weights for growth and wood stiffness is highly recommended for selective breeding.

@article{wu_inheritance_2017,
	title = {Inheritance and {Genetic} {Gain} in {Wood} {Stiffness} in {Radiata} {Pine} {Assessed} {Acoustically} in {Young} {Standing} {Trees}},
	volume = {57},
	url = {https://www.sciendo.com/article/10.1515/sg-2008-0009},
	doi = {10/gkhnmw},
	abstract = {Wood stiffness, measured in terms of its modulus of elasticity (MoE) is an important characteristic of radiata pine for structural products. To select high stiffness radiata pine for breeding purpose, rapid, inexpensive methods for measuring wood stiffness are desirable. In this study, we explored acoustic instruments to measure stiffness of young standing trees in radiata pine and examined inheritance and genetic gain for stiffness in an Australian national breeding program. Time of flight of sound waves was recorded in standing trees in two progeny trials, one in eastern Victoria (Flynn) aged 8 years and the other in South Australia (Kromelite) aged 7 years. Average time of flight at Kromelite was higher than at Flynn, (519 μs/metre compared to 463 μs/metre) which corresponds to 3.7 GPa and 4.7 GPa for MoE, respectively. Heritability for time of flight was higher at Flynn (h2 = 0.67 ± 0.10) than at Kromelite (h2 = 0.30 ± 0.14). Selection of the best 10\% for time of flight based on pooled data would result in 21\% genetic gain in wood stiffness.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-10},
	journal = {Silvae Genetica},
	author = {Wu, H. X.},
	month = oct,
	year = {2017},
	pages = {56--64},
}

Wood stiffness, measured in terms of its modulus of elasticity (MoE) is an important characteristic of radiata pine for structural products. To select high stiffness radiata pine for breeding purpose, rapid, inexpensive methods for measuring wood stiffness are desirable. In this study, we explored acoustic instruments to measure stiffness of young standing trees in radiata pine and examined inheritance and genetic gain for stiffness in an Australian national breeding program. Time of flight of sound waves was recorded in standing trees in two progeny trials, one in eastern Victoria (Flynn) aged 8 years and the other in South Australia (Kromelite) aged 7 years. Average time of flight at Kromelite was higher than at Flynn, (519 μs/metre compared to 463 μs/metre) which corresponds to 3.7 GPa and 4.7 GPa for MoE, respectively. Heritability for time of flight was higher at Flynn (h2 = 0.67 ± 0.10) than at Kromelite (h2 = 0.30 ± 0.14). Selection of the best 10% for time of flight based on pooled data would result in 21% genetic gain in wood stiffness.

@article{chen_patterns_2017,
	title = {Patterns of additive genotype-by-environment interaction in tree height of {Norway} spruce in southern and central {Sweden}},
	volume = {13},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-017-1103-6},
	doi = {10.1007/s11295-017-1103-6},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Chen, Zhi-Qiang and Karlsson, Bo and Wu, Harry X.},
	month = feb,
	year = {2017},
	pages = {25},
}

@article{bian_spatial_2017,
	title = {Spatial analysis increases efficiency of progeny testing of {Chinese} fir},
	volume = {28},
	issn = {1007-662X, 1993-0607},
	url = {http://link.springer.com/10.1007/s11676-016-0341-z},
	doi = {10.1007/s11676-016-0341-z},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Journal of Forestry Research},
	author = {Bian, Liming and Zheng, Renhua and Su, Shunde and Lin, Huazhong and Xiao, Hui and Wu, Harry Xiaming and Shi, Jisen},
	month = may,
	year = {2017},
	pages = {445--452},
}

@article{hall_estimation_2016,
	title = {Estimation of number and size of {QTL} effects in forest tree traits},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1073-0},
	doi = {10.1007/s11295-016-1073-0},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Hall, David and Hallingbäck, Henrik R. and Wu, Harry X.},
	month = dec,
	year = {2016},
	pages = {110},
}

@article{chen_genetic_2016,
	title = {Genetic analysis of fiber dimensions and their correlation with stem diameter and solid-wood properties in {Norway} spruce},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1065-0},
	doi = {10.1007/s11295-016-1065-0},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Chen, Zhi-Qiang and Karlsson, Bo and Mörling, Tommy and Olsson, Lars and Mellerowicz, Ewa J. and Wu, Harry X. and Lundqvist, Sven-Olof and Gil, María Rosario García},
	month = dec,
	year = {2016},
	pages = {123},
}

@article{zheng_inheritance_2016,
	title = {Inheritance of growth and survival in two 9-year-old, open-pollinated progenies of an advanced breeding population of {Chinese} firs in southeastern {China}},
	volume = {27},
	issn = {1007-662X, 1993-0607},
	url = {http://link.springer.com/10.1007/s11676-016-0250-1},
	doi = {10.1007/s11676-016-0250-1},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Journal of Forestry Research},
	author = {Zheng, Renhua and Hong, Zhou and Su, Shunde and Bian, Liming and Xiao, Hui and Shi, Jisen and Wu, Harry X.},
	month = oct,
	year = {2016},
	pages = {1067--1075},
}

@article{chen_method_2016,
	title = {Method for accurate fiber length determination from increment cores for large-scale population analyses in {Norway} spruce},
	volume = {70},
	issn = {1437-434X, 0018-3830},
	url = {https://www.degruyter.com/document/doi/10.1515/hf-2015-0138/html},
	doi = {10/f3rwht},
	abstract = {Abstract
            
              Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce (
              Picea abies
              (L.) Karst) trees on fibers from rings 8–11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7\% and low scatter. Length-weighing and length
              2
              -weighing gave biases of -7.3\% and +9.3\%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.},
	number = {9},
	urldate = {2021-06-07},
	journal = {Holzforschung},
	author = {Chen, Zhi-Qiang and Abramowicz, Konrad and Raczkowski, Rafal and Ganea, Stefana and Wu, Harry X. and Lundqvist, Sven-Olof and Mörling, Tommy and de Luna, Sara Sjöstedt and García Gil, María Rosario and Mellerowicz, Ewa J.},
	month = sep,
	year = {2016},
	pages = {829--838},
}

Abstract Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce ( Picea abies (L.) Karst) trees on fibers from rings 8–11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7% and low scatter. Length-weighing and length 2 -weighing gave biases of -7.3% and +9.3%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.

@article{wu_performance_2016,
	title = {Performance of {Seven} {Tree} {Breeding} {Strategies} {Under} {Conditions} of {Inbreeding} {Depression}},
	volume = {6},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/6/3/529/6027276},
	doi = {10.1534/g3.115.025767},
	abstract = {Abstract
            In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Wu, Harry X and Hallingbäck, Henrik R and Sánchez, Leopoldo},
	month = mar,
	year = {2016},
	pages = {529--540},
}

Abstract In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term.

@article{hong_age_2015,
	title = {Age trend of heritability, genetic correlation, and efficiency of early selection for wood quality traits in {Scots} pine},
	volume = {45},
	issn = {0045-5067},
	url = {://WOS:000357136800004},
	doi = {10.1139/cjfr-2014-0465},
	abstract = {To examine the efficiency of early selection for wood quality traits in the Scots pine (Pinus sylvestris L.) breeding program in Sweden, a total of 778 wood increment cores were sampled from 179 full-sib families in a single progeny trial at 40 years of age. Age trend of inheritance, age-age genetic correlation, and early selection efficiency for eight wood traits including annual ring width, wood density, microfibril angle (MFA), modulus of elasticity (i.e., wood stiffness; MOE), and fibre dimensions were studied. Heritabilities for the eight wood traits reached a plateau between age 5 years and age 15 years, with the highest heritability for radial fibre width and fibre coarseness (similar to 0.6) and the lowest heritability for ring width (similar to 0.2). Heritability reached about 0.4 for both wood density and MFA but only reached about 0.3 for MOE. Genetic correlation from early to reference age 30 years reached a very high level ({\textgreater}0.8) for all eight wood traits at age 5 years. Early selection was effective for wood quality traits in Scots pine, and selection at age 8 years is recommended for MOE in Scots pine.},
	language = {English},
	number = {7},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hong, Z. and Fries, A. and Wu, H. X.},
	month = jul,
	year = {2015},
	keywords = {2 locations, density, early selection, genetic parameters, growth traits, juvenile, mature wood, microfibril angle, parameters, picea-abies, pinus sylvestris, radiata pine, sylvestris, wood properties},
	pages = {817--825},
}

To examine the efficiency of early selection for wood quality traits in the Scots pine (Pinus sylvestris L.) breeding program in Sweden, a total of 778 wood increment cores were sampled from 179 full-sib families in a single progeny trial at 40 years of age. Age trend of inheritance, age-age genetic correlation, and early selection efficiency for eight wood traits including annual ring width, wood density, microfibril angle (MFA), modulus of elasticity (i.e., wood stiffness; MOE), and fibre dimensions were studied. Heritabilities for the eight wood traits reached a plateau between age 5 years and age 15 years, with the highest heritability for radial fibre width and fibre coarseness (similar to 0.6) and the lowest heritability for ring width (similar to 0.2). Heritability reached about 0.4 for both wood density and MFA but only reached about 0.3 for MOE. Genetic correlation from early to reference age 30 years reached a very high level (\textgreater0.8) for all eight wood traits at age 5 years. Early selection was effective for wood quality traits in Scots pine, and selection at age 8 years is recommended for MOE in Scots pine.

@article{chen_estimating_2015,
	title = {Estimating solid wood properties using {Pilodyn} and acoustic velocity on standing trees of {Norway} spruce},
	volume = {72},
	issn = {1286-4560},
	url = {://WOS:000354388400010},
	doi = {10.1007/s13595-015-0458-9},
	abstract = {Strong genetic correlations were observed between Pilodyn measurement and wood density, and between acoustic velocity and MFA. Combination of Pilodyn penetration and acoustic velocity measurements from standing trees can provide reliable prediction of stiffness of Norway spruce for breeding selection.
Traditional methods for the estimation of solid wood quality traits of standing tree such as wood density, microfibril angle (MFA), and modulus of elasticity (MOE) are time-consuming and expensive, which render them unsuitable for rapidly screening a large number of trees in tree breeding programs.
This study aims to evaluate the suitability of using Pilodyn penetration and acoustic velocity (nondestructive evaluation) to assess wood density, MFA, and MOE for Norway spruce.
Pilodyn penetration and Hitman acoustic velocity, as well as wood density, MFA, and MOE using benchmark SilviScan were measured on 5618 standing trees of 524 open-pollinated families in two 21-year-old Norway spruce (Picea abies) progeny trials in southern Sweden.
Strong genetic correlations were observed between Pilodyn measurement and wood density (r (g) = -0.96), and between acoustic velocity and MFA (r (g) = -0.94). Combination of Pilodyn penetration and Hitman acoustic velocity measurements () obtained from standing trees showed a genetic correlation with benchmark MOE of 0.99. This combined had higher selection efficiency for benchmark MOE (92 \%) compared to 58-60 \% using acoustic velocity alone and 78 \% using Pilodyn penetration alone.
Combination of Pilodyn penetration with Hitman acoustic velocity provided very high selection efficiency for the three most important quality traits for wood mechanical properties in Norway spruce.},
	language = {English},
	number = {4},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Chen, Z. Q. and Karlsson, B. and Lundqvist, S. O. and Gil, M. R. G. and Olsson, L. and Wu, H. X.},
	month = jun,
	year = {2015},
	keywords = {douglas-fir, genetic-improvement, mature wood, microfibril angle, modulus of elasticity, near-infrared spectroscopy, new-zealand, nondestructive evaluation, norway spruce, picea-abies, pinus-radiata, quality traits, rapid assessment, stiffness, wood density},
	pages = {499--508},
}

Strong genetic correlations were observed between Pilodyn measurement and wood density, and between acoustic velocity and MFA. Combination of Pilodyn penetration and acoustic velocity measurements from standing trees can provide reliable prediction of stiffness of Norway spruce for breeding selection. Traditional methods for the estimation of solid wood quality traits of standing tree such as wood density, microfibril angle (MFA), and modulus of elasticity (MOE) are time-consuming and expensive, which render them unsuitable for rapidly screening a large number of trees in tree breeding programs. This study aims to evaluate the suitability of using Pilodyn penetration and acoustic velocity (nondestructive evaluation) to assess wood density, MFA, and MOE for Norway spruce. Pilodyn penetration and Hitman acoustic velocity, as well as wood density, MFA, and MOE using benchmark SilviScan were measured on 5618 standing trees of 524 open-pollinated families in two 21-year-old Norway spruce (Picea abies) progeny trials in southern Sweden. Strong genetic correlations were observed between Pilodyn measurement and wood density (r (g) = -0.96), and between acoustic velocity and MFA (r (g) = -0.94). Combination of Pilodyn penetration and Hitman acoustic velocity measurements () obtained from standing trees showed a genetic correlation with benchmark MOE of 0.99. This combined had higher selection efficiency for benchmark MOE (92 %) compared to 58-60 % using acoustic velocity alone and 78 % using Pilodyn penetration alone. Combination of Pilodyn penetration with Hitman acoustic velocity provided very high selection efficiency for the three most important quality traits for wood mechanical properties in Norway spruce.

@article{hong_measuring_2015,
	title = {Measuring stiffness using acoustic tool for {Scots} pine breeding selection},
	volume = {30},
	issn = {0282-7581},
	url = {://WOS:000352893900012},
	doi = {10/f3rwh9},
	abstract = {Stiffness (modulus of elasticity, MOE) of conifer trees is the most important trait for structural wood products. Finding a fast, reliable and non-destructive way to measure MOE is a priority for screening large progeny trials in tree breeding programmes. For Scots pine, time-of-flight (TOF) velocity measured on standing trees accounted for 47\% of the variation to the benchmark SilviScan-based clearwood MOE (MOEs), under the assumption of constant wood density. If wood density was included, 59\% of the variation was accounted for. The TOF stiffness measurements on standing trees were, however, more related to the clearwood MOEs in the outerwood, and the prediction was the most reliable at breast height compared to the stem base and the top section. Microfibril angle (MFA) had higher correlation with acoustic velocity (VEL) of standing trees than wood density, and among the early, transition and latewood density, the latewood density had the highest correlation with stiffness measurements on standing trees. VEL measured at breast height in combination with wood density was the most reliable predictor of MOE of standing trees for selection and breeding in Scots pine.},
	language = {English},
	number = {4},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Hong, Z. and Fries, A. and Lundqvist, S. O. and Gull, B. A. and Wu, H. X.},
	month = may,
	year = {2015},
	keywords = {acoustic velocity, economic weights, genetic correlations, logs, mature wood, microfibril angle, modulus of elasticity (moe), non-destructive evaluation, pinus sylvestris, radiata, standing trees, traits, velocity, wood stiffness},
	pages = {363--372},
}

Stiffness (modulus of elasticity, MOE) of conifer trees is the most important trait for structural wood products. Finding a fast, reliable and non-destructive way to measure MOE is a priority for screening large progeny trials in tree breeding programmes. For Scots pine, time-of-flight (TOF) velocity measured on standing trees accounted for 47% of the variation to the benchmark SilviScan-based clearwood MOE (MOEs), under the assumption of constant wood density. If wood density was included, 59% of the variation was accounted for. The TOF stiffness measurements on standing trees were, however, more related to the clearwood MOEs in the outerwood, and the prediction was the most reliable at breast height compared to the stem base and the top section. Microfibril angle (MFA) had higher correlation with acoustic velocity (VEL) of standing trees than wood density, and among the early, transition and latewood density, the latewood density had the highest correlation with stiffness measurements on standing trees. VEL measured at breast height in combination with wood density was the most reliable predictor of MOE of standing trees for selection and breeding in Scots pine.

@article{ivkovic_pattern_2015,
	title = {Pattern of genotype by environment interaction for radiata pine in southern {Australia}},
	volume = {72},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-014-0437-6},
	doi = {10/gkf559},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Ivković, Miloš and Gapare, Washington and Yang, Huixiao and Dutkowski, Gregory and Buxton, Peter and Wu, Harry},
	month = may,
	year = {2015},
	pages = {391--401},
}

@article{li_characterizing_2014,
	title = {Characterizing compression wood formed in radiata pine branches},
	volume = {35},
	issn = {0928-1541, 2294-1932},
	url = {https://brill.com/view/journals/iawa/35/4/article-p385_4.xml},
	doi = {10/f3p3vv},
	abstract = {The formation of reaction wood is an adaptive feature of trees in response to various mechanical forces. In gymnosperms, reaction wood consists of compression wood (CW) and opposite wood (OW) that are formed on the underside and upperside of bent trunks and branches. Although reaction wood formed in bent trunks has been extensively investigated, relatively little has been reported from conifer branches. In this study SilviScan® technology was used to characterize radiata pine branches at high resolution. Compared to OW formed in the branches, CW showed greater growth, darker colour, thicker tracheid walls, higher coarseness, larger microfibril angle (MFA), higher wood density, lower extensional stiffness and smaller internal specific surface area. However, tracheids of CW were similar to those of OW in their radial and tangential diameters. These results indicated that gravity influenced tracheid cell division and secondary wall formation but had limited impact on primary wall expansion. Furthermore, seasonal patterns of CW formation were not observed in the branches from cambial age 4 while earlywood and latewood were clearly separated in all rings of OW. The marked change of MFA during reaction wood formation suggested that branches could be ideal materials for further study of cellulose microfibril orientation.},
	number = {4},
	urldate = {2021-06-08},
	journal = {IAWA Journal},
	author = {Li, Xinguo and Evans, Robert and Gapare, Washington and Yang, Xiaohui and Wu, Harry X.},
	month = dec,
	year = {2014},
	pages = {385--394},
}

The formation of reaction wood is an adaptive feature of trees in response to various mechanical forces. In gymnosperms, reaction wood consists of compression wood (CW) and opposite wood (OW) that are formed on the underside and upperside of bent trunks and branches. Although reaction wood formed in bent trunks has been extensively investigated, relatively little has been reported from conifer branches. In this study SilviScan® technology was used to characterize radiata pine branches at high resolution. Compared to OW formed in the branches, CW showed greater growth, darker colour, thicker tracheid walls, higher coarseness, larger microfibril angle (MFA), higher wood density, lower extensional stiffness and smaller internal specific surface area. However, tracheids of CW were similar to those of OW in their radial and tangential diameters. These results indicated that gravity influenced tracheid cell division and secondary wall formation but had limited impact on primary wall expansion. Furthermore, seasonal patterns of CW formation were not observed in the branches from cambial age 4 while earlywood and latewood were clearly separated in all rings of OW. The marked change of MFA during reaction wood formation suggested that branches could be ideal materials for further study of cellulose microfibril orientation.

@article{zhang_comparison_2014,
	title = {Comparison of allelic diversity between native gene resource plantings and selections in open-pollinated progeny test of {Pinus} radiata {D}. {Don}.},
	volume = {63},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2014-0027},
	doi = {10/gjcm3w},
	abstract = {Genetic diversity within radiata pine first generation of open-pollinated selections (OPS) from the native resource stands was compared with that observed in native populations to monitor potential changes in genetic diversity during domestication. Genetic diversity was estimated using 58 single nucleotide polymorphisms (SNPs) from 8 expressed genes. Nucleotide diversity maintained in first generation of selections (OPS) (mean ␲ = 0.0036; mean ␪w = 0.0058) was similar to that found within the native population material (mean ␲ = 0.0043; mean for ␪w = 0.0065). Likewise, mean values for expected heterozygosity (H ) within E and between native population material and OPS were similar (mean = 0.27 ± 0.04) and not significantly different (P = 0.068). Also, the overall distribution of allele frequency classes was not significantly different between native population material and OPS. These results point to no evidence of loss of diversity in OPS due to artificial selection. One possible reason is that the domestication of the OPS is at a very early stage. Another may be that artificial selection in the OPS was based on tree growth and form, not wood properties. The genes selected in this study are mostly involved in cell wall formation, thus genetic diversity of these genes should remain stable between natural population and OPS, unless there was a significant sampling bias in the OPS. Although the SNP information suggests similarities among mainland populations, results from quantitative genetic studies found large provenance differences for growth-, morphological-, stem-form traits, and disease resistance. Determining the threshold at which genetic diversity levels will be significantly reduced during selection should help breeders to make informed decisions regarding the intensity of selection in managed breeding populations as well as gene resource populations.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Zhang, L. and Huanqiong, N. and Gapare, Washington J. and Dillon, S. K. and Li, X. and Wu, H. X.},
	month = dec,
	year = {2014},
	pages = {213--221},
}

Genetic diversity within radiata pine first generation of open-pollinated selections (OPS) from the native resource stands was compared with that observed in native populations to monitor potential changes in genetic diversity during domestication. Genetic diversity was estimated using 58 single nucleotide polymorphisms (SNPs) from 8 expressed genes. Nucleotide diversity maintained in first generation of selections (OPS) (mean ␲ = 0.0036; mean ␪w = 0.0058) was similar to that found within the native population material (mean ␲ = 0.0043; mean for ␪w = 0.0065). Likewise, mean values for expected heterozygosity (H ) within E and between native population material and OPS were similar (mean = 0.27 ± 0.04) and not significantly different (P = 0.068). Also, the overall distribution of allele frequency classes was not significantly different between native population material and OPS. These results point to no evidence of loss of diversity in OPS due to artificial selection. One possible reason is that the domestication of the OPS is at a very early stage. Another may be that artificial selection in the OPS was based on tree growth and form, not wood properties. The genes selected in this study are mostly involved in cell wall formation, thus genetic diversity of these genes should remain stable between natural population and OPS, unless there was a significant sampling bias in the OPS. Although the SNP information suggests similarities among mainland populations, results from quantitative genetic studies found large provenance differences for growth-, morphological-, stem-form traits, and disease resistance. Determining the threshold at which genetic diversity levels will be significantly reduced during selection should help breeders to make informed decisions regarding the intensity of selection in managed breeding populations as well as gene resource populations.

@article{lin_effect_2014,
	title = {Effect of genotype-by-spacing interaction on radiata pine wood density},
	volume = {77},
	issn = {0004-9158},
	url = {http://www.tandfonline.com/doi/abs/10.1080/00049158.2014.980878},
	doi = {10/f3p3hg},
	language = {en},
	number = {3-4},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	author = {Lin, Yuanzhen and Yang, Huixiao and Ivković, Miloš and Gapare, Washington J. and Matheson, A. Colin and Wu, Harry X.},
	month = oct,
	year = {2014},
	pages = {203--211},
}

@article{bian_genetic_2014,
	title = {Genetic parameters and genotype–environment interactions of {Chinese} fir ( \textit{{Cunninghamia} lanceolata} ) in {Fujian} {Province}},
	volume = {44},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2013-0427},
	doi = {10/f3pxpf},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is the most commercially important conifer in China, and the Nanjing Forestry University – Fujian Province Chinese fir Cooperation (NJFU – Fujian Cooperation) breeding program has advanced it into the third cycle of selection and breeding. In this paper, we estimated genetic parameters from four sites for 80 half-sib families and summarized previous estimates of genetic parameters in Chinese fir with an objective to propose optimal breeding strategy. Heritability averaged 0.20 and 0.14 for height and diameter at breast height (DBH), respectively, for the four sites. A significant genotype–environment interaction (G × E) for growth was also observed among the four sites, with the greatest interactions between a marginal site and the three central sites in the Fujian Province Chinese fir plantation region. The average estimated type-B genetic correlation between the marginal site and the three central sites was 0.08 for height and –0.09 for DBH. However, the highly productive families were among the most stable across the four sites. The results from this study in combination with summarized genetic parameters from literature were used to discuss and propose an optimal breeding strategy for the third generation of the breeding program for Chinese firs in Fujian Province.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Canadian Journal of Forest Research},
	author = {Bian, Liming and Shi, Jisen and Zheng, Renhua and Chen, Jinhui and Wu, Harry X.},
	month = jun,
	year = {2014},
	pages = {582--592},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is the most commercially important conifer in China, and the Nanjing Forestry University – Fujian Province Chinese fir Cooperation (NJFU – Fujian Cooperation) breeding program has advanced it into the third cycle of selection and breeding. In this paper, we estimated genetic parameters from four sites for 80 half-sib families and summarized previous estimates of genetic parameters in Chinese fir with an objective to propose optimal breeding strategy. Heritability averaged 0.20 and 0.14 for height and diameter at breast height (DBH), respectively, for the four sites. A significant genotype–environment interaction (G × E) for growth was also observed among the four sites, with the greatest interactions between a marginal site and the three central sites in the Fujian Province Chinese fir plantation region. The average estimated type-B genetic correlation between the marginal site and the three central sites was 0.08 for height and –0.09 for DBH. However, the highly productive families were among the most stable across the four sites. The results from this study in combination with summarized genetic parameters from literature were used to discuss and propose an optimal breeding strategy for the third generation of the breeding program for Chinese firs in Fujian Province.

@article{hong_high_2014,
	title = {High negative genetic correlations between growth traits and wood properties suggest incorporating multiple traits selection including economic weights for the future {Scots} pine breeding programs},
	volume = {71},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-014-0359-3},
	doi = {10/f3p4zt},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Hong, Zhou and Fries, Anders and Wu, Harry X.},
	month = jun,
	year = {2014},
	pages = {463--472},
}

@article{chen_inheritance_2014,
	title = {Inheritance of growth and solid wood quality traits in a large {Norway} spruce population tested at two locations in southern {Sweden}},
	volume = {10},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-014-0761-x},
	doi = {10/f3ndqx},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Chen, Zhi-Qiang and Gil, María Rosario García and Karlsson, Bo and Lundqvist, Sven-Olof and Olsson, Lars and Wu, Harry X.},
	month = oct,
	year = {2014},
	pages = {1291--1303},
}

@article{hallingback_single_2014,
	title = {Single versus subdivided population strategies in breeding against an adverse genetic correlation},
	volume = {10},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-014-0707-3},
	doi = {10/f3p5jd},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Hallingbäck, Henrik R. and Sánchez, Leopoldo and Wu, Harry X.},
	month = jun,
	year = {2014},
	pages = {605--617},
}

@article{fries_stem_2014,
	title = {Stem damage of lodgepole pine clonal cuttings in relation to wood and fiber traits, acoustic velocity, and spiral grain},
	volume = {29},
	issn = {0282-7581, 1651-1891},
	url = {http://www.tandfonline.com/doi/abs/10.1080/02827581.2014.978886},
	doi = {10/f3pxdm},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Scandinavian Journal of Forest Research},
	author = {Fries, Anders and Ulvcrona, Thomas and Wu, Harry X. and Kroon, Johan},
	month = nov,
	year = {2014},
	pages = {764--776},
}

@article{lin_effect_2013,
	title = {Effect of genotype by spacing interaction on radiata pine genetic parameters for height and diameter growth},
	volume = {304},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112713003149},
	doi = {10/f23mtw},
	language = {en},
	urldate = {2021-06-08},
	journal = {Forest Ecology and Management},
	author = {Lin, Yuanzhen and Yang, Huixiao and Ivković, Miloš and Gapare, Washington J. and Colin Matheson, A. and Wu, Harry X.},
	month = sep,
	year = {2013},
	pages = {204--211},
}

@article{ivkovic_influence_2013,
	title = {Influence of cambial age and climate on ring width and wood density in {Pinus} radiata families},
	volume = {70},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-013-0290-z},
	doi = {10/f4zz7w},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Ivković, Miloš and Gapare, Washington and Wu, Harry and Espinoza, Sergio and Rozenberg, Philippe},
	month = jul,
	year = {2013},
	pages = {525--534},
}

@article{li_transcriptome_2013,
	title = {Transcriptome profiling of radiata pine branches reveals new insights into reaction wood formation with implications in plant gravitropism},
	volume = {14},
	issn = {1471-2164},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-768},
	doi = {10/f23ncd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genomics},
	author = {Li, Xinguo and Yang, Xiaohui and Wu, Harry X},
	year = {2013},
	pages = {768},
}

@article{gapare_genetic_2012,
	title = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 1: growth and form traits},
	volume = {8},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 1},
	url = {http://link.springer.com/10.1007/s11295-011-0449-4},
	doi = {10/c4rg94},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gapare, Washington J. and Ivković, Miloš and Dutkowski, Gregory W. and Spencer, David J. and Buxton, Peter and Wu, Harry X.},
	month = apr,
	year = {2012},
	pages = {391--407},
}

@article{gapare_genetic_2012,
	title = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 2: wood properties},
	volume = {8},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Genetic parameters and provenance variation of {Pinus} radiata {D}. {Don}. ‘{Eldridge} collection’ in {Australia} 2},
	url = {http://link.springer.com/10.1007/s11295-012-0475-x},
	doi = {10/f3p3cs},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gapare, Washington J. and Ivković, Miloš and Dillon, Shannon K. and Chen, Fiona and Evans, Robert and Wu, Harry X.},
	month = aug,
	year = {2012},
	pages = {895--910},
}

@article{li_identification_2012,
	title = {Identification of putative candidate genes for juvenile wood density in {Pinus} radiata},
	volume = {32},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tps060},
	doi = {10/f24jz3},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Li, X. and Wu, H. X. and Southerton, S. G.},
	month = aug,
	year = {2012},
	pages = {1046--1057},
}

@article{abrahamsson_inheritance_2012,
	title = {Inheritance of height growth and autumn cold hardiness based on two generations of full-sib and half-sib families of \textit{{Pinus} sylvestris}},
	volume = {27},
	issn = {0282-7581, 1651-1891},
	url = {http://www.tandfonline.com/doi/abs/10.1080/02827581.2012.663403},
	doi = {10/f25q9r},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Scandinavian Journal of Forest Research},
	author = {Abrahamsson, Sara and Nilsson, Jan-Erik and Wu, Harry and García Gil, MarÍa Rosario and Andersson, Bengt},
	month = jul,
	year = {2012},
	pages = {405--413},
}

@article{chen_phylogeography_2012,
	title = {Phylogeography of {Quercus} variabilis {Based} on {Chloroplast} {DNA} {Sequence} in {East} {Asia}: {Multiple} {Glacial} {Refugia} and {Mainland}-{Migrated} {Island} {Populations}},
	volume = {7},
	issn = {1932-6203},
	shorttitle = {Phylogeography of {Quercus} variabilis {Based} on {Chloroplast} {DNA} {Sequence} in {East} {Asia}},
	url = {https://dx.plos.org/10.1371/journal.pone.0047268},
	doi = {10/f23cz3},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Chen, Dongmei and Zhang, Xianxian and Kang, Hongzhang and Sun, Xiao and Yin, Shan and Du, Hongmei and Yamanaka, Norikazu and Gapare, Washington and Wu, Harry X. and Liu, Chunjiang},
	editor = {Shaw, Peter},
	month = oct,
	year = {2012},
	pages = {e47268},
}

@article{bian_genetic_2011,
	title = {Genetic variation between and within \textit{ex-situ} native-provenance collections of \textit{{Pinus} radiata} {D}. {Don} planted in {Australia} and {New} {Zealand}},
	volume = {60},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2011-0036},
	doi = {10/gjcmm5},
	abstract = {Abstract
            
              A total of 1226 increment cores were sampled from two provenance trials of
              Pinus radiata
              D. Don planted in New Zealand (Kaingaroa) and Australia (Kangaroovale), to study variation and inheritance of wood density in selections from three mainland California natural populations: Año Nuevo, Monterey and Cambria. The study represents a back-to-back comparison of the same provenance and family material on contrasting sites between New Zealand and Australia. Monterey was significantly different to Año Nuevo and Cambria at Kaingaroa (
              p
              {\textless}0.05), and had slightly higher density, whereas all provenances were almost identical and not significantly different at Kangaroovale. However, there were significant differences for wood density at family level for Año Nuevo and Cambria at Kangaroovale. No significant provenance or family differences were detected for core length at either site. The estimates of heritability for wood density were all above 0.50 and generally higher at Kaingaroa than at Kangaroovale. Estimates of additive genetic correlations between wood density and core length were imprecise. Genotype × site interactions for density appeared minor (estimated type-B genetic correlation= 0.70) despite substantial differences in rainfall and soils. The similarity of Cambria to Año Nuevo for density is an interesting result because the genetic base of the present Australian and New Zealand plantations has been shown to be from Año Nuevo and Monterey. Infusion of Cambria material would increase the overall genetic base of the radiata pine breeding programs, with potential long-term benefits, despite the often disappointing growth performance of material collected from Cambria.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Bian, L. and Gapare, W. J. and Ivković, M. and Jefferson, P. and Wu, H. X.},
	month = dec,
	year = {2011},
	pages = {276--285},
}

Abstract A total of 1226 increment cores were sampled from two provenance trials of Pinus radiata D. Don planted in New Zealand (Kaingaroa) and Australia (Kangaroovale), to study variation and inheritance of wood density in selections from three mainland California natural populations: Año Nuevo, Monterey and Cambria. The study represents a back-to-back comparison of the same provenance and family material on contrasting sites between New Zealand and Australia. Monterey was significantly different to Año Nuevo and Cambria at Kaingaroa ( p \textless0.05), and had slightly higher density, whereas all provenances were almost identical and not significantly different at Kangaroovale. However, there were significant differences for wood density at family level for Año Nuevo and Cambria at Kangaroovale. No significant provenance or family differences were detected for core length at either site. The estimates of heritability for wood density were all above 0.50 and generally higher at Kaingaroa than at Kangaroovale. Estimates of additive genetic correlations between wood density and core length were imprecise. Genotype × site interactions for density appeared minor (estimated type-B genetic correlation= 0.70) despite substantial differences in rainfall and soils. The similarity of Cambria to Año Nuevo for density is an interesting result because the genetic base of the present Australian and New Zealand plantations has been shown to be from Año Nuevo and Monterey. Infusion of Cambria material would increase the overall genetic base of the radiata pine breeding programs, with potential long-term benefits, despite the often disappointing growth performance of material collected from Cambria.

@article{gapare_inheritance_2011,
	title = {Inheritance of spiral grain in the juvenile core of {Pinus} radiata},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x06-202},
	doi = {10/c2hfh2},
	abstract = {Spiral grain is the angular arrangement of fibres in a tangential plane with reference to the pith or vertical tree axis. Spiral grain angles exceeding 5° can cause wood to twist, which may result ...},
	language = {en},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press Ottawa, Canada},
	author = {Gapare, Washington and Hathorn, Adrian and Kain, Dominic and Matheson, Colin and Wu, Harry},
	month = dec,
	year = {2011},
}

Spiral grain is the angular arrangement of fibres in a tangential plane with reference to the pith or vertical tree axis. Spiral grain angles exceeding 5° can cause wood to twist, which may result ...

@article{gapare_performance_2011,
	title = {Performance differences among ex situ native-provenance collections of {Pinus} radiata {D}. {Don}. 1: potential for infusion into breeding populations in {Australia} and {New} {Zealand}},
	volume = {7},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Performance differences among ex situ native-provenance collections of {Pinus} radiata {D}. {Don}. 1},
	url = {http://link.springer.com/10.1007/s11295-010-0343-5},
	doi = {10/cjz6bv},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gapare, Washington J. and Baltunis, Brian S. and Ivković, Miloš and Low, Charlie B. and Jefferson, Paul and Wu, Harry X.},
	month = apr,
	year = {2011},
	pages = {409--419},
}

@article{li_transcriptome_2011,
	title = {Transcriptome profiling of {Pinus} radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics},
	volume = {12},
	issn = {1471-2164},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-480},
	doi = {10/cg5tp5},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genomics},
	author = {Li, Xinguo and Wu, Harry X and Southerton, Simon G},
	month = dec,
	year = {2011},
	pages = {480},
}

@article{li_transcriptome_2011,
	title = {Transcriptome profiling of wood maturation in {Pinus} radiata identifies differentially expressed genes with implications in juvenile and mature wood variation},
	volume = {487},
	issn = {03781119},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378111911003659},
	doi = {10/dc32cg},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Gene},
	author = {Li, Xinguo and Wu, Harry X. and Southerton, Simon G.},
	month = nov,
	year = {2011},
	pages = {62--71},
}

@article{dillon_allelic_2010,
	title = {Allelic {Variation} in {Cell} {Wall} {Candidate} {Genes} {Affecting} {Solid} {Wood} {Properties} in {Natural} {Populations} and {Land} {Races} of \textit{{Pinus} radiata}},
	volume = {185},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/185/4/1477/6063711},
	doi = {10/fdj9jt},
	abstract = {Abstract
            Forest trees are ideally suited to association mapping due to their high levels of diversity and low genomic linkage disequilibrium. Using an association mapping approach, single-nucleotide polymorphism (SNP) markers influencing quantitative variation in wood quality were identified in a natural population of Pinus radiata. Of 149 sites examined, 10 demonstrated significant associations (P \< 0.05, q \< 0.1) with one or more traits after accounting for population structure and experimentwise error. Without accounting for marker interactions, phenotypic variation attributed to individual SNPs ranged from 2 to 6.5\%. Undesirable negative correlations between wood quality and growth were not observed, indicating potential to break negative correlations by selecting for individual SNPs in breeding programs. Markers that yielded significant associations were reexamined in an Australian land race. SNPs from three genes (PAL1, PCBER, and SUSY) yielded significant associations. Importantly, associations with two of these genes validated associations with density previously observed in the discovery population. In both cases, decreased wood density was associated with the minor allele, suggesting that these SNPs may be under weak negative purifying selection for density in the natural populations. These results demonstrate the utility of LD mapping to detect associations, even when the power to detect SNPs with small effect is anticipated to be low.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Genetics},
	author = {Dillon, S K and Nolan, M and Li, W and Bell, C and Wu, H X and Southerton, S G},
	month = aug,
	year = {2010},
	pages = {1477--1487},
}

Abstract Forest trees are ideally suited to association mapping due to their high levels of diversity and low genomic linkage disequilibrium. Using an association mapping approach, single-nucleotide polymorphism (SNP) markers influencing quantitative variation in wood quality were identified in a natural population of Pinus radiata. Of 149 sites examined, 10 demonstrated significant associations (P < 0.05, q < 0.1) with one or more traits after accounting for population structure and experimentwise error. Without accounting for marker interactions, phenotypic variation attributed to individual SNPs ranged from 2 to 6.5%. Undesirable negative correlations between wood quality and growth were not observed, indicating potential to break negative correlations by selecting for individual SNPs in breeding programs. Markers that yielded significant associations were reexamined in an Australian land race. SNPs from three genes (PAL1, PCBER, and SUSY) yielded significant associations. Importantly, associations with two of these genes validated associations with density previously observed in the discovery population. In both cases, decreased wood density was associated with the minor allele, suggesting that these SNPs may be under weak negative purifying selection for density in the natural populations. These results demonstrate the utility of LD mapping to detect associations, even when the power to detect SNPs with small effect is anticipated to be low.

@article{dillon_association_2010,
	title = {Association genetics reveal candidate gene {SNPs} affecting wood properties in \textit{{Pinus} radiata}},
	volume = {73},
	issn = {0004-9158, 2325-6087},
	url = {https://www.tandfonline.com/doi/full/10.1080/00049158.2010.10676326},
	doi = {10/gkgfrf},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	author = {Dillon, S. K. and Nolan, M. F. and Wu, H. and Southerton, S. G.},
	month = jan,
	year = {2010},
	pages = {185--190},
}

@article{dillon_association_2010,
	title = {Association genetics reveal candidate gene {SNPs} affecting wood properties in {Pinus} radiata},
	volume = {73},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2010.10676326},
	doi = {10/gkgfrf},
	abstract = {Association or linkage disequilibrium (LD) mapping is an emerging approach for identifying molecular markers linked to phenotypic variation. Forest trees are ideally suited to association mapping due to their low genomic LD which permits highresolution mapping of marker associations. Using this approach several single-nucleotide polymorphisms (SNPs) potentially influencing economically important wood traits (density, cellulose microfibril angle and modulus of elasticity) were identified in a Pinus radiata provenance trial. One hundred and forty-nine SNP markers from 44 cell wall candidate genes were examined. After accounting for population structure and multiple testing, 15 SNPs demonstrated significant associations at P {\textless} 0.05. We have demonstrated that linkage disequilibrium in the native populations of P. radiata decays within the length of a gene. Therefore, the identified associations may result from the SNP under examination, or at least a linked SNP within the same gene. Without accounting for multi-colinearity between markers, the proportion of trait variance attributed to individual SNPs ranged from 1.5\% to 6.5\%. SNP associations are presently undergoing validation in a second-generation Southern Tree Breeding Association progeny trial. The small proportion of total quantitative variation contributed by individual SNPs indicates molecular breeding strategies would achieve greatest gains using combinations of SNPs for marker-assisted selection. Establishing methods for efficient transfer of validated SNPs into breeding selection models is essential for the uptake of the marker technology identified here, and is the focus of ongoing research.},
	number = {3},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	publisher = {Taylor \& Francis},
	author = {Dillon, S. K. and Nolan, M. F. and Wu, H. and Southerton, S. G.},
	month = jan,
	year = {2010},
	note = {\_eprint: https://doi.org/10.1080/00049158.2010.10676326},
	keywords = {Pinus radiata, genetic variation, marker-aided selection, molecular markers, phenotypic variation, wood properties},
	pages = {185--190},
}

Association or linkage disequilibrium (LD) mapping is an emerging approach for identifying molecular markers linked to phenotypic variation. Forest trees are ideally suited to association mapping due to their low genomic LD which permits highresolution mapping of marker associations. Using this approach several single-nucleotide polymorphisms (SNPs) potentially influencing economically important wood traits (density, cellulose microfibril angle and modulus of elasticity) were identified in a Pinus radiata provenance trial. One hundred and forty-nine SNP markers from 44 cell wall candidate genes were examined. After accounting for population structure and multiple testing, 15 SNPs demonstrated significant associations at P \textless 0.05. We have demonstrated that linkage disequilibrium in the native populations of P. radiata decays within the length of a gene. Therefore, the identified associations may result from the SNP under examination, or at least a linked SNP within the same gene. Without accounting for multi-colinearity between markers, the proportion of trait variance attributed to individual SNPs ranged from 1.5% to 6.5%. SNP associations are presently undergoing validation in a second-generation Southern Tree Breeding Association progeny trial. The small proportion of total quantitative variation contributed by individual SNPs indicates molecular breeding strategies would achieve greatest gains using combinations of SNPs for marker-assisted selection. Establishing methods for efficient transfer of validated SNPs into breeding selection models is essential for the uptake of the marker technology identified here, and is the focus of ongoing research.

@article{ivkovic_bio-economic_2010,
	title = {Bio-economic {Modelling} as a {Method} for {Determining} {Economic} {Weights} for {Optimal} {Multiple}-{Trait} {Tree} {Selection}},
	volume = {59},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2010-0010},
	doi = {10/gkgftk},
	abstract = {Abstract
            A bio-economic model provides a framework for simultaneously considering breeding, management, and production decisions. Such a model should result in optimal breeding (and silvicultural) objectives if main goals of a production system are well defined. Historically estimation of economic weights for breeding-objective traits has been based on partial regressions and profit functions relating only to certain parts of the production system. A bio-economic model includes effects of growth rate, branching, form, and wood quality on all production system components and on overall profitability of an integrated production system. However, long rotation cycles in forestry make determination of relative economic values for the breeding-objective traits particularly difficult. When modelling complex systems under uncertainty about future production goals, there are necessary trade offs between the complexity of the model and the use of simplifying assumptions.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Ivković, M. and Wu, H. and Kumar, S.},
	month = dec,
	year = {2010},
	pages = {77--90},
}

Abstract A bio-economic model provides a framework for simultaneously considering breeding, management, and production decisions. Such a model should result in optimal breeding (and silvicultural) objectives if main goals of a production system are well defined. Historically estimation of economic weights for breeding-objective traits has been based on partial regressions and profit functions relating only to certain parts of the production system. A bio-economic model includes effects of growth rate, branching, form, and wood quality on all production system components and on overall profitability of an integrated production system. However, long rotation cycles in forestry make determination of relative economic values for the breeding-objective traits particularly difficult. When modelling complex systems under uncertainty about future production goals, there are necessary trade offs between the complexity of the model and the use of simplifying assumptions.

@article{ivkovic_breeding_2010,
	title = {Breeding against dothistroma needle blight of radiata pine in {Australia}},
	volume = {40},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/X10-097},
	doi = {10/b72bt5},
	abstract = {Pine needle blight, caused by Dothistroma septosporum (Dorog.) M. Morelet, is one of the most serious foliar diseases of Pinus spp. in Australia and New Zealand. In 16 Pinus radiata (D.Don.) progeny trials in northeastern Victoria, Australia, Dothistroma-caused defoliation varied widely among trials and assessment years, ranging from 5\% to 65\%. The estimated narrow sense heritability ranged from nonsignificant to as high as 0.69 with a median of 0.36. Spatial autocorrelation of residuals accounted for a significant proportion of residual variance, and that increased heritability estimates. Genetic correlation between defoliation scores at an early age and growth at a later age was negative with a median value of –0.39. Phenotypic correlation between defoliation and survival was low and negative with a median value of –0.11. Economic analyses indicated that at sites with a high risk of infection, the effect of reducing defoliation on profitability was comparable with that of increasing growth at sites free from infection. The genetic parameters and economic impacts of Dothistroma were used to derive selection indices and include resistance to defoliation into the current breeding objective for radiata pine.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Canadian Journal of Forest Research},
	author = {Ivković, Miloš and Baltunis, Brian and Gapare, Washington and Sasse, Jo and Dutkowski, Gregory and Elms, Stephen and Wu, Harry},
	month = aug,
	year = {2010},
	pages = {1653--1660},
}

Pine needle blight, caused by Dothistroma septosporum (Dorog.) M. Morelet, is one of the most serious foliar diseases of Pinus spp. in Australia and New Zealand. In 16 Pinus radiata (D.Don.) progeny trials in northeastern Victoria, Australia, Dothistroma-caused defoliation varied widely among trials and assessment years, ranging from 5% to 65%. The estimated narrow sense heritability ranged from nonsignificant to as high as 0.69 with a median of 0.36. Spatial autocorrelation of residuals accounted for a significant proportion of residual variance, and that increased heritability estimates. Genetic correlation between defoliation scores at an early age and growth at a later age was negative with a median value of –0.39. Phenotypic correlation between defoliation and survival was low and negative with a median value of –0.11. Economic analyses indicated that at sites with a high risk of infection, the effect of reducing defoliation on profitability was comparable with that of increasing growth at sites free from infection. The genetic parameters and economic impacts of Dothistroma were used to derive selection indices and include resistance to defoliation into the current breeding objective for radiata pine.

@article{li_comparative_2010,
	title = {Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants},
	volume = {10},
	issn = {1471-2148},
	url = {http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-190},
	doi = {10/bwhkfp},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Evolutionary Biology},
	author = {Li, Xinguo and Wu, Harry X and Southerton, Simon G},
	year = {2010},
	pages = {190},
}

@article{sanchez_effect_2010,
	title = {Effect of selection method on genetic correlation and gain in a two-trait selection scheme},
	volume = {74},
	doi = {10/f2467c},
	abstract = {Adverse genetic correlations between wood volume and quality traits are one of the main constraints in advancing radiata pine and other pine breeding programs. To overcome or deal with adverse genetic correlation in radiata pine and other conifer breeding programs, a Monte Carlo simulation study for the adversely correlated traits DBH and wood density was conducted using allele-based models. Two allelic models were generated for the study: a mixed-loci model using independent and pleiotropic loci (i.e. each locus affecting more than one trait) for adversely correlated traits and an all-antagonistic-pleiotropic-loci model. Selection was conducted for three scenarios: the first was based on a single trait, the second on index selection for two adversely correlated traits (DBH and wood density) with equal or, third, unequal economic weights. Results indicated that: 1. Adverse genetic correlation tends to increase under pleiotropic models with selection. 2. Genetic gains for adversely correlated traits (such as DBH and wood density) could be made for many generations with selective breeding if there are independent loci for individual traits. 3. New alleles (from infusion or mutation) with less antagonistic effect are required for further genetic gain in the two adversely correlated traits simultaneously if all independent alleles are fixed (i.e. without allelic variation) and pleiotropic loci with antagonistic effects are not fixed. 4. For short-term genetic gain in adversely correlated traits, selection based on two traits simultaneously is more effective than selection based on a single trait. Developing economic weights through breeding objectives is a sound approach for short-term breeding programs. Economic weights will influence genetic gain for individual traits and genetic correla tion between traits. 5. For long-term genetic gain, dissecting the genetic basis of traits using a large association population is recommended. When the genetic mechanisms controlling adversely correlated traits are better understood, an allele model could be developed to study optimal strategies under different gene actions.},
	journal = {Australian Forestry},
	author = {Sanchez, Leopoldo and Wu, Harry},
	month = dec,
	year = {2010},
	pages = {36--42},
}

Adverse genetic correlations between wood volume and quality traits are one of the main constraints in advancing radiata pine and other pine breeding programs. To overcome or deal with adverse genetic correlation in radiata pine and other conifer breeding programs, a Monte Carlo simulation study for the adversely correlated traits DBH and wood density was conducted using allele-based models. Two allelic models were generated for the study: a mixed-loci model using independent and pleiotropic loci (i.e. each locus affecting more than one trait) for adversely correlated traits and an all-antagonistic-pleiotropic-loci model. Selection was conducted for three scenarios: the first was based on a single trait, the second on index selection for two adversely correlated traits (DBH and wood density) with equal or, third, unequal economic weights. Results indicated that: 1. Adverse genetic correlation tends to increase under pleiotropic models with selection. 2. Genetic gains for adversely correlated traits (such as DBH and wood density) could be made for many generations with selective breeding if there are independent loci for individual traits. 3. New alleles (from infusion or mutation) with less antagonistic effect are required for further genetic gain in the two adversely correlated traits simultaneously if all independent alleles are fixed (i.e. without allelic variation) and pleiotropic loci with antagonistic effects are not fixed. 4. For short-term genetic gain in adversely correlated traits, selection based on two traits simultaneously is more effective than selection based on a single trait. Developing economic weights through breeding objectives is a sound approach for short-term breeding programs. Economic weights will influence genetic gain for individual traits and genetic correla tion between traits. 5. For long-term genetic gain, dissecting the genetic basis of traits using a large association population is recommended. When the genetic mechanisms controlling adversely correlated traits are better understood, an allele model could be developed to study optimal strategies under different gene actions.

@article{baltunis_genetic_2010,
	title = {Genetic {Parameters} and {Genotype} by {Environment} {Interaction} in {Radiata} {Pine} for {Growth} and {Wood} {Quality} {Traits} in {Australia}},
	volume = {59},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2010-0014},
	doi = {10/gkgfsb},
	abstract = {Abstract
            
              The phenotypic response of genotypes across different environments can be quantified by estimating the genotype by environment interaction (GxE). In a practical sense, GxE means that the relative performance of genotypes does not remain constant under all test conditions. Genetic parameters and genotype by environment interactions for wood density, growth, branching characteristics and stem straightness were investigated in eight radiata pine progeny trials derived from a second generation breeding population in Australia. Five trials were on the mainland, while three trials were in Tasmania. Generally, ĥ
              2
              for density {\textgreater} branch angle {\textgreater} stem straightness {\textgreater} tree diameter {\textgreater} branch size; and significant ĥ
              2
              was observed for all traits and at all trials with only two exceptions. Genetic correlations were estimated among the five traits, and a large negative genetic correlation observed between wood density and tree diameter indicated that a selection strategy should be developed in dealing with this adverse genetic correlation in advanced generations of breeding for radiata pine. Interactions for density, branch angle, and stem straightness were small within the two regions. Overall, branch angle had the least GxE, followed by density and stem straightness. Growth traits (tree diameter and branch size) tended to be the most interactive with substantial GxE present. Genotype by regional interactions (Mainland versus Tasmania) revealed that density and branch angle had the least interactions (ȓ
              B
              = 0.98 and ȓ
              B
              = 0.95, respectively). Branch size and tree diameter had the highest interactions among the two regions (ȓ
              B
              = 0.55 and ȓ
              B
              = 0.63, respectively). Within Tasmania, only branch size and tree diameter had a sizable interaction within the three sites. In contrast, there was little interaction for tree diameter among the Mainland trials. Branch size in the Mainland trials had a similar size of interaction as in Tasmania. Further research is recommended in identifying the cause of GxE for tree diameter and branch size in radiata pine across the entire radiata pine estate in Australia.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Baltunis, Brian. S. and Gapare, W. J. and Wu, H. X.},
	month = dec,
	year = {2010},
	pages = {113--124},
}

Abstract The phenotypic response of genotypes across different environments can be quantified by estimating the genotype by environment interaction (GxE). In a practical sense, GxE means that the relative performance of genotypes does not remain constant under all test conditions. Genetic parameters and genotype by environment interactions for wood density, growth, branching characteristics and stem straightness were investigated in eight radiata pine progeny trials derived from a second generation breeding population in Australia. Five trials were on the mainland, while three trials were in Tasmania. Generally, ĥ 2 for density \textgreater branch angle \textgreater stem straightness \textgreater tree diameter \textgreater branch size; and significant ĥ 2 was observed for all traits and at all trials with only two exceptions. Genetic correlations were estimated among the five traits, and a large negative genetic correlation observed between wood density and tree diameter indicated that a selection strategy should be developed in dealing with this adverse genetic correlation in advanced generations of breeding for radiata pine. Interactions for density, branch angle, and stem straightness were small within the two regions. Overall, branch angle had the least GxE, followed by density and stem straightness. Growth traits (tree diameter and branch size) tended to be the most interactive with substantial GxE present. Genotype by regional interactions (Mainland versus Tasmania) revealed that density and branch angle had the least interactions (ȓ B = 0.98 and ȓ B = 0.95, respectively). Branch size and tree diameter had the highest interactions among the two regions (ȓ B = 0.55 and ȓ B = 0.63, respectively). Within Tasmania, only branch size and tree diameter had a sizable interaction within the three sites. In contrast, there was little interaction for tree diameter among the Mainland trials. Branch size in the Mainland trials had a similar size of interaction as in Tasmania. Further research is recommended in identifying the cause of GxE for tree diameter and branch size in radiata pine across the entire radiata pine estate in Australia.

@article{gapare_genetic_2010,
	title = {Genetic stability of wood density and diameter in {Pinus} radiata {D}. {Don} plantation estate across {Australia}},
	volume = {6},
	copyright = {2009 Springer-Verlag},
	issn = {1614-2950},
	url = {https://link.springer.com/article/10.1007/s11295-009-0233-x},
	doi = {10/dg26z4},
	abstract = {Genetic variation for wood quality traits and diameter growth for radiata pine (Pinus radiata D. Don) at age 20/21 years was estimated from eight trials in Australia. The traits studied were wood density, acoustic time-of-flight (an indirect measure of stiffness) and diameter at breast height (DBH). Wood density and DBH exhibited significant additive genetic variation whereas non-additive effects were not significantly different from zero. Time of flight was also not significantly different from zero for both additive and non-additive effects, respectively. Average single-site heritability estimates (±SE) for wood density and DBH were 0.38 ± 0.10 and 0.16 ± 0.08, respectively. Pooled-site heritability estimates for wood density and DBH were 0.38 ± 0.10 and 0.08 ± 0.10, respectively. For density, there was little evidence of genotype-by-environment interaction (GEI) across the eight trials at the additive level (type B additive genetic correlation; r BADD = 0.73 ± 0.08) and type B genetic correlation for full-sib families (r BFS = 0.64 ± 0.08). In contrast, the type B additive genetic correlation for DBH was lower, (r BADD = 0.51 ± 0.14), suggesting evidence of GEI. However, type B genetic correlation for full-sib families was moderate (0.63 ± 0.11) for DBH, suggesting that there may be some stable full-sib families. On the basis of the results of this study, GEI should be considered in order to optimise deployment of improved germplasm in Australia.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	publisher = {Springer-Verlag},
	author = {Gapare, Washington J. and Ivković, Miloš and Baltunis, Brian S. and Matheson, Colin A. and Wu, Harry X.},
	month = jan,
	year = {2010},
	note = {Company: Springer
Distributor: Springer
Institution: Springer
Label: Springer
Number: 1},
	pages = {113--125},
}

Genetic variation for wood quality traits and diameter growth for radiata pine (Pinus radiata D. Don) at age 20/21 years was estimated from eight trials in Australia. The traits studied were wood density, acoustic time-of-flight (an indirect measure of stiffness) and diameter at breast height (DBH). Wood density and DBH exhibited significant additive genetic variation whereas non-additive effects were not significantly different from zero. Time of flight was also not significantly different from zero for both additive and non-additive effects, respectively. Average single-site heritability estimates (±SE) for wood density and DBH were 0.38 ± 0.10 and 0.16 ± 0.08, respectively. Pooled-site heritability estimates for wood density and DBH were 0.38 ± 0.10 and 0.08 ± 0.10, respectively. For density, there was little evidence of genotype-by-environment interaction (GEI) across the eight trials at the additive level (type B additive genetic correlation; r BADD = 0.73 ± 0.08) and type B genetic correlation for full-sib families (r BFS = 0.64 ± 0.08). In contrast, the type B additive genetic correlation for DBH was lower, (r BADD = 0.51 ± 0.14), suggesting evidence of GEI. However, type B genetic correlation for full-sib families was moderate (0.63 ± 0.11) for DBH, suggesting that there may be some stable full-sib families. On the basis of the results of this study, GEI should be considered in order to optimise deployment of improved germplasm in Australia.

@article{baltunis_genotype_2010,
	title = {Genotype by {Environmental} {Interaction} for {DBH}, {Wood} {Density}, {Branch} {Angle}, {Branch} {Size}, and {Stem} {Straightness} in {Eight} {Young} {Pinus} radiata {D}. {Don} {Trials} in {Australia}},
	journal = {Silvae Genetica},
	author = {Baltunis, Brian and Gapare, Washington and {WJ} and Wu, Harry},
	month = jan,
	year = {2010},
	keywords = {⛔ No DOI found},
}

@article{ivkovic_risks_2010,
	title = {Risks affecting breeding objectives for radiata pine in {Australia}},
	volume = {73},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2010.10676338},
	doi = {10/gkgfsd},
	abstract = {This paper examines the effects of climatic and biotic risks—drought, Essigella aphid, Dothistroma needle blight and Fusarium pitch canker—on the Pinus radiata production system in Australia. These risks were examined in relation to climatic variables in order to develop ‘hazard ratings’ for planting sites. Bio-economic models were developed to link the risks with the established breeding objective for solid wood production. Economic weights were derived for resistance traits that can be used in index selection for breeding and deployment. Under one scenario, drought-affected sites can achieve an internal rate of return of {\textgreater}7.0\% only if the land rental is sufficiently low, that is {\textgreater}\$25 ha−1 y−1, but replanting costs and volume losses due to mortality can be significant. An average of 13.5\% defoliation caused by Essigella aphid would reduce volume growth over a rotation period by about 10\%. A modest increase in profitability can be achieved through deployment of Essigella-resistant genotypes. Reduction of volume growth by Dothistroma defoliation at an early age (4–10 y) had a relatively small effect on subsequent yield reduction. At a site with a high level of infection, however, the profitability of improving Dothistroma resistance was similar to that for improving growth on uninfected sites. The economic importance of risk traits relative to MAI over the entire radiata pine plantation estate was generally low: 4\% for pine aphid, 0.6\% for needle blight and 1.3\% for pitch canker resistance. Essigella pine aphid is the most important pest currently affecting the productivity of radiata pine plantations in Australia.},
	number = {4},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	publisher = {Taylor \& Francis},
	author = {Ivković, M. and Gapare, W. J. and Wharton, T. and Jovanovic, T. and Elms, S. and McRae, T. A. and Wu, H. X.},
	month = jan,
	year = {2010},
	note = {\_eprint: https://doi.org/10.1080/00049158.2010.10676338},
	keywords = {Dothistroma septosporum, Essigella californica, Fusarium circinatum, Pinus radiata, breeding, diseases, economic analysis, insect pests, objectives, risk assessment},
	pages = {265--278},
}

This paper examines the effects of climatic and biotic risks—drought, Essigella aphid, Dothistroma needle blight and Fusarium pitch canker—on the Pinus radiata production system in Australia. These risks were examined in relation to climatic variables in order to develop ‘hazard ratings’ for planting sites. Bio-economic models were developed to link the risks with the established breeding objective for solid wood production. Economic weights were derived for resistance traits that can be used in index selection for breeding and deployment. Under one scenario, drought-affected sites can achieve an internal rate of return of \textgreater7.0% only if the land rental is sufficiently low, that is \textgreater$25 ha−1 y−1, but replanting costs and volume losses due to mortality can be significant. An average of 13.5% defoliation caused by Essigella aphid would reduce volume growth over a rotation period by about 10%. A modest increase in profitability can be achieved through deployment of Essigella-resistant genotypes. Reduction of volume growth by Dothistroma defoliation at an early age (4–10 y) had a relatively small effect on subsequent yield reduction. At a site with a high level of infection, however, the profitability of improving Dothistroma resistance was similar to that for improving growth on uninfected sites. The economic importance of risk traits relative to MAI over the entire radiata pine plantation estate was generally low: 4% for pine aphid, 0.6% for needle blight and 1.3% for pitch canker resistance. Essigella pine aphid is the most important pest currently affecting the productivity of radiata pine plantations in Australia.

@article{li_seasonal_2010,
	title = {Seasonal reorganization of the xylem transcriptome at different tree ages reveals novel insights into wood formation in {Pinus} radiata},
	volume = {187},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/j.1469-8137.2010.03333.x},
	doi = {10/bhvgjx},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Li, Xinguo and Wu, Harry X. and Southerton, Simon G.},
	month = aug,
	year = {2010},
	pages = {764--776},
}

@article{li_use_2010,
	title = {Use of chromosome walking in discovery of single-nucleotide polymorphism in noncoding regions of a candidate actin gene in {Pinus} radiata},
	volume = {51},
	issn = {2190-3883},
	doi = {10/d5385t},
	abstract = {Untranslated regions (UTRs) of eukaryotic mRNAs play crucial roles in post-transcriptional regulation of gene expression via the modulation of nucleocytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Single-nucleotide polymorphisms (SNPs) in UTRs of a candidate gene may also change the post-transcriptional regulation of a gene or function by nucleotide mutation. For species that have not been entirely sequenced genomically, new methods need to be devised to discover SNPs in noncoding regions of candidate genes. In this study, based on the expressed sequence tag (EST) of Pinus radiata (Monterey pine), we obtained all the sequences of UTRs of the actin gene by using a chromosome walking method. We also detected all the SNPs in and around the coding region of the actin gene. In this way, the full genomic sequence (2154 bp) of the actin gene was identified, including the 5\’UTR, introns, the coding sequence, and the 3\’UTR. PCR amplification and DNA fragment sequencing from 200 unrelated P. radiata trees revealed a total of 21 SNPs in the actin gene, of which 3 were located in the 5\’UTR, 3 in the introns, 10 in the coding sequence, and 5 in the 3\’UTR. We show that chromosome walking can be used for obtaining the sequence of UTRs, and then, based on this sequence, to discover SNPs in the noncoding regions of candidate genes from this species without an entire genomic sequence.},
	language = {eng},
	number = {3},
	journal = {Journal of Applied Genetics},
	author = {Li, W. and Li, H. and Wu, H. and Chen, X.-Y.},
	year = {2010},
	keywords = {Actins, Base Sequence, Chromosome Walking, Expressed Sequence Tags, Genes, Plant, Genome, Plant, Molecular Sequence Data, Pinus, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Untranslated Regions},
	pages = {275--281},
}

Untranslated regions (UTRs) of eukaryotic mRNAs play crucial roles in post-transcriptional regulation of gene expression via the modulation of nucleocytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Single-nucleotide polymorphisms (SNPs) in UTRs of a candidate gene may also change the post-transcriptional regulation of a gene or function by nucleotide mutation. For species that have not been entirely sequenced genomically, new methods need to be devised to discover SNPs in noncoding regions of candidate genes. In this study, based on the expressed sequence tag (EST) of Pinus radiata (Monterey pine), we obtained all the sequences of UTRs of the actin gene by using a chromosome walking method. We also detected all the SNPs in and around the coding region of the actin gene. In this way, the full genomic sequence (2154 bp) of the actin gene was identified, including the 5’UTR, introns, the coding sequence, and the 3’UTR. PCR amplification and DNA fragment sequencing from 200 unrelated P. radiata trees revealed a total of 21 SNPs in the actin gene, of which 3 were located in the 5’UTR, 3 in the introns, 10 in the coding sequence, and 5 in the 3’UTR. We show that chromosome walking can be used for obtaining the sequence of UTRs, and then, based on this sequence, to discover SNPs in the noncoding regions of candidate genes from this species without an entire genomic sequence.

@article{baltunis_comparisons_2009,
	title = {Comparisons of genetic parameters and clonal value predictions from clonal trials and seedling base population trials of radiata pine},
	volume = {5},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-008-0172-y},
	doi = {10/bwq6cq},
	abstract = {Different methods for predicting clonal values were explored for diameter growth (diameter at breast height (DBH)) in a radiata pine clonal forestry program: (1) clones were analyzed with a full model in which the total genetic variation was partitioned into additive, dominance, and epistasis (Clone Only—Full Model); (2) clones were analyzed together with seedling base population data (Clone Plus Seedling (CPS)), and (3) clones were analyzed with a reduced model in which the only genetic term was the total genetic variance (Clone Only—Reduced Model). DBH was assessed at age 5 for clones and between ages 4 to 13 at the seedling trials. Significant additive, dominance, and epistatic genetic effects were estimated for DBH using the CPS model. Nonadditive genetic effects for DBH were 87\% as large as additive genetic effects. Narrow-sense (\$\${\textbackslash}hat h{\textasciicircum}2 \$\$) and broad-sense (\$\${\textbackslash}hat H{\textasciicircum}2 \$\$) heritability estimates for DBH using the CPS model were 0.14 ± 0.01 and 0.26 ± 0.01, respectively. Accuracy of predicted clonal values increased 4\% by combining the clone and seedling data over using clonal data alone, resulting in greater confidence in the predicted genetic performance of clones. Our results indicate that exploiting nonadditive genetic effects in clonal varieties will generate greater gains than that typically obtainable from conventional family-based forestry of radiata pine. The predicted genetic gain for DBH from deployment of the top 5\% of clones was 24.0\%—an improvement of more than 100\% over family forestry at the same selection intensity. We conclude that it is best practice to predict clonal values by incorporating seedling base population data in the clonal analysis.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Baltunis, Brian S. and Wu, Harry X. and Dungey, Heidi S. and Mullin, T. J. “Tim” and Brawner, Jeremy T.},
	month = jan,
	year = {2009},
	pages = {269--278},
}

Different methods for predicting clonal values were explored for diameter growth (diameter at breast height (DBH)) in a radiata pine clonal forestry program: (1) clones were analyzed with a full model in which the total genetic variation was partitioned into additive, dominance, and epistasis (Clone Only—Full Model); (2) clones were analyzed together with seedling base population data (Clone Plus Seedling (CPS)), and (3) clones were analyzed with a reduced model in which the only genetic term was the total genetic variance (Clone Only—Reduced Model). DBH was assessed at age 5 for clones and between ages 4 to 13 at the seedling trials. Significant additive, dominance, and epistatic genetic effects were estimated for DBH using the CPS model. Nonadditive genetic effects for DBH were 87% as large as additive genetic effects. Narrow-sense ($$\hat h\textasciicircum2 $$) and broad-sense ($$\hat H\textasciicircum2 $$) heritability estimates for DBH using the CPS model were 0.14 ± 0.01 and 0.26 ± 0.01, respectively. Accuracy of predicted clonal values increased 4% by combining the clone and seedling data over using clonal data alone, resulting in greater confidence in the predicted genetic performance of clones. Our results indicate that exploiting nonadditive genetic effects in clonal varieties will generate greater gains than that typically obtainable from conventional family-based forestry of radiata pine. The predicted genetic gain for DBH from deployment of the top 5% of clones was 24.0%—an improvement of more than 100% over family forestry at the same selection intensity. We conclude that it is best practice to predict clonal values by incorporating seedling base population data in the clonal analysis.

@article{zhang_discussion_2009,
	title = {Discussion on {Role} of {Forest} to {Control} {Agricultural} {Non}-{Point} {Source} {Pollution} in {Taihu} {Lake} {Basin}-{Based} on {Source}-{Sink} {Analysis}},
	volume = {1},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	url = {http://www.scirp.org/Journal/Paperabs.aspx?paperid=865},
	doi = {10/cfkp6v},
	abstract = {Taihu Lake is located at the center of Changjiang delta region, the Lake and its effluent rivers are important water sources for 40 million around inhabitants and rapidly increasing industrial factories in Shanghai, Ji-angsu and Zhejiang. The pollutants originate mainly from acidy rain, home sewage of the vast number of inhabitants, livestock manure, agricultural fertilizers \& pesticides applied over fields in the drainage basin, and the industrial sewage. Due to the kinds of pollutants, the Lake water is getting highly eutrophic, with frequent blooms of blue-green algae. Compared with point-source pollutants, diffuse pollution is much com-plicated and difficult to control. Thus combating non-point pollution (NPP) is paid much great attention. Based on analysis on source-sink of NPP in Taihu Lake basin, it is concluded that the function of forests on NPP control is multiple and important by both source reduction and sink expansion. The primary objective of planting trees through constructing forested wetlands and establishing riparian forest buffers is to control soil \& water erosion, decrease agrochemicals application, and improve farming conditions in the region of Taihu Lake basin. Moreover forests help to intercept acidy rain, protect streambanks, uptake nutrients, hold up pollutants and provide habitat for wildlife.},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Journal of Water Resource and Protection},
	publisher = {Scientific Research Publishing},
	author = {Zhang, Jianfeng and Jiang, Jingmin and Zhang, Zhijian and Shan, Qihua and Chen, Guangcai and Wang, Ying and Xu, Yonghui and Wu, Harry and Abarquez, Aljoy},
	month = nov,
	year = {2009},
	note = {Number: 5},
	pages = {345--350},
}

Taihu Lake is located at the center of Changjiang delta region, the Lake and its effluent rivers are important water sources for 40 million around inhabitants and rapidly increasing industrial factories in Shanghai, Ji-angsu and Zhejiang. The pollutants originate mainly from acidy rain, home sewage of the vast number of inhabitants, livestock manure, agricultural fertilizers & pesticides applied over fields in the drainage basin, and the industrial sewage. Due to the kinds of pollutants, the Lake water is getting highly eutrophic, with frequent blooms of blue-green algae. Compared with point-source pollutants, diffuse pollution is much com-plicated and difficult to control. Thus combating non-point pollution (NPP) is paid much great attention. Based on analysis on source-sink of NPP in Taihu Lake basin, it is concluded that the function of forests on NPP control is multiple and important by both source reduction and sink expansion. The primary objective of planting trees through constructing forested wetlands and establishing riparian forest buffers is to control soil & water erosion, decrease agrochemicals application, and improve farming conditions in the region of Taihu Lake basin. Moreover forests help to intercept acidy rain, protect streambanks, uptake nutrients, hold up pollutants and provide habitat for wildlife.

@article{li_generation_2009,
	title = {Generation and analysis of expressed sequence tags from six developing xylem libraries in {Pinus} radiata {D}. {Don}},
	volume = {10},
	issn = {1471-2164},
	doi = {10/b946xz},
	abstract = {BACKGROUND: Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. Pinus radiata D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine.
RESULTS: Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0\% of the 5,952 ESTs and 96.1\% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9\% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1\%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0\% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including CesA, tubulin, AGP, SAMS, actin, laccase, CCoAMT, MetE, phytocyanin, pectate lyase, cellulase, SuSy, expansin, chitinase and UDP-glucose dehydrogenase. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.
CONCLUSION: The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.},
	language = {eng},
	journal = {BMC genomics},
	author = {Li, Xinguo and Wu, Harry X. and Dillon, Shannon K. and Southerton, Simon G.},
	month = jan,
	year = {2009},
	keywords = {Cell Wall, Expressed Sequence Tags, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Library, Genes, Plant, Genome, Plant, Genomics, Pinus, RNA, Plant, Transcription Factors, Xylem},
	pages = {41},
}

BACKGROUND: Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. Pinus radiata D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine. RESULTS: Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0% of the 5,952 ESTs and 96.1% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including CesA, tubulin, AGP, SAMS, actin, laccase, CCoAMT, MetE, phytocyanin, pectate lyase, cellulase, SuSy, expansin, chitinase and UDP-glucose dehydrogenase. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development. CONCLUSION: The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.

@article{gapare_genetic_2009,
	title = {Genetic correlations among juvenile wood quality and growth traits and implications for selection strategy in {Pinus} radiata {D}. {Don}},
	volume = {66},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1051/forest/2009044},
	doi = {10/bbnt8q},
	abstract = {Juvenile wood quality in Pinus radiata is affected by factors such as low density, stiffness, and high microfibril angle, spiral grain, and shrinkage. Adverse genetic correlations between growth and wood quality traits remain as one of the main constraints in radiata pine advanced generation selection breeding program.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Gapare, Washington J. and Baltunis, Brian S. and Ivković, Miloš and Wu, Harry X.},
	month = jan,
	year = {2009},
	pages = {606--606},
}

Juvenile wood quality in Pinus radiata is affected by factors such as low density, stiffness, and high microfibril angle, spiral grain, and shrinkage. Adverse genetic correlations between growth and wood quality traits remain as one of the main constraints in radiata pine advanced generation selection breeding program.

@article{ding_mm_application_2008,
	title = {Application of {GGE} biplot analysis to evaluate genotype ({G}), environment ({E}) and {GxE} interaction on {Pinus} radiata: a case study},
	number = {38},
	urldate = {2021-06-10},
	journal = {N.Z.J. For. Sci.},
	author = {{Ding MM} and {Tier B} and {Yan W} and {Wu HX}},
	year = {2008},
	keywords = {⛔ No DOI found},
	pages = {132--142},
}

@article{wu_breeding_2008,
	title = {Breeding for {Wood} {Quality} and {Profit} in {Radiata} {Pine}: {A} {Review} of {Genetic} {Parameters}},
	volume = {38},
	shorttitle = {Breeding for {Wood} {Quality} and {Profit} in {Radiata} {Pine}},
	author = {Wu, Harry and Ivković, Miloš and Gapare, Washington and Matheson, Alastair and Baltunis, Brian and Powell, Michael and McRae, T.},
	month = jan,
	year = {2008},
}

@article{gapare_genetics_2008,
	title = {Genetics of {Shrinkage} in {Juvenile} {Trees} of {Pinus} radiata {D}. {Don} {From} {Two} {Test} {Sites} in {Australia}},
	volume = {57},
	url = {https://www.sciendo.com/article/10.1515/sg-2008-0022},
	doi = {10/gnj3pf},
	abstract = {To examine the genetic control of wood shrinkage (radial, tangential and longitudinal) in juvenile wood of radiata pine (Pinus radiata D. Don), we assessed samples collected at breast height in two related progeny tests of age 8 and 9 years, established at two different sites in Australia. Green to oven-dry tangential and radial shrinkage for the outer-rings was similar at both sites. Similarly, mean longitudinal shrinkage for the outer-rings was similar at both sites (0.3\%, ranging from 0.1 to 1.9 at Flynn and 0.4\%, ranging from 0.02 to 1.6, at Kromelite). Mean longitudinal shrinkage for the inner-rings was 4 times greater than that of the outerrings at both sites. The magnitude of the gradient of longitudinal shrinkage from pith to bark (0.001 to 2.9\%) is large enough to cause distortion problems including twist and warp, during drying of sawn boards. These values also suggest that shrinkage in the juvenile core of radiata pine is of major economic importance and therefore should be improved either through genetics or silviculture. Individual-tree narrow-sense individual heritability for tangential and radial shrinkage in the outer-rings (4-6) was moderate at Flynn (0.24 ± 0.09 and 0.26±0.07, respectively). There was a lack of significant genetic variation},
	language = {en},
	number = {1-6},
	urldate = {2021-11-22},
	journal = {Silvae Genetica},
	author = {Gapare, W. J. and Ivković, M. and Powell, M. B. and McRae, T. A. and Wu, H. X.},
	month = dec,
	year = {2008},
	pages = {145--151},
}

To examine the genetic control of wood shrinkage (radial, tangential and longitudinal) in juvenile wood of radiata pine (Pinus radiata D. Don), we assessed samples collected at breast height in two related progeny tests of age 8 and 9 years, established at two different sites in Australia. Green to oven-dry tangential and radial shrinkage for the outer-rings was similar at both sites. Similarly, mean longitudinal shrinkage for the outer-rings was similar at both sites (0.3%, ranging from 0.1 to 1.9 at Flynn and 0.4%, ranging from 0.02 to 1.6, at Kromelite). Mean longitudinal shrinkage for the inner-rings was 4 times greater than that of the outerrings at both sites. The magnitude of the gradient of longitudinal shrinkage from pith to bark (0.001 to 2.9%) is large enough to cause distortion problems including twist and warp, during drying of sawn boards. These values also suggest that shrinkage in the juvenile core of radiata pine is of major economic importance and therefore should be improved either through genetics or silviculture. Individual-tree narrow-sense individual heritability for tangential and radial shrinkage in the outer-rings (4-6) was moderate at Flynn (0.24 ± 0.09 and 0.26±0.07, respectively). There was a lack of significant genetic variation

@article{matheson_inheritance_2008,
	title = {Inheritance and genetic gain in wood stiffness in radiata pine assessed acoustically in young standing trees},
	volume = {57},
	number = {2},
	journal = {Silvae Genetica},
	author = {Matheson, A. C. and Gapare, W. J. and Ilic, J. and Wu, Harry X.},
	year = {2008},
	pages = {56--64},
}

@article{ding_multi-environment_2008,
	title = {Multi-environment trial analysis for {Pinus} radiata},
	volume = {38},
	abstract = {A stem-diameter data set of five combined trials of Pinus radiata D. Don was used to identify and determine the nature of genetics by environment (GxE) interaction. The restricted maximum likelihood approach was applied to handle the main issues of the multi-environment trial analysis: (1) Testing sources of heterogeneity of variance and lack of between-sites genetic correlation; (2) Modelling the heterogeneity of error variance among trials and micro-environmental variation within each trial; and (3) Selecting the best model for prediction of breeding values. Model comparison was based on the criterion of log-likelihood. The significance of variance components was tested by the likelihood ratio test which showed that all sources of GxE interactions were highly significant, indicating that GxE interactions occurred in these five trials due to both the heterogeneity of variances and the lack of correlation. Estimates of Type B genetic correlations were increased slightly by correcting for the heterogeneity of variances. The full model, which accommodated heterogeneity of error variances between trials, spatial variation within trials, and fitting a separate GxE interaction variance for each trial, was superior to other models for this multi-environment trial.},
	journal = {New Zealand Journal of Forestry Science},
	author = {Ding, M. and Tier, Bruce and Dutkowski, G.W. and Wu, Harry and Powell, Michael and McRae, T.A.},
	month = jan,
	year = {2008},
	keywords = {⛔ No DOI found},
	pages = {143--159},
}

A stem-diameter data set of five combined trials of Pinus radiata D. Don was used to identify and determine the nature of genetics by environment (GxE) interaction. The restricted maximum likelihood approach was applied to handle the main issues of the multi-environment trial analysis: (1) Testing sources of heterogeneity of variance and lack of between-sites genetic correlation; (2) Modelling the heterogeneity of error variance among trials and micro-environmental variation within each trial; and (3) Selecting the best model for prediction of breeding values. Model comparison was based on the criterion of log-likelihood. The significance of variance components was tested by the likelihood ratio test which showed that all sources of GxE interactions were highly significant, indicating that GxE interactions occurred in these five trials due to both the heterogeneity of variances and the lack of correlation. Estimates of Type B genetic correlations were increased slightly by correcting for the heterogeneity of variances. The full model, which accommodated heterogeneity of error variances between trials, spatial variation within trials, and fitting a separate GxE interaction variance for each trial, was superior to other models for this multi-environment trial.

@article{ivkovic_prediction_2008,
	title = {Prediction of wood stiffness, strength, and shrinkage in juvenile wood of radiata pine},
	volume = {43},
	issn = {1432-5225},
	url = {https://doi.org/10.1007/s00226-008-0232-3},
	doi = {10/bsmjjc},
	abstract = {Development of optimal ways to predict juvenile wood stiffness, strength, and stability using wood properties that can be measured with relative ease and low cost is a priority for tree breeding and silviculture. Wood static modulus of elasticity (MOE), modulus of rupture (MOR), radial, tangential, and longitudinal shrinkage (RS, TS, LS), wood density (DEN), sound wave velocity (SWV), spiral grain (SLG), and microfibril angle (MFA) were measured on juvenile wood samples from lower stem sections in two radiata pine test plantations. Variation between inner (rings 1–2 from pith) and outer (rings 3–6 from pith) rings was generally larger than that among trees. MOE and MOR were lower (50\%) in inner-rings than in outer-rings. RS and TS were higher (30–50\%) for outer-rings than inner-rings, but LS decreased rapidly ({\textgreater}200\%) from inner-rings to outer-rings. DEN had a higher correlation with MOR than with MOE, while MFA had a higher correlation with dry wood MOE than with MOR. SLG had higher significant correlation with MOE than with MOR. DEN and MOE had a weak, significant linear relationship with RS and TS, while MOE had a strong negative non-linear relationship with LS. Multiple regressions had a good potential as a method for predicting billet stiffness (R2 {\textgreater} 0.42), but had only a weak potential to predict wood strength and shrinkage (R2 {\textless} 0.22). For wood stiffness acoustic velocity measurements seemed to be the most practical, and for wood strength and stability acoustic velocity plus core density seemed to be the most practical measurements for predicting lower stem average in young trees.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Wood Science and Technology},
	author = {Ivković, Miloš and Gapare, Washington J. and Abarquez, Aljoy and Ilic, Jugo and Powell, Michael B. and Wu, Harry X.},
	month = oct,
	year = {2008},
	pages = {237},
}

Development of optimal ways to predict juvenile wood stiffness, strength, and stability using wood properties that can be measured with relative ease and low cost is a priority for tree breeding and silviculture. Wood static modulus of elasticity (MOE), modulus of rupture (MOR), radial, tangential, and longitudinal shrinkage (RS, TS, LS), wood density (DEN), sound wave velocity (SWV), spiral grain (SLG), and microfibril angle (MFA) were measured on juvenile wood samples from lower stem sections in two radiata pine test plantations. Variation between inner (rings 1–2 from pith) and outer (rings 3–6 from pith) rings was generally larger than that among trees. MOE and MOR were lower (50%) in inner-rings than in outer-rings. RS and TS were higher (30–50%) for outer-rings than inner-rings, but LS decreased rapidly (\textgreater200%) from inner-rings to outer-rings. DEN had a higher correlation with MOR than with MOE, while MFA had a higher correlation with dry wood MOE than with MOR. SLG had higher significant correlation with MOE than with MOR. DEN and MOE had a weak, significant linear relationship with RS and TS, while MOE had a strong negative non-linear relationship with LS. Multiple regressions had a good potential as a method for predicting billet stiffness (R2 \textgreater 0.42), but had only a weak potential to predict wood strength and shrinkage (R2 \textless 0.22). For wood stiffness acoustic velocity measurements seemed to be the most practical, and for wood strength and stability acoustic velocity plus core density seemed to be the most practical measurements for predicting lower stem average in young trees.

@article{li_single_2008,
	title = {Single nucleotide polymorphism discovery of {Pinus} radiata with chromosome walking {PCR} method},
	volume = {3},
	issn = {1673-3630},
	url = {https://doi.org/10.1007/s11461-008-0055-2},
	doi = {10/djzr4f},
	abstract = {In this paper, the basic principle of chromosome walking is presented and we used an actin gene of radiata pine (Pinus radiata) as an example to conduct upstream and downstream chromosome walking for EST sequences. The full genomic sequence (2154 bp) of the actin gene, including promoters 5′ UTR, CDS and 3′ UTR, was identified by chromosome walking. PCR amplification and DNA band sequencing from 200 unrelated radiata pine trees revealed a total of 21 SNPs for the actin gene, three in the promoter region, 15 in CDS and 4 in 3′ UTR. The results of this experiment provide a technical framework for SNPs discovery in none coding regions of candidate genes.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Frontiers of Forestry in China},
	author = {Li, Wei and Li, Hui and Chen, Xiaoyang and Wu, Harry},
	month = sep,
	year = {2008},
	pages = {352--356},
}

In this paper, the basic principle of chromosome walking is presented and we used an actin gene of radiata pine (Pinus radiata) as an example to conduct upstream and downstream chromosome walking for EST sequences. The full genomic sequence (2154 bp) of the actin gene, including promoters 5′ UTR, CDS and 3′ UTR, was identified by chromosome walking. PCR amplification and DNA band sequencing from 200 unrelated radiata pine trees revealed a total of 21 SNPs for the actin gene, three in the promoter region, 15 in CDS and 4 in 3′ UTR. The results of this experiment provide a technical framework for SNPs discovery in none coding regions of candidate genes.

@article{wu_achievements_2007,
	title = {Achievements in forest tree improvement in {Australia} and {New} {Zealand} 8. {Successful} introduction and breeding of radiata pine in {Australia}},
	volume = {70},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2007.10675023},
	doi = {10/gkhp99},
	abstract = {Radiata pine (Pinus radiata) was originally known as Pinus insignis or ‘remarkable pine’, an apt name for a tree which has had such a dramatic impact on the world timber scene. It is a native conifer of California, USA, and was first introduced into Australia around 1857 for ornamental plantings. There were two major sources of original importation, one through Ferdinand von Mueller to Victoria and South Australia in the 1860s, and the second through New Zealand seed merchants. Forty-year-old trees were clearfelled for sawing in 1908 in Victoria. The fast early growth of radiata pine in Mount Gambier and north of Adelaide in the 1870s and 80s prompted the state forest services of South Australia, Victoria and New South Wales to advocate planting of the remarkable pine as an exotic conifer to compensate for the relative paucity of indigenous softwood in Australia. There was some plantation development in the 1920s and 1930s, but planting almost stopped during World War II. Large-scale planting of radiata pine started again only in the late 1950s. Up to the late 1960s, unimproved seeds used to establish plantations in Australia were at first from early ornamental plantings, then from small plantations and later, in part, imported from New Zealand. Initial research and breeding were undertaken by the Forestry and Timber Bureau (at Canberra and Mt Gambier) and the Queensland Forestry Department — both studied reproductive biology, selected superior trees and established progeny tests in the early 1950s. Following the Seventh British Commonwealth Forestry Conference in Australia and New Zealand in 1957, the other five state forest services and two private companies initiated genetic improvement work in the late 1950s. After establishment of the first grafted seed orchard in 1957, a total of 145 ha of seed orchard was established by 1968. Large-scale plantings using improved seeds started in the early 1970s. Many clones were received from NZ before the 1970s, and a range-wide seed collection was made in the five native stands in California in 1978. In 1983, the Southern Tree Breeding Association (STBA) was formed to coordinate the national breeding program of radiata pine, and it now serves about half of Australia's radiata pine estate. The other half is controlled by Forests New South Wales (FNSW) and the Western Australian Forest Products Commission (FPC). Radiata pine has been bred for three generations since the 1950s, with realised genetic gain up to 33\% for volume from the first generation and more than 10\% gain predicted from the second generation. The focus of the third-generation breeding in STBA has shifted to wood quality traits with: • integration of quantitative genetics, molecular genetics and wood science • development of economic breeding objectives • application of best linear unbiased prediction (BLUP) and a Web-based interactive database for customised delivery of breeding values. During 50 years of breeding radiata pine in southern Australia, several changes in strategic directions have been developed and implemented. Options for such flexibility must be maintained. To further increase genetic gain, infusion of new genetic material from the range-wide collections, increased recombination rate and selection intensity, purging of inbreeding depression, deployment by clonal forestry, and development of strategies dealing with adverse genetic correlation between wood volume and quality traits will be critical.},
	number = {4},
	urldate = {2021-06-10},
	journal = {Australian Forestry},
	publisher = {Taylor \& Francis},
	author = {Wu, Harry X. and Eldridge, Ken G. and Matheson, A. Colin and Powell, Mike B. and McRae, Tony A. and Butcher, Trevor B. and Johnson, Ian G.},
	month = jan,
	year = {2007},
	note = {\_eprint: https://doi.org/10.1080/00049158.2007.10675023},
	keywords = {breeding programs, economics, genetic improvement, genetic resources, growth rate, history, information systems, provenance, radiata pine, traits, wood properties},
	pages = {215--225},
}

Radiata pine (Pinus radiata) was originally known as Pinus insignis or ‘remarkable pine’, an apt name for a tree which has had such a dramatic impact on the world timber scene. It is a native conifer of California, USA, and was first introduced into Australia around 1857 for ornamental plantings. There were two major sources of original importation, one through Ferdinand von Mueller to Victoria and South Australia in the 1860s, and the second through New Zealand seed merchants. Forty-year-old trees were clearfelled for sawing in 1908 in Victoria. The fast early growth of radiata pine in Mount Gambier and north of Adelaide in the 1870s and 80s prompted the state forest services of South Australia, Victoria and New South Wales to advocate planting of the remarkable pine as an exotic conifer to compensate for the relative paucity of indigenous softwood in Australia. There was some plantation development in the 1920s and 1930s, but planting almost stopped during World War II. Large-scale planting of radiata pine started again only in the late 1950s. Up to the late 1960s, unimproved seeds used to establish plantations in Australia were at first from early ornamental plantings, then from small plantations and later, in part, imported from New Zealand. Initial research and breeding were undertaken by the Forestry and Timber Bureau (at Canberra and Mt Gambier) and the Queensland Forestry Department — both studied reproductive biology, selected superior trees and established progeny tests in the early 1950s. Following the Seventh British Commonwealth Forestry Conference in Australia and New Zealand in 1957, the other five state forest services and two private companies initiated genetic improvement work in the late 1950s. After establishment of the first grafted seed orchard in 1957, a total of 145 ha of seed orchard was established by 1968. Large-scale plantings using improved seeds started in the early 1970s. Many clones were received from NZ before the 1970s, and a range-wide seed collection was made in the five native stands in California in 1978. In 1983, the Southern Tree Breeding Association (STBA) was formed to coordinate the national breeding program of radiata pine, and it now serves about half of Australia's radiata pine estate. The other half is controlled by Forests New South Wales (FNSW) and the Western Australian Forest Products Commission (FPC). Radiata pine has been bred for three generations since the 1950s, with realised genetic gain up to 33% for volume from the first generation and more than 10% gain predicted from the second generation. The focus of the third-generation breeding in STBA has shifted to wood quality traits with: • integration of quantitative genetics, molecular genetics and wood science • development of economic breeding objectives • application of best linear unbiased prediction (BLUP) and a Web-based interactive database for customised delivery of breeding values. During 50 years of breeding radiata pine in southern Australia, several changes in strategic directions have been developed and implemented. Options for such flexibility must be maintained. To further increase genetic gain, infusion of new genetic material from the range-wide collections, increased recombination rate and selection intensity, purging of inbreeding depression, deployment by clonal forestry, and development of strategies dealing with adverse genetic correlation between wood volume and quality traits will be critical.

@article{wu_efficiency_2007,
	title = {Efficiency of early selection for rotation-aged wood quality traits in radiata pine},
	volume = {64},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	url = {http://dx.doi.org/10.1051/forest:2006082},
	doi = {10/dsj2r9},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Annals of Forest Science},
	publisher = {EDP Sciences},
	author = {Wu, Harry X. and Powell, Mike B. and Yang, Junli L. and Ivković, Milo and McRae, Tony A.},
	month = jan,
	year = {2007},
	pages = {1--9},
}

Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry

@article{baltunis_inheritance_2007,
	title = {Inheritance of density, microfibril angle, and modulus of elasticity in juvenile wood of {Pinus} radiata at two locations in {Australia}},
	copyright = {2007},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/X07-061},
	doi = {10/b2z5mv},
	abstract = {A total of 1640 increment cores from 343 radiata pine (Pinus radiata D. Don) families were sampled at two second-generation progeny trials, aged 6 and 7 years, for a detailed genetic study of juven...},
	language = {en},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	author = {Baltunis, Brian S. BaltunisB S. and Wu, H. X. and Powell, Mike B. PowellM B.},
	month = nov,
	year = {2007},
}

A total of 1640 increment cores from 343 radiata pine (Pinus radiata D. Don) families were sampled at two second-generation progeny trials, aged 6 and 7 years, for a detailed genetic study of juven...

@article{gapare_inheritance_2007,
	title = {Inheritance of spiral grain in the juvenile core of {Pinus} radiata},
	volume = {37},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/x06-202},
	doi = {10.1139/x06-202},
	abstract = {Spiral grain is the angular arrangement of fibres in a tangential plane with reference to the pith or vertical tree axis. Spiral grain angles exceeding 5° can cause wood to twist, which may result in a considerable amount of waste and degrade. We assessed spiral grain at breast height in two related progeny tests of radiata pine (Pinus radiata D. Don) aged 8 and 9 years established at two different sites in Australia. Radial trends for grain angle at the two sites were similar. Mean spiral grain (MSG) across the two trials was 4.3° with a standard deviation of 1.5° and a range of 0.8–10°. Estimates of individual tree heritabilities on a single-site basis for individual rings and MSG suggested that spiral grain is lowly to highly inherited (h2 = 0.11 ± 0.08 to 0.66 ± 0.21 for individual rings and 0.44 ± 0.12 for MSG). Additive genotypic correlations between individual rings grain angle and MSG were generally high, above 0.71, suggesting a favourable expected correlated response of mean grain angle in the juvenile wood to selection for grain angle of individual rings. Selection to reduce spiral grain on any of rings 2–4 (at a selection intensity of 1.755, i.e., selecting the best 10\% of trees) would result in a predicted correlated genetic gain in MSG of 1.0°. Our results suggest that selection could be performed in any of the individual rings 2, 3, or 4 (equivalent to ages 4–6) and still achieve at least 75\% of the genetic gain possible from selection on the mean of all rings 1–5 (MSG). This suggests that there is an optimum stage (rings 2–4) in which selection for this trait should take place. Our results suggest that a reduction in spiral grain angle in the juvenile core is one strategy to reduce the amount of lower grade timber owing to twist.},
	number = {1},
	urldate = {2026-09-08},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press},
	author = {Gapare, Washington and Hathorn, Adrian and Kain, Dominic and Matheson, Colin and Wu, Harry},
	month = jan,
	year = {2007},
	pages = {116--127},
}

Spiral grain is the angular arrangement of fibres in a tangential plane with reference to the pith or vertical tree axis. Spiral grain angles exceeding 5° can cause wood to twist, which may result in a considerable amount of waste and degrade. We assessed spiral grain at breast height in two related progeny tests of radiata pine (Pinus radiata D. Don) aged 8 and 9 years established at two different sites in Australia. Radial trends for grain angle at the two sites were similar. Mean spiral grain (MSG) across the two trials was 4.3° with a standard deviation of 1.5° and a range of 0.8–10°. Estimates of individual tree heritabilities on a single-site basis for individual rings and MSG suggested that spiral grain is lowly to highly inherited (h2 = 0.11 ± 0.08 to 0.66 ± 0.21 for individual rings and 0.44 ± 0.12 for MSG). Additive genotypic correlations between individual rings grain angle and MSG were generally high, above 0.71, suggesting a favourable expected correlated response of mean grain angle in the juvenile wood to selection for grain angle of individual rings. Selection to reduce spiral grain on any of rings 2–4 (at a selection intensity of 1.755, i.e., selecting the best 10% of trees) would result in a predicted correlated genetic gain in MSG of 1.0°. Our results suggest that selection could be performed in any of the individual rings 2, 3, or 4 (equivalent to ages 4–6) and still achieve at least 75% of the genetic gain possible from selection on the mean of all rings 1–5 (MSG). This suggests that there is an optimum stage (rings 2–4) in which selection for this trait should take place. Our results suggest that a reduction in spiral grain angle in the juvenile core is one strategy to reduce the amount of lower grade timber owing to twist.

@article{ivkovic_modelling_2007,
	title = {Modelling the effects of stem sweep, branch size and wood stiffness of radiata pine on structural timber production},
	volume = {70},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2007.10675018},
	doi = {10/gkhqbc},
	abstract = {The effects of changing three important biological traits — stem sweep (SWE), branch size (BRS) and modulus of elasticity (MoE) — on the radiata pine production system were examined using data obtained from the Australian radiata pine industry and from scientific experiments. Significant improvements in sawlog grade, structural timber grade recovery and the proportion of higher-grade timber can be obtained by reducing SWE and BRS and by increasing MoE. A 10\% reduction in sweep reduced sawlog degrade by 17.1\% and increased green timber recovery by about 0.5\%. A 10\% reduction in BRS decreased the volume of degraded sawlog by 68\% and increased structural timber recovery by 0.6–1.6\%. An increase of 10\% in MoE increased structural timber recovery by 12.3–13.1\%. The main advantage of modelling the effects of biological traits using data from industry is greater reliability relative to models based on assumptions. The modelling provides quantitative information that the timber industry can use to increase its productivity and profitability.},
	number = {3},
	urldate = {2021-06-10},
	journal = {Australian Forestry},
	publisher = {Taylor \& Francis},
	author = {Ivković, M. and Wu, H. X. and Spencer, D. J. and McRae, T. A.},
	month = jan,
	year = {2007},
	note = {\_eprint: https://doi.org/10.1080/00049158.2007.10675018},
	keywords = {Pinus radiala, models, production, profitability, structural timbers, traits, wood properties},
	pages = {173--184},
}

The effects of changing three important biological traits — stem sweep (SWE), branch size (BRS) and modulus of elasticity (MoE) — on the radiata pine production system were examined using data obtained from the Australian radiata pine industry and from scientific experiments. Significant improvements in sawlog grade, structural timber grade recovery and the proportion of higher-grade timber can be obtained by reducing SWE and BRS and by increasing MoE. A 10% reduction in sweep reduced sawlog degrade by 17.1% and increased green timber recovery by about 0.5%. A 10% reduction in BRS decreased the volume of degraded sawlog by 68% and increased structural timber recovery by 0.6–1.6%. An increase of 10% in MoE increased structural timber recovery by 12.3–13.1%. The main advantage of modelling the effects of biological traits using data from industry is greater reliability relative to models based on assumptions. The modelling provides quantitative information that the timber industry can use to increase its productivity and profitability.

@article{ivkovic_developing_2006,
	title = {Developing breeding objectives for radiata pine structural wood production. {I}. {Bioeconomic} model and economic weights},
	volume = {36},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/x06-161},
	doi = {10.1139/x06-161},
	abstract = {Economic breeding objectives were developed for production of radiata pine (Pinus radiata D. Don) structural timber in Australia. Production systems of eight companies, including plantation growers, sawmills, and integrated-system companies, were examined. A bioeconomic model linking the breeding-objective traits mean annual increment (MAI), stem sweep, average branch size, and modulus of elasticity (MoE) with production-system components was constructed using data obtained from industry and published sources. For a plantation grower the most important trait for improvement was MAI (31\% improvement of net present value after a 10\% trait improvement). For a sawmill the most important trait was MoE (29\% improvement of profit after a 10\% trait improvement). For an integrated-system company the two most important traits were MoE and MAI (24\% and 21\% improvement of net present value after a 10\% trait improvement, respectively). There was a high correlation between breeding objectives of plantation growers within a region (rG {\textgreater} 0.99), but a negative correlation between breeding objectives of plantation growers and sawmills (rGS = –0.32) and only an intermediate correlation (rGI {\textless} 0.65) between those of growers and integrated-system companies.},
	number = {11},
	urldate = {2026-09-08},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press},
	author = {Ivković, Miloš and Wu, Harry X and McRae, Tony A and Powell, Mike B},
	month = nov,
	year = {2006},
	pages = {2920--2931},
}

Economic breeding objectives were developed for production of radiata pine (Pinus radiata D. Don) structural timber in Australia. Production systems of eight companies, including plantation growers, sawmills, and integrated-system companies, were examined. A bioeconomic model linking the breeding-objective traits mean annual increment (MAI), stem sweep, average branch size, and modulus of elasticity (MoE) with production-system components was constructed using data obtained from industry and published sources. For a plantation grower the most important trait for improvement was MAI (31% improvement of net present value after a 10% trait improvement). For a sawmill the most important trait was MoE (29% improvement of profit after a 10% trait improvement). For an integrated-system company the two most important traits were MoE and MAI (24% and 21% improvement of net present value after a 10% trait improvement, respectively). There was a high correlation between breeding objectives of plantation growers within a region (rG \textgreater 0.99), but a negative correlation between breeding objectives of plantation growers and sawmills (rGS = –0.32) and only an intermediate correlation (rGI \textless 0.65) between those of growers and integrated-system companies.

@article{ivkovic_developing_2006,
	title = {Developing breeding objectives for radiata pine structural wood production. {II}. {Sensitivity} analyses},
	volume = {36},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x06-162},
	doi = {10.1139/x06-162},
	abstract = {In a companion paper we describe a bioeconomic model of a production system for radiata pine (Pinus radiata D. Don) structural timber and estimated economic weights for four breeding-objective traits: mean annual increment, stem sweep, average branch size, and modulus of elasticity. In this paper we show estimation errors and the sensitivity of the economic weights to the input parameters of the production-system model. We also illustrate the linearity and independence of the economic weights and the sensitivity of selection indices to variation in economic weights and genetic parameters. Estimated standard errors of economic weights were generally low. Among the production-system parameters studied, discount rate and roundwood and sawn-timber prices had the largest impact on the estimates of economic weights. The relationship between the change in values of breeding-objective traits and the corresponding change in profit was nonlinear. The profit change due to change in one objective trait was not independent of the values of the other traits. The most important factors affecting the sensitivity of the selection index were the phenotypic variances of early selection traits such as tree diameter and wood basic density and the economic weights of mean annual increment and modulus of elasticity.},
	number = {11},
	urldate = {2026-09-08},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press},
	author = {Ivković, Miloš and Wu, Harry X and McRae, Tony A and Matheson, Colin A},
	month = nov,
	year = {2006},
	pages = {2932--2942},
}

In a companion paper we describe a bioeconomic model of a production system for radiata pine (Pinus radiata D. Don) structural timber and estimated economic weights for four breeding-objective traits: mean annual increment, stem sweep, average branch size, and modulus of elasticity. In this paper we show estimation errors and the sensitivity of the economic weights to the input parameters of the production-system model. We also illustrate the linearity and independence of the economic weights and the sensitivity of selection indices to variation in economic weights and genetic parameters. Estimated standard errors of economic weights were generally low. Among the production-system parameters studied, discount rate and roundwood and sawn-timber prices had the largest impact on the estimates of economic weights. The relationship between the change in values of breeding-objective traits and the corresponding change in profit was nonlinear. The profit change due to change in one objective trait was not independent of the values of the other traits. The most important factors affecting the sensitivity of the selection index were the phenotypic variances of early selection traits such as tree diameter and wood basic density and the economic weights of mean annual increment and modulus of elasticity.

@article{gapare_genetic_2006,
	title = {Genetic control of the time of transition from juvenile to mature wood in {Pinus} radiata {D}. {Don}},
	volume = {63},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	url = {http://dx.doi.org/10.1051/forest:2006070},
	doi = {10/c9gr4h},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {8},
	urldate = {2021-06-11},
	journal = {Annals of Forest Science},
	publisher = {EDP Sciences},
	author = {Gapare, Washington J. and Wu, Harry X. and Abarquez, Aljoy},
	month = dec,
	year = {2006},
	pages = {871--878},
}

Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry

@article{li_efficiency_2005,
	title = {Efficiency of early selection for rotation-aged growth and wood density traits in {Pinus} radiata},
	volume = {35},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/x05-134},
	doi = {10.1139/x05-134},
	abstract = {A total of 1097 cross-sectional wood disks from breast height were sampled from two rotation-aged (27 and 31 years from planting) genetic trials of radiata pine (Pinus radiata D. Don) in Australia to estimate the genetic correlation between early and rotation-aged growth and wood quality traits and the efficiency of early selection. Annual growth-ring width and density, diameter at breast height (DBH), and area-weighted density (AD) from 30 open-pollinated families were measured using X-ray densitometry. Genotype × site interactions were not significant for density and growth traits. Ring density increased steadily from the pith to cambial age 14, and then density had little change in the following years. For AD, the family and individual heritability estimates were about 0.60 and 0.30 after the first 2 years. For DBH, family and individual narrow-sense heritability estimates increased steadily after the first 4 years, and family heritability increased to 0.7 at a cambial age of 11 and had little change thereafter. Individual heritability estimate increased to 0.4 at cambial age 14 and was similar for the later ages. Beyond a cambial age of 5 years, there were strong negative genetic correlations of around –0.80 between AD and DBH. Age–age genetic correlations for AD were high and reached 0.80 and above after cambial age 3. Age–age genetic correlations for DBH were similar to AD, except the first two years. The most efficient early selection year was between ages 4 and 6 years after planting for AD, and between ages 8 and 11 years for DBH.},
	number = {8},
	urldate = {2026-09-08},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press},
	author = {Li, Li and Wu, Harry X},
	month = aug,
	year = {2005},
	pages = {2019--2029},
}

A total of 1097 cross-sectional wood disks from breast height were sampled from two rotation-aged (27 and 31 years from planting) genetic trials of radiata pine (Pinus radiata D. Don) in Australia to estimate the genetic correlation between early and rotation-aged growth and wood quality traits and the efficiency of early selection. Annual growth-ring width and density, diameter at breast height (DBH), and area-weighted density (AD) from 30 open-pollinated families were measured using X-ray densitometry. Genotype × site interactions were not significant for density and growth traits. Ring density increased steadily from the pith to cambial age 14, and then density had little change in the following years. For AD, the family and individual heritability estimates were about 0.60 and 0.30 after the first 2 years. For DBH, family and individual narrow-sense heritability estimates increased steadily after the first 4 years, and family heritability increased to 0.7 at a cambial age of 11 and had little change thereafter. Individual heritability estimate increased to 0.4 at cambial age 14 and was similar for the later ages. Beyond a cambial age of 5 years, there were strong negative genetic correlations of around –0.80 between AD and DBH. Age–age genetic correlations for AD were high and reached 0.80 and above after cambial age 3. Age–age genetic correlations for DBH were similar to AD, except the first two years. The most efficient early selection year was between ages 4 and 6 years after planting for AD, and between ages 8 and 11 years for DBH.

@article{wu_genotype_2005,
	title = {Genotype by environment interactions in an {Australia}-wide radiata pine diallel mating experiment: implications for regionalized breeding},
	volume = {51},
	issn = {0015-749X},
	shorttitle = {Genotype by environment interactions in an {Australia}-wide radiata pine diallel mating experiment},
	abstract = {Genotype by site interactions were studied in an Australia-wide diallel experiment covering 10 testing sites for stem dbh, stem straightness, branch angle and size, and number of branch clusters on the stem at age 10.5 to 11.5 years. The size and practical importance of genotype by site interactions were examined by four approaches: (1) the ratio of interaction variance to general combining ability (GCA) variance; (2) additive genetic correlations among sites; (3) testing whether the interaction was a result of a few families reacting more than others; and (4) by the size of genetic gains through a proposed regionalization. The genotype by site interaction for dbh observed in this experiment was larger than reported earlier for radiata pine because two high-elevation sites were included. There were more interactions between the two high-elevation sites and other lower elevation sites than interactions between lower elevation sites. The large genotype by region interaction was attributed to the extensive snow loading at the two higher elevation sites. Gain predictions from five regionalization schemes in this experiment favor regionalization of radiata pine breeding into two main regions: higher elevation and lower elevation sites. FOR. SCI. 51(1):29-40.},
	language = {eng},
	number = {1},
	journal = {Forest science.},
	author = {Wu, H. X. and Matheson, A. C.},
	month = feb,
	year = {2005},
	keywords = {⛔ No DOI found},
	pages = {29--40},
}

Genotype by site interactions were studied in an Australia-wide diallel experiment covering 10 testing sites for stem dbh, stem straightness, branch angle and size, and number of branch clusters on the stem at age 10.5 to 11.5 years. The size and practical importance of genotype by site interactions were examined by four approaches: (1) the ratio of interaction variance to general combining ability (GCA) variance; (2) additive genetic correlations among sites; (3) testing whether the interaction was a result of a few families reacting more than others; and (4) by the size of genetic gains through a proposed regionalization. The genotype by site interaction for dbh observed in this experiment was larger than reported earlier for radiata pine because two high-elevation sites were included. There were more interactions between the two high-elevation sites and other lower elevation sites than interactions between lower elevation sites. The large genotype by region interaction was attributed to the extensive snow loading at the two higher elevation sites. Gain predictions from five regionalization schemes in this experiment favor regionalization of radiata pine breeding into two main regions: higher elevation and lower elevation sites. FOR. SCI. 51(1):29-40.

@article{wu_predicting_2005,
	title = {Predicting site productivity and pest hazard in lodgepole pine using biogeoclimatic system and geographic variables in {British} {Columbia}},
	volume = {62},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	url = {http://dx.doi.org/10.1051/forest:2004089},
	doi = {10/d2rsm7},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {Annals of Forest Science},
	publisher = {EDP Sciences},
	author = {Wu, Harry X. and Ying, Cheng C. and Ju, Hong-Bo},
	month = jan,
	year = {2005},
	pages = {31--42},
}

Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry

@article{wu_general_2004,
	title = {General and specific combining ability from partial diallels of radiata pine: implications for utility of {SCA} in breeding and deployment populations},
	volume = {108},
	issn = {1432-2242},
	shorttitle = {General and specific combining ability from partial diallels of radiata pine},
	url = {https://doi.org/10.1007/s00122-004-1598-8},
	doi = {10/d84w8d},
	abstract = {Variances for general combining ability (GCA) and specific combining ability (SCA) and the relationship between mid-parental GCA and SCA effects were estimated for tree diameter (DBH) from a series of 20 sets of 6×6 half-diallel mating experiments in radiata pine, planted at ten sites across Australia. Significant SCA variance for DBH was almost equal to GCA variance for the combined analysis of all ten sites. The importance of SCA variance varied among sites, from non-significant to SCA variance accounting for all genetic variation among full-sib families. Significant SCA × site interaction was detected among the ten sites. A significant and positive correlation between mid-parental breeding values and best linear unbiased predictions of the SCA effects was observed. About a quarter of extra genetic gain is achievable through use of SCA variance if selection is based on the best breeding values. To fully exploit genetic gain from SCA variance in a deployment population, positive assortative matings are required for the best parents. It is estimated that the additional deployment gain of 46.0\% for ten sites combined, or 52.9\% for four sites combined that had significant GCA as well as SCA effects, were achievable relative to gain from GCA only, if all SCA variance within this breeding population was exploited. For a breeding population, selection for breeding values may be sufficient due to positive correlations between breeding values and SCA values. For a deployment population to capture more SCA genetic gain, it is preferable to make more pair-wise mating for parents with higher breeding values.},
	language = {en},
	number = {8},
	urldate = {2021-06-15},
	journal = {Theoretical and Applied Genetics},
	author = {Wu, Harry X. and Matheson, A. Colin},
	month = may,
	year = {2004},
	pages = {1503--1512},
}

Variances for general combining ability (GCA) and specific combining ability (SCA) and the relationship between mid-parental GCA and SCA effects were estimated for tree diameter (DBH) from a series of 20 sets of 6×6 half-diallel mating experiments in radiata pine, planted at ten sites across Australia. Significant SCA variance for DBH was almost equal to GCA variance for the combined analysis of all ten sites. The importance of SCA variance varied among sites, from non-significant to SCA variance accounting for all genetic variation among full-sib families. Significant SCA × site interaction was detected among the ten sites. A significant and positive correlation between mid-parental breeding values and best linear unbiased predictions of the SCA effects was observed. About a quarter of extra genetic gain is achievable through use of SCA variance if selection is based on the best breeding values. To fully exploit genetic gain from SCA variance in a deployment population, positive assortative matings are required for the best parents. It is estimated that the additional deployment gain of 46.0% for ten sites combined, or 52.9% for four sites combined that had significant GCA as well as SCA effects, were achievable relative to gain from GCA only, if all SCA variance within this breeding population was exploited. For a breeding population, selection for breeding values may be sufficient due to positive correlations between breeding values and SCA values. For a deployment population to capture more SCA genetic gain, it is preferable to make more pair-wise mating for parents with higher breeding values.

@article{wu_geographic_2004,
	title = {Geographic pattern of local optimality in natural populations of lodgepole pine},
	volume = {194},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112704001380},
	doi = {10/dt45ng},
	abstract = {Adaptive optimality of local populations is central to evolutionary biology. It also provides a genetic framework for planning gene conservation. We examined local optimality using 20-year height growth as an indicator of population fitness. The height growth data were obtained from a network of 57 long-term field trials in interior British Columbia involving a range-wide samples of 142 lodgepole pine (Pinus contorta Doug) populations. Local optimality was defined statistically and tested, and its geographic patterns were examined in both multi-dimensional mode and component dimensions along latitude, longitude and elevation. Fitness values of local and optimal populations were derived by fitting population variation to response functions for individual sites. Local optimality was an interval estimate, i.e. within the 95\% confidence limit of the projected fitness value of the optimal populations. Both biological and physical distances between local and optimal population were used to examine geographic pattern of local optimality. Study leads to following key results: (1) local optimality prevails at majority of sites; (2) populations at northeast bordering the northern Rocky Mountain Trench are most local optimal, whereas non-local optimality most evident along the eastern foothills of the Coastal Mountains in the coast-interior transition climate zone and the high mountains in the southern interior; (3) there is a geographic cline oriented from southwest to northeast, but with a steep west-east incline; and (4) along component dimensions, a steep longitudinal cline, i.e. the farther the west, the lesser the local optimality, and an elevational cline, i.e. the higher the elevation, the lesser the local optimality. Based on the ecological and life-history characteristics of the species and the climate in interior British Columbia, we propose that a selection gradient coupled with directional gene flow was the process influencing the formation of the observed geographic pattern. The selection gradient parallels the general climate pattern from continental northeast to sub-continental southwest. The gene flow brought the migration of undesirable genes from the coastal subspecies contorta to interior populations of the subspecies latifolia, which further diminished the effectiveness of natural selection. Practical applications through seed transfer in reforestation and genetic resources management are discussed.},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {Forest Ecology and Management},
	author = {Wu, Harry X. and Ying, Cheng C.},
	month = jun,
	year = {2004},
	keywords = {Adaptation, Gene flow, Local optimality, Lodgepole pine, Natural selection},
	pages = {177--198},
}

Adaptive optimality of local populations is central to evolutionary biology. It also provides a genetic framework for planning gene conservation. We examined local optimality using 20-year height growth as an indicator of population fitness. The height growth data were obtained from a network of 57 long-term field trials in interior British Columbia involving a range-wide samples of 142 lodgepole pine (Pinus contorta Doug) populations. Local optimality was defined statistically and tested, and its geographic patterns were examined in both multi-dimensional mode and component dimensions along latitude, longitude and elevation. Fitness values of local and optimal populations were derived by fitting population variation to response functions for individual sites. Local optimality was an interval estimate, i.e. within the 95% confidence limit of the projected fitness value of the optimal populations. Both biological and physical distances between local and optimal population were used to examine geographic pattern of local optimality. Study leads to following key results: (1) local optimality prevails at majority of sites; (2) populations at northeast bordering the northern Rocky Mountain Trench are most local optimal, whereas non-local optimality most evident along the eastern foothills of the Coastal Mountains in the coast-interior transition climate zone and the high mountains in the southern interior; (3) there is a geographic cline oriented from southwest to northeast, but with a steep west-east incline; and (4) along component dimensions, a steep longitudinal cline, i.e. the farther the west, the lesser the local optimality, and an elevational cline, i.e. the higher the elevation, the lesser the local optimality. Based on the ecological and life-history characteristics of the species and the climate in interior British Columbia, we propose that a selection gradient coupled with directional gene flow was the process influencing the formation of the observed geographic pattern. The selection gradient parallels the general climate pattern from continental northeast to sub-continental southwest. The gene flow brought the migration of undesirable genes from the coastal subspecies contorta to interior populations of the subspecies latifolia, which further diminished the effectiveness of natural selection. Practical applications through seed transfer in reforestation and genetic resources management are discussed.

@article{wu_inbreeding_2004,
	title = {Inbreeding in {Pinus} radiata - {V}. {The} effects of inbreeding on fecundity},
	volume = {53},
	issn = {00375349},
	url = {https://www.mendeley.com/catalogue/15b5790a-f00c-327c-805e-9fd9b8b7ed12/},
	doi = {10/gkm3fw},
	abstract = {(2004) Wu et al. Silvae Genetica. A successful inbreeding and hybrid breeding strategy in tree improvement requires that 1) inbreeding (selfing) can produce superior inbred lines (effective purging...},
	language = {en-GB},
	number = {2},
	urldate = {2021-08-26},
	journal = {Silvae Genetica},
	author = {Wu, H. X. and Owen, J. V. and Abarquez, A. and Matheson, A. C.},
	year = {2004},
	note = {Number: 2},
	pages = {80--87},
}

(2004) Wu et al. Silvae Genetica. A successful inbreeding and hybrid breeding strategy in tree improvement requires that 1) inbreeding (selfing) can produce superior inbred lines (effective purging...

@article{glaubitz_impacts_2003,
	title = {Impacts of silviculture on genetic diversity in the native forest species {Eucalyptus} sieberi},
	volume = {4},
	issn = {1572-9737},
	url = {https://doi.org/10.1023/A:1024025331750},
	doi = {10/ddfq62},
	abstract = {Potential impacts of regeneration practices ongenetic diversity in the Australian nativeforest species Eucalyptus sieberi L.A.S.Johnson. (silvertop ash) were assessed usingDNA markers. Three different silviculturaltreatments were examined: clear-felling withaerial re-sowing, and the seed tree system withsite preparation by either burning ormechanical disturbance. In addition, twounharvested stands were chosen as controls. Atotal sample of 825 trees were genotyped at 35Mendelian markers: 26 single-copy nuclear RFLPsand 9 microsatellites. No significantdifferences were found among the treatments inany of four population genetic statistics:allelic richness, effective number of alleles,expected heterozygosity and the panmictic index(f). Rare alleles were prevalent, and a MonteCarlo simulation showed that the apparent lossof four rare alleles from the saplingregenerants was highly statisticallysignificant. There was no evidence for recentbottlenecks from analyses of either the levelsof expected heterozygosity relative to thatexpected under mutation drift equilibrium, orthe allele frequency profiles. A dendrogram ofthe relationships between the sampledpopulations suggested that the seed tree systemmay result in the promotion of genetic drift(slight expansion of the dendrogram) whileaerial re-sowing of clear falls with the sameseedlot will lead to genetic homogenisation(contraction of the dendrogram). The apparentgenetic robustness of E. sieberi tonative forest regeneration practices isattributed to its local abundance combined withthe favourable properties of its reproductivebiology, as well as to the limitation that onlya single rotation was examined.},
	language = {en},
	number = {3},
	urldate = {2021-07-05},
	journal = {Conservation Genetics},
	author = {Glaubitz, Jeffrey C. and Wu, Harry X. and Moran, Gavin F.},
	month = may,
	year = {2003},
	pages = {275--287},
}

Potential impacts of regeneration practices ongenetic diversity in the Australian nativeforest species Eucalyptus sieberi L.A.S.Johnson. (silvertop ash) were assessed usingDNA markers. Three different silviculturaltreatments were examined: clear-felling withaerial re-sowing, and the seed tree system withsite preparation by either burning ormechanical disturbance. In addition, twounharvested stands were chosen as controls. Atotal sample of 825 trees were genotyped at 35Mendelian markers: 26 single-copy nuclear RFLPsand 9 microsatellites. No significantdifferences were found among the treatments inany of four population genetic statistics:allelic richness, effective number of alleles,expected heterozygosity and the panmictic index(f). Rare alleles were prevalent, and a MonteCarlo simulation showed that the apparent lossof four rare alleles from the saplingregenerants was highly statisticallysignificant. There was no evidence for recentbottlenecks from analyses of either the levelsof expected heterozygosity relative to thatexpected under mutation drift equilibrium, orthe allele frequency profiles. A dendrogram ofthe relationships between the sampledpopulations suggested that the seed tree systemmay result in the promotion of genetic drift(slight expansion of the dendrogram) whileaerial re-sowing of clear falls with the sameseedlot will lead to genetic homogenisation(contraction of the dendrogram). The apparentgenetic robustness of E. sieberi tonative forest regeneration practices isattributed to its local abundance combined withthe favourable properties of its reproductivebiology, as well as to the limitation that onlya single rotation was examined.

@article{kumar_reciprocal_2003,
	title = {Reciprocal and {Maternal} {Effects} on {Growth} and {Form} {Traits} in {Radiata} {Pine} in {New} {Zealand}},
	abstract = {The information from two experiments was used to study reciprocal and maternal effects on several growth and form traits in Pinus radiata. In Experiment 1, 10 families and their reciprocals obtained from a 5 x 5 diallel experiment were planted across three sites. In Experiment 2, 17 parents were used in a partial diallel design and all available crosses were planted at a single site. All three sites for Experiment 1 were assessed at 9 years of age. The site for Experiment 2 was assessed at the age of 6-years. Four growth and form traits, namely diameter at breast height (DBH), straightness (STR), branching (BR) and malformation (MAL) were measured in both experiments while needle retention (NRA) was assessed only in Experiment 1.},
	language = {en},
	number = {52},
	author = {Kumar, S and Wu, H X},
	year = {2003},
	pages = {2},
}

The information from two experiments was used to study reciprocal and maternal effects on several growth and form traits in Pinus radiata. In Experiment 1, 10 families and their reciprocals obtained from a 5 x 5 diallel experiment were planted across three sites. In Experiment 2, 17 parents were used in a partial diallel design and all available crosses were planted at a single site. All three sites for Experiment 1 were assessed at 9 years of age. The site for Experiment 2 was assessed at the age of 6-years. Four growth and form traits, namely diameter at breast height (DBH), straightness (STR), branching (BR) and malformation (MAL) were measured in both experiments while needle retention (NRA) was assessed only in Experiment 1.

@article{matheson_inbreeding_2002,
	title = {Inbreeding in {Pinus} radiata {III}: the effect of inbreeding on age-age correlation and early selection efficiency},
	shorttitle = {Inbreeding in {Pinus} radiata {III}},
	abstract = {A breeding strategy involving inbreeding followed by crossbreeding of inbreds requires that the production of superior inbred lines must be possible, but crosses between lines should exhibit heterosis, inbreeding should not substantially delay reproduction, and early selection between lines to be effective. Age-age correlation and the effectiveness of early selection have been extensively reported for outcrossed populations of different species, but there are no reports for inbred populations. In this study, age-age correlations based on both family means and individual trees were investigated and compared in radiata pine populations with five different inbreeding levels (F = 0, 0.125, 0.25, 0.5 and 0.75). Trends in additive genetic variance, environmental variance, heritability and age-age additive genetic correlations were estimated from an outcrossed population (F = 0). For cross-sectional area at breast height, additive genetic variance increased from 3.7\% at age 3 to 29.4\% at age 5, remained at about 30\% up to age 10, then declined to 15.6\% at age 13.},
	number = {51},
	urldate = {2021-11-22},
	journal = {Silvae Genetica},
	author = {Matheson, A. Colin and Wu, Harry X. and Spencer, David J. and Raymond, Carolyn A. and Griffin, A. Rod},
	year = {2002},
	keywords = {⛔ No DOI found},
	pages = {115--122},
}

A breeding strategy involving inbreeding followed by crossbreeding of inbreds requires that the production of superior inbred lines must be possible, but crosses between lines should exhibit heterosis, inbreeding should not substantially delay reproduction, and early selection between lines to be effective. Age-age correlation and the effectiveness of early selection have been extensively reported for outcrossed populations of different species, but there are no reports for inbred populations. In this study, age-age correlations based on both family means and individual trees were investigated and compared in radiata pine populations with five different inbreeding levels (F = 0, 0.125, 0.25, 0.5 and 0.75). Trends in additive genetic variance, environmental variance, heritability and age-age additive genetic correlations were estimated from an outcrossed population (F = 0). For cross-sectional area at breast height, additive genetic variance increased from 3.7% at age 3 to 29.4% at age 5, remained at about 30% up to age 10, then declined to 15.6% at age 13.

@article{wu_inbreeding_2002,
	title = {Inbreeding in {Pinus} radiata. {IV}: the effect of inbreeding on wood density},
	volume = {59},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	shorttitle = {Inbreeding in {Pinus} radiata. {IV}},
	url = {http://dx.doi.org/10.1051/forest:2002041},
	doi = {10/c8jbk5},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {5-6},
	urldate = {2021-08-26},
	journal = {Annals of Forest Science},
	publisher = {EDP Sciences},
	author = {Wu, Harry X. and Matheson, A. Colin and Abarquez, Aljoy},
	month = jul,
	year = {2002},
	pages = {557--562},
}

Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry

@article{wu_study_2002,
	title = {Study of early selection in tree breeding 4. {Efficiency} of {Marker}-{Aided} {Early} {Selection} ({MAES})},
	volume = {51},
	abstract = {One of the main attractions of Marker-Aided Selection (MAS) in tree breeding is its potential for early selection through juvenile traits as Marker-Aided Early Selection (MAES). The theoretical advantages of incorporating molecular markers into early selection in tree breeding are examined. Equations were derived to answer the following questions: (1) how effective is the use of markers for early selection relative to conventional late (mature) selection? (2) what is the efficiency of using markers for early selection relative to early selection based on morphological traits? (3) how effective is incorporating markers into an early selection index relative to an early selection index based on morphological traits alone? (4) what are the efficiencies when MAS is used only for within-family selection in the combined family and within family selection approach, relative to selection using combined family and within family phenotypic information alone? and (5) how effective is selection when MAES is used for within-family selection only in the combined family and within family early selection approach, relative to early selection using combined family and within family phenotypic information alone? These equations could be used to compare relative efficiencies of MAES and QAES (QTL-Aided Early Selection) relative to traditional phenotypic selection in breeding programs. For Marker-Aided Early Selection or QTL-Aided Early Selection to be applicable in tree breeding populations, it may be necessary to demonstrate that efficiency from MAES or QAES is higher than efficiency of early selection using less expensive early phenotypic traits. Furthermore, the relative efficiency of MAES or QAES is higher when genetic correlation of early-mature trait and/or heritability of the early trait is lower and is less for full-sib family than for half-sib family selection.},
	journal = {Silvae Genetica},
	author = {Wu, H.X.},
	month = jan,
	year = {2002},
	keywords = {⛔ No DOI found},
	pages = {261--269},
}

One of the main attractions of Marker-Aided Selection (MAS) in tree breeding is its potential for early selection through juvenile traits as Marker-Aided Early Selection (MAES). The theoretical advantages of incorporating molecular markers into early selection in tree breeding are examined. Equations were derived to answer the following questions: (1) how effective is the use of markers for early selection relative to conventional late (mature) selection? (2) what is the efficiency of using markers for early selection relative to early selection based on morphological traits? (3) how effective is incorporating markers into an early selection index relative to an early selection index based on morphological traits alone? (4) what are the efficiencies when MAS is used only for within-family selection in the combined family and within family selection approach, relative to selection using combined family and within family phenotypic information alone? and (5) how effective is selection when MAES is used for within-family selection only in the combined family and within family early selection approach, relative to early selection using combined family and within family phenotypic information alone? These equations could be used to compare relative efficiencies of MAES and QAES (QTL-Aided Early Selection) relative to traditional phenotypic selection in breeding programs. For Marker-Aided Early Selection or QTL-Aided Early Selection to be applicable in tree breeding populations, it may be necessary to demonstrate that efficiency from MAES or QAES is higher than efficiency of early selection using less expensive early phenotypic traits. Furthermore, the relative efficiency of MAES or QAES is higher when genetic correlation of early-mature trait and/or heritability of the early trait is lower and is less for full-sib family than for half-sib family selection.

@article{wu_analysis_2001,
	title = {Analysis of half-diallel mating designs with missing crosses: {Theory} and {SAS} program for testing and estimating {GCA} and {SCA} variance components},
	volume = {50},
	number = {5-6},
	journal = {Silvae Genetica},
	author = {Wu, Harry X. and Matheson, A. C.},
	year = {2001},
}

@article{wu_reciprocal_2001,
	title = {Reciprocal, maternal and non-maternal effects in radiata pine diallel mating experiment on four {Australia} sites},
	volume = {8},
	abstract = {To investigate the importance of the reciprocal effect in a series of Australia-wide radiata pine 6 × 6 half-diallel matings, one diallel mating set was deliberately mated to include reciprocal crosses. At age ten and a half, five traits (DBH, stem straightness, branch angle, branch size and cluster whorl number) were assessed at four sites, and the reciprocal effects were estimated and partitioned into the maternal and non-maternal components. General combined ability was significant (P {\textless} 0.001) for DBH, stem straightness, branch angle, and branch size while specific combined ability was significant (P {\textless} 0.039) for stem straightness, branch angle, and cluster number. The overall reciprocal effect was significant for branch angle only; however, there were reciprocal effects in individual pair-crosses for DBH, branch size and cluster number. A partitioning of these significant reciprocal effects suggests either maternal (e.g. cytoplasmic DNA effect) and non-maternal effects (e.g. interaction effect between nuclear and cytoplasmic DNA) or purely non-maternal interaction may be the causes of the reciprocal effects. The observed overall weak reciprocal effect in this experiment indicates that (1) reciprocal mating could be used if it is easier or cheaper to use a particular parent as female for commercial production in radiata pine, and (2) half-diallel mating is suitable for the mating design to estimate genetic parameters and variance components, and pooling reciprocal crosses into a half-diallel mating structure should be acceptable for the standard half-diallel genetic analysis.},
	journal = {Forest Genetics},
	author = {Wu, H.X. and Matheson, A.C.},
	month = sep,
	year = {2001},
	pages = {205--212},
}

To investigate the importance of the reciprocal effect in a series of Australia-wide radiata pine 6 × 6 half-diallel matings, one diallel mating set was deliberately mated to include reciprocal crosses. At age ten and a half, five traits (DBH, stem straightness, branch angle, branch size and cluster whorl number) were assessed at four sites, and the reciprocal effects were estimated and partitioned into the maternal and non-maternal components. General combined ability was significant (P \textless 0.001) for DBH, stem straightness, branch angle, and branch size while specific combined ability was significant (P \textless 0.039) for stem straightness, branch angle, and cluster number. The overall reciprocal effect was significant for branch angle only; however, there were reciprocal effects in individual pair-crosses for DBH, branch size and cluster number. A partitioning of these significant reciprocal effects suggests either maternal (e.g. cytoplasmic DNA effect) and non-maternal effects (e.g. interaction effect between nuclear and cytoplasmic DNA) or purely non-maternal interaction may be the causes of the reciprocal effects. The observed overall weak reciprocal effect in this experiment indicates that (1) reciprocal mating could be used if it is easier or cheaper to use a particular parent as female for commercial production in radiata pine, and (2) half-diallel mating is suitable for the mating design to estimate genetic parameters and variance components, and pooling reciprocal crosses into a half-diallel mating structure should be acceptable for the standard half-diallel genetic analysis.

@article{wu_variation_2001,
	title = {Variation on reaction norm in lodgepole pine natural populations},
	volume = {103},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s001220100540},
	doi = {10.1007/s001220100540},
	abstract = {Variations on the norm of reaction among ten natural lodgepole pine populations sampled from three lodgepole pine subspecies (Pinus contorta ssp. contorta, ssp. latifolia and ssp. murrayana) were studied by using 20 year heights measured in 57 provenance test sites across interior British Columbia (B.C.). There were significant population by site interactions. Concurrent joint regression and the AMMI model were used to dissect these population by environmental interactions. Joint regression analysis indicated that three populations (from the northwest) had a negative linear regression coefficient with environmental deviation, three (from central and southeast sites) had a positive regression coefficient and four (from the southwest) had a zero regression coefficient. The AMMI model revealed a similar pattern of reaction norm among the ten populations. But the three significant IPCA axes, which captured twice as much of the G × E sum of squares than joint regression, were more effective in separating the ten populations and associating their performance with the climate of test sites and their origin. The variation patterns of reaction norm in lodgepole pine populations demonstrated that adaptation of lodgepole pine natural populations to the various physical environments, at sub-species as well as at population level, was due largely to a balance between selection for high growth potential in less severe environments and selection for high cold hardiness in severe environments.},
	language = {en},
	number = {2},
	urldate = {2021-11-02},
	journal = {Theoretical and Applied Genetics},
	author = {Wu, H. X. and Ying, C. C.},
	month = aug,
	year = {2001},
	pages = {331--345},
}

Variations on the norm of reaction among ten natural lodgepole pine populations sampled from three lodgepole pine subspecies (Pinus contorta ssp. contorta, ssp. latifolia and ssp. murrayana) were studied by using 20 year heights measured in 57 provenance test sites across interior British Columbia (B.C.). There were significant population by site interactions. Concurrent joint regression and the AMMI model were used to dissect these population by environmental interactions. Joint regression analysis indicated that three populations (from the northwest) had a negative linear regression coefficient with environmental deviation, three (from central and southeast sites) had a positive regression coefficient and four (from the southwest) had a zero regression coefficient. The AMMI model revealed a similar pattern of reaction norm among the ten populations. But the three significant IPCA axes, which captured twice as much of the G × E sum of squares than joint regression, were more effective in separating the ten populations and associating their performance with the climate of test sites and their origin. The variation patterns of reaction norm in lodgepole pine populations demonstrated that adaptation of lodgepole pine natural populations to the various physical environments, at sub-species as well as at population level, was due largely to a balance between selection for high growth potential in less severe environments and selection for high cold hardiness in severe environments.

@article{wu_accounting_2000,
	title = {{ACCOUNTING} {FOR} {BREEDING} {VALUES}, {HETEROGENEOUS} {VARIANCES} {AND} {MATERNAL} {EFFECTS} {IN} {ESTIMATING} {SELFING} {DEPRESSION} {FOR} {INDIVIDUAL} {PEDIGREES}},
	volume = {7},
	abstract = {Inbreeding depression (ID) has been estimated for populations and individual pedigrees in many tree species by comparing the mean performance of selfed progeny with related outcrossed progeny. The traditional use of outcrossed progeny as the reference population (F= 0) can introduce bias into the estimation of ID for individual pedigreesas well as forpopulationsdueto unequal contributionsof parentalbreeding valuesto selfed and outcrossed progeny. In addition,maternaleffectsandheterogeneous variancesamong selfed and outcrossedfamiliesmay further distort estimates of population and individual ID.},
	language = {en},
	journal = {Forest Genetics},
	author = {Wu, Harry X and Burdon, Rowland D},
	month = aug,
	year = {2000},
	pages = {267--275},
}

Inbreeding depression (ID) has been estimated for populations and individual pedigrees in many tree species by comparing the mean performance of selfed progeny with related outcrossed progeny. The traditional use of outcrossed progeny as the reference population (F= 0) can introduce bias into the estimation of ID for individual pedigreesas well as forpopulationsdueto unequal contributionsof parentalbreeding valuesto selfed and outcrossed progeny. In addition,maternaleffectsandheterogeneous variancesamong selfed and outcrossedfamiliesmay further distort estimates of population and individual ID.

@article{wu_study_2000,
	title = {Study of early selection in tree breeding: 3. {A} case study using early information to enhance selection efficiency in late trait in lodgepole pine ({Pinus} contorta spp. {Latifolia})},
	volume = {49},
	shorttitle = {Study of early selection in tree breeding},
	abstract = {We present a selection procedure that combines early performance from retrospective study and late performance from field testing into an index designed for enhancing the selection efficiency of the late performance. The prerequisite is that early performance from retrospective study and late performance from field testing must correlate genetically. This selection index procedure is particularly applicable when practical considerations make seedling selection of early traits preferable. An example is the study of biomass partitioning where young trees could offer a solution for large scale evaluation and serve as a useful first approximation to what might be expected in older trees. To numerically illustrate this selection procedure, we present a case study of retrospective early selection in 110 open-pollinated families from Alberta lodgepole pine (Pinus contorta spp. latifolia). Twenty-eight glasshouse traits in seedlings and the 9-year tree height of their siblings on four sites were conceived as the early and late traits, respectively. Five greenhouse traits having highest genetic correlations with overall field performance were selected and indices of one and two traits from these five glasshouse traits with 9-year tree height averaged 3.0\% and 6\% more efficient, respectively, relative to selection based on 9-year tree height alone. 24 seedling traits which had highest correlations with the field site height were selected for combination with 9-year tree height of one site. Their efficiencies, relative to selection based on 9-year tree height alone, for indices of one and two of glasshouse traits averaged 40\% and 55\% greater, respectively, than selection based on 9-year tree height alone. This demonstrates the potential of early retrospective genetic study to enhance later mature selection.},
	journal = {Silvae Genetica},
	author = {Wu, H.X. and Yeh, Francis and Pharis, R.P. and Dhir, N. and Dancik, Bruce},
	month = jan,
	year = {2000},
	keywords = {⛔ No DOI found},
	pages = {152--158},
}

We present a selection procedure that combines early performance from retrospective study and late performance from field testing into an index designed for enhancing the selection efficiency of the late performance. The prerequisite is that early performance from retrospective study and late performance from field testing must correlate genetically. This selection index procedure is particularly applicable when practical considerations make seedling selection of early traits preferable. An example is the study of biomass partitioning where young trees could offer a solution for large scale evaluation and serve as a useful first approximation to what might be expected in older trees. To numerically illustrate this selection procedure, we present a case study of retrospective early selection in 110 open-pollinated families from Alberta lodgepole pine (Pinus contorta spp. latifolia). Twenty-eight glasshouse traits in seedlings and the 9-year tree height of their siblings on four sites were conceived as the early and late traits, respectively. Five greenhouse traits having highest genetic correlations with overall field performance were selected and indices of one and two traits from these five glasshouse traits with 9-year tree height averaged 3.0% and 6% more efficient, respectively, relative to selection based on 9-year tree height alone. 24 seedling traits which had highest correlations with the field site height were selected for combination with 9-year tree height of one site. Their efficiencies, relative to selection based on 9-year tree height alone, for indices of one and two of glasshouse traits averaged 40% and 55% greater, respectively, than selection based on 9-year tree height alone. This demonstrates the potential of early retrospective genetic study to enhance later mature selection.

@article{wu_study_1999,
	title = {Study of early selection in tree breeding. 2. {Advantage} of early selection through shortening the breeding cycle},
	volume = {48},
	issn = {0037-5349},
	abstract = {Three main advantages from early selection in tree breeding
have been recognized: 1.) increased selection intensity or reduc-
ed field-testing size; 2.) shorter generation interval; and 3.)
genetic information from early testing can be used to enhance
selection efficiency at later ages. The second advantage is
obtained through quicker realisation of genetic gain or by
breeding several generations within a conventional breeding
cycle from mature selection. To quantify the second advantage
from early selection it is necessary to estimate genetic gain
from indirect selection over several generations. In this paper,
a method is derived to estimate genetic gain from several gen-
erations of early indirect selection and is used to study the
advantage of early selection through shortening the tree breed-
ing cycle relative to mature selection. The results show that
genetic variance, heritability and selection response for the cor-
related (mature) trait as well as genetic correlation between
directly selected (early) and correlated (mature) traits will
decline after each generation of selection. When the number of
generations approaches infinity, genetic variance, heritability
and selection response for the correlated trait and the genetic
correlation between directly selected and correlated traits each
approach corresponding limiting values under F ISHER’s infinite
genetic loci model. The reduction in genetic variance, heritabil-
ity and selection response for the correlated trait is slower than
the reduction of genetic variance for the trait under direct
selection. The method is applied to a lodgepole pine early selec-
tion study.},
	language = {eng},
	number = {2},
	journal = {Silvae genetica},
	author = {Wu, H. X.},
	month = jan,
	year = {1999},
	keywords = {⛔ No DOI found},
	pages = {78--83},
}

Three main advantages from early selection in tree breeding have been recognized: 1.) increased selection intensity or reduc- ed field-testing size; 2.) shorter generation interval; and 3.) genetic information from early testing can be used to enhance selection efficiency at later ages. The second advantage is obtained through quicker realisation of genetic gain or by breeding several generations within a conventional breeding cycle from mature selection. To quantify the second advantage from early selection it is necessary to estimate genetic gain from indirect selection over several generations. In this paper, a method is derived to estimate genetic gain from several gen- erations of early indirect selection and is used to study the advantage of early selection through shortening the tree breed- ing cycle relative to mature selection. The results show that genetic variance, heritability and selection response for the cor- related (mature) trait as well as genetic correlation between directly selected (early) and correlated (mature) traits will decline after each generation of selection. When the number of generations approaches infinity, genetic variance, heritability and selection response for the correlated trait and the genetic correlation between directly selected and correlated traits each approach corresponding limiting values under F ISHER’s infinite genetic loci model. The reduction in genetic variance, heritabil- ity and selection response for the correlated trait is slower than the reduction of genetic variance for the trait under direct selection. The method is applied to a lodgepole pine early selec- tion study.

@article{wu_inbreeding_1998,
	title = {{INBREEDING} {IN} {PINUS} {RADIATA}. {II}: {TIME} {COURSE} {OF} {INBREEDING} {DEPRESSION} {AND} {EFFECT} {ON} {GROWTH} {CURVE}},
	shorttitle = {{INBREEDING} {IN} {PINUS} {RADIATA}. {II}},
	url = {https://www.semanticscholar.org/paper/INBREEDING-IN-PINUS-RADIATA.-II%3A-TIME-COURSE-OF-AND-Wu-Matheson/b06a022fa94bf2d8947e226f626ecebd67470af6},
	abstract = {Changes in the effects of inbreeding on sectional area at breast height (1.3 m) each year from ages 1 to 13 were studied in Pinus radiata D.Don of five different inbreeding levels: F = 0, outcrosses; F = 0.125, resulting from half-sib matings; F = 0.25, resulting from full-sib matings; F = 0.5, resulting from selfing; and F = 0.75, resulting from two generations of selfing. The experimental material was derived from eight founder clones. Inbreeding had a significant impact on both cumulative and annual increments in sectional area from age 3, i.e., 2 years after outplanting when most trees had reached 1.3 m in height. At age 4, trees with the highest inbreeding levels (F = 0.5 and 0.75) had significantly less sectional area increment than those with lower inbreeding levels (F = 0, 0.125, 0.25). From age 11 on, trees had differentiated into three groups: outcrosses (F = 0) were best, sib matings (F = 0.125 and 0.25) were intermediate, and selfs (F = 0.5 and 0.75) were worst for cumulative and yearly increment of sectional area. An apparent bimodal time trend in inbreeding depression (ID) of annual increment was observed, being highest at the initial stage of stand development, disappearing at about the time of crown closure in the outcrossed population, and reappearing later. This bimodal trend was believed to be associated with the different times at which crown closure began for the different inbreeding levels, and indicates that inbreeding depression is a dynamic process associated with stage of stand development, spacing, and design of field layout. In fitted Gompertz growth curves, all parameters were affected by inbreeding, including maximum growth rate, time to reach maximum growth rate, and the maximum sectional area achievable. There were significant differences in response to inbreeding among pedigrees.},
	urldate = {2026-09-08},
	journal = {New Zealand journal of forestry science},
	author = {Wu, H. and Matheson, A. C. and Spencer, D.},
	year = {1998},
}

Changes in the effects of inbreeding on sectional area at breast height (1.3 m) each year from ages 1 to 13 were studied in Pinus radiata D.Don of five different inbreeding levels: F = 0, outcrosses; F = 0.125, resulting from half-sib matings; F = 0.25, resulting from full-sib matings; F = 0.5, resulting from selfing; and F = 0.75, resulting from two generations of selfing. The experimental material was derived from eight founder clones. Inbreeding had a significant impact on both cumulative and annual increments in sectional area from age 3, i.e., 2 years after outplanting when most trees had reached 1.3 m in height. At age 4, trees with the highest inbreeding levels (F = 0.5 and 0.75) had significantly less sectional area increment than those with lower inbreeding levels (F = 0, 0.125, 0.25). From age 11 on, trees had differentiated into three groups: outcrosses (F = 0) were best, sib matings (F = 0.125 and 0.25) were intermediate, and selfs (F = 0.5 and 0.75) were worst for cumulative and yearly increment of sectional area. An apparent bimodal time trend in inbreeding depression (ID) of annual increment was observed, being highest at the initial stage of stand development, disappearing at about the time of crown closure in the outcrossed population, and reappearing later. This bimodal trend was believed to be associated with the different times at which crown closure began for the different inbreeding levels, and indicates that inbreeding depression is a dynamic process associated with stage of stand development, spacing, and design of field layout. In fitted Gompertz growth curves, all parameters were affected by inbreeding, including maximum growth rate, time to reach maximum growth rate, and the maximum sectional area achievable. There were significant differences in response to inbreeding among pedigrees.

@article{wu_inbreeding_1998,
	title = {Inbreeding in {Pinus} radiata. {I}. {The} effect of inbreeding on growth, survival and variance},
	volume = {97},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s001220051018},
	doi = {10.1007/s001220051018},
	abstract = {The effects of inbreeding on growth, survival and variance in a 12-year-old radiata pine trial were studied in five populations each inbred to one of five different levels: outcross (F=0), half-sib (F=0.125), full-sib (F=0.25), selfing (S1, F=0.5), and two-generations of selfing (S2, F=0.75). These five populations were derived from a founder population of eight clones. Inbreeding reduced diameter, growth, and survival but increased the variance for diameter. Inbreeding depression at F=0.125, 0.25, 0.5, and 0.75 was 5\%, 6\%, 15\%, and 19\% respectively for DBH; −3\%, 1\%, 7\%, and 11\% respectively, for survival. The standard deviation for diameter increased by 10\%, 10\%, 30\%, and 25\% respectively for F=0.125, 0.25, 0.5, and 0.75 and, similarly, the coefficient of variation increased by 17\%, 16\%, 53\%, and 55\% respectively. There were significant differences among the eight founder clones in their response to inbreeding. The best clone in the trial showed no inbreeding depression. Overall, inbreeding depression was found to be linearly related to the inbreeding coefficient F with no significant quadratic effects for any trait at any population level. However, two individual clones had a quadratic relationship with F for DBH and one clone had a similar relationship for survival. A significant correlation (r=0.96) between S2 and the breeding values of founder clones was observed while the correlation (r=0.58) between S1 and breeding values was insignificant. The low inbreeding depression in radiata pine relative to other conifers may indicate that historical purging of detrimental alleles through small geographic populations, a higher degree of population subdivision, and the relative high fecundity of inbred progenies has rendered radiata pine an ideal species to use inbreeding as a breeding tool.},
	language = {en},
	number = {8},
	urldate = {2026-09-08},
	journal = {Theoretical and Applied Genetics},
	author = {Wu, H. X. and Matheson, A. C. and Spencer, D.},
	month = dec,
	year = {1998},
	keywords = {Growth, Inbreeding depression, Key words Pinus radiata, Purging, Survival, Variance},
	pages = {1256--1268},
}

The effects of inbreeding on growth, survival and variance in a 12-year-old radiata pine trial were studied in five populations each inbred to one of five different levels: outcross (F=0), half-sib (F=0.125), full-sib (F=0.25), selfing (S1, F=0.5), and two-generations of selfing (S2, F=0.75). These five populations were derived from a founder population of eight clones. Inbreeding reduced diameter, growth, and survival but increased the variance for diameter. Inbreeding depression at F=0.125, 0.25, 0.5, and 0.75 was 5%, 6%, 15%, and 19% respectively for DBH; −3%, 1%, 7%, and 11% respectively, for survival. The standard deviation for diameter increased by 10%, 10%, 30%, and 25% respectively for F=0.125, 0.25, 0.5, and 0.75 and, similarly, the coefficient of variation increased by 17%, 16%, 53%, and 55% respectively. There were significant differences among the eight founder clones in their response to inbreeding. The best clone in the trial showed no inbreeding depression. Overall, inbreeding depression was found to be linearly related to the inbreeding coefficient F with no significant quadratic effects for any trait at any population level. However, two individual clones had a quadratic relationship with F for DBH and one clone had a similar relationship for survival. A significant correlation (r=0.96) between S2 and the breeding values of founder clones was observed while the correlation (r=0.58) between S1 and breeding values was insignificant. The low inbreeding depression in radiata pine relative to other conifers may indicate that historical purging of detrimental alleles through small geographic populations, a higher degree of population subdivision, and the relative high fecundity of inbred progenies has rendered radiata pine an ideal species to use inbreeding as a breeding tool.

@article{wu_stability_1998,
	title = {Stability of resistance to western gall rust and needle cast in lodgepole pine provenances},
	volume = {28},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/x98-009},
	doi = {10.1139/x98-009},
	abstract = {Stability of 76 interior lodgepole pine (Pinus contorta ssp. latifolia Engelm.) provenances in resistance to western gall rust (Endocronartium harknessii (J.P. More) Y. Hiratsuka) and needle cast (Lophodermella concolor (Dearn.) Darker) was investigated from 19 and 23 sites in the British Columbia interior, respectively. Provenances, sites, and provenance by site interaction had significant effects on severity level of infection of both diseases. Susceptible provenances contributed mainly to the interaction. The resistant provenances to both diseases were very stable and essentially homeostatic across sites (regression coefficient approaching 0). Resistant provenances were concentrated in the jack pine (Pinus banksiana Lamb.) - lodgepole pine hybrid zone and adjacent areas, and provenances from the low-elevation interior wetbelt were also very resistant to needle cast. Geographic patterns of provenance variation revealed that the closer a lodgepole pine provenance is to the limit of jack pine distribution, the higher and more stable is its resistance to western gall rust and needle cast. The current multiple-site evaluation supports for the hypothesis that jack pine introgression influences pest defence in lodgepole pine and suggests genetic selection can be effective.},
	number = {3},
	urldate = {2026-09-08},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press},
	author = {Wu, Harry X and Ying, Cheng C},
	month = mar,
	year = {1998},
	pages = {439--449},
}

Stability of 76 interior lodgepole pine (Pinus contorta ssp. latifolia Engelm.) provenances in resistance to western gall rust (Endocronartium harknessii (J.P. More) Y. Hiratsuka) and needle cast (Lophodermella concolor (Dearn.) Darker) was investigated from 19 and 23 sites in the British Columbia interior, respectively. Provenances, sites, and provenance by site interaction had significant effects on severity level of infection of both diseases. Susceptible provenances contributed mainly to the interaction. The resistant provenances to both diseases were very stable and essentially homeostatic across sites (regression coefficient approaching 0). Resistant provenances were concentrated in the jack pine (Pinus banksiana Lamb.) - lodgepole pine hybrid zone and adjacent areas, and provenances from the low-elevation interior wetbelt were also very resistant to needle cast. Geographic patterns of provenance variation revealed that the closer a lodgepole pine provenance is to the limit of jack pine distribution, the higher and more stable is its resistance to western gall rust and needle cast. The current multiple-site evaluation supports for the hypothesis that jack pine introgression influences pest defence in lodgepole pine and suggests genetic selection can be effective.

@article{wu_study_1998,
	title = {Study of early selection in tree breeding: 1. {Advantage} of early selection through increase of selection intensity and reduction of field test size},
	volume = {47},
	journal = {Silvae Genetica},
	author = {Wu, Harry X.},
	year = {1998},
	pages = {146--155},
}

@article{wu_genetic_1997,
	title = {Genetic {Parameters} and {Selection} {Efficiencies} in {Resistance} to {Western} {Gall} {Rust}, {Stalactiform} {Blister} {Rust}, {Needle} {Cast}, and {Sequoia} {Pitch} {Moth} in {Lodgepole} {Pine}},
	volume = {43},
	issn = {1938-3738},
	url = {https://doi.org/10.1093/forestscience/43.4.571},
	doi = {10.1093/forestscience/43.4.571},
	abstract = {Genetic variances, heritabilities, and between-trait genetic correlations in resistance to western gall rust (Endocronartium harknessii), stalactiform blister rust (Cronartium coleosporioides), needle cast (Lophodermella concolor), and sequoia pitch moth (Synanthedon sequoiae) (Lepidoptera: Sesiidae) were investigated in a 21-yr-old lodgepole pine (Pinus contorta spp. latifolia) provenance-family trial with 778 wind-pollinated families in interior British Columbia. Selection efficiencies in expected improvement in resistance were compared among mass, family, sequential family-and-within-family, and combined family/individual index selection. Efficiencies in multitrait selection for overall resistance to the four pests based on different selection indices were also compared.},
	language = {en},
	number = {4},
	urldate = {2026-09-08},
	journal = {Forest Science},
	author = {Wu, Harry X. and Ying, Cheng C.},
	month = nov,
	year = {1997},
	keywords = {Heritability, genetic correlation, index selection, indirect selection},
	pages = {571--581},
}

Genetic variances, heritabilities, and between-trait genetic correlations in resistance to western gall rust (Endocronartium harknessii), stalactiform blister rust (Cronartium coleosporioides), needle cast (Lophodermella concolor), and sequoia pitch moth (Synanthedon sequoiae) (Lepidoptera: Sesiidae) were investigated in a 21-yr-old lodgepole pine (Pinus contorta spp. latifolia) provenance-family trial with 778 wind-pollinated families in interior British Columbia. Selection efficiencies in expected improvement in resistance were compared among mass, family, sequential family-and-within-family, and combined family/individual index selection. Efficiencies in multitrait selection for overall resistance to the four pests based on different selection indices were also compared.

@article{wu_genetic_1997,
	title = {Genetic effect on biomass partition and breeding for tree architecture in {Pinus} contorta ssp. latifolia},
	journal = {Forest Genetics},
	author = {Wu, Harry X. and Yeh, F.C.},
	year = {1997},
	pages = {123--130},
}

@article{wu_genotype_1997,
	title = {Genotype by environment interaction and genetic correlation of greenhouse and field performance in {Pinus} contorta ssp. latifolia},
	volume = {46},
	number = {2-3},
	journal = {Silvae Genetica},
	author = {Wu, Harry X. and Yeh, F.C. and Dhir, N. and Pharis, R. P. and Dancik, B. P.},
	year = {1997},
}

@article{wu_effect_1996,
	title = {Effect of geographic variation and jack pine introgression on disease and insect resistance in lodgepole pine},
	volume = {26},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/x26-081},
	doi = {10.1139/x26-081},
	abstract = {Incidence of western gall rust (Endocronartiumharknessii (J.P. Moore) Y. Hiratsuka), stalactiform blister rust (Cronartiumcoleosporioides Arth.), needle cast (Lophodermellaconcolor (Dearn.) Darker), and sequoia pitch moth (Synanthedonsequoiae (Hy. Edwards) (Lepidoptera: Sesiidae)) attacks were investigated in a lodgepole pine (Pinuscontorta Dougl. ex Loud, van latifolia Engelm.) provenance–family test plantation located at Red Rock Tree Improvement Station, Prince George, British Columbia. This plantation contains 778 wind-pollinated families from 53 provenances in British Columbia, Alberta, and the Yukon Territory. Pest incidence was assessed in 1993 when the plantation was 21 years old. Provenance had a significant effect on resistance to the four disease and insect attacks. Regression models using latitude, longitude, and elevation as predictors accounted for 38\% to 80\% of the provenance variation in pest incidence. Geographic patterns of genetic variation in pest resistance essentially followed longitudinal and elevational clines. The most interesting finding is the strong relationship between pest incidence and provenance distance to the western limit of the natural range of jack pine (Pinusbanksiana Lamb,): the closer a lodgepole pine provenance is to the edge of jack pine distribution, the higher is its resistance to the pests. We hypothesize that jack pine introgression may have played a significant role in the evolution of pest defense in lodgepole pine. Effective selection and breeding for pest resistance in lodgepole pine may have to look beyond the intraspecific gene pool.},
	number = {5},
	urldate = {2026-09-08},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press},
	author = {Wu, Harry X. and Ying, Cheng C. and Muir, John A.},
	month = may,
	year = {1996},
	pages = {711--726},
}

Incidence of western gall rust (Endocronartiumharknessii (J.P. Moore) Y. Hiratsuka), stalactiform blister rust (Cronartiumcoleosporioides Arth.), needle cast (Lophodermellaconcolor (Dearn.) Darker), and sequoia pitch moth (Synanthedonsequoiae (Hy. Edwards) (Lepidoptera: Sesiidae)) attacks were investigated in a lodgepole pine (Pinuscontorta Dougl. ex Loud, van latifolia Engelm.) provenance–family test plantation located at Red Rock Tree Improvement Station, Prince George, British Columbia. This plantation contains 778 wind-pollinated families from 53 provenances in British Columbia, Alberta, and the Yukon Territory. Pest incidence was assessed in 1993 when the plantation was 21 years old. Provenance had a significant effect on resistance to the four disease and insect attacks. Regression models using latitude, longitude, and elevation as predictors accounted for 38% to 80% of the provenance variation in pest incidence. Geographic patterns of genetic variation in pest resistance essentially followed longitudinal and elevational clines. The most interesting finding is the strong relationship between pest incidence and provenance distance to the western limit of the natural range of jack pine (Pinusbanksiana Lamb,): the closer a lodgepole pine provenance is to the edge of jack pine distribution, the higher is its resistance to the pests. We hypothesize that jack pine introgression may have played a significant role in the evolution of pest defense in lodgepole pine. Effective selection and breeding for pest resistance in lodgepole pine may have to look beyond the intraspecific gene pool.

@article{wu_genetic_1995,
	title = {Genetic parameters of greenhouse growth and performance of 2‐year pinus contorta subsp. latifolia},
	volume = {10},
	issn = {0282-7581},
	url = {https://doi.org/10.1080/02827589509382861},
	doi = {10.1080/02827589509382861},
	abstract = {Stand differentiation, heritabilities and genetic correlations in 16 growth, bud and branch traits in Pinus contorta subsp. latifolia were studied for two growth periods in the greenhouse. Data for analyses were based on 116. open‐pollinated families from 33 stands in one breeding region in central Alberta, Canada. Family effect was significant at the 1\% level of probability for all traits. The narrow‐sense heritabilities (h2) from 0.43 + 0.09 to 0.71 + 0.12 for traits of absolute height and diameter were the highest reported for growth traits in this conifer. In contrast, h2 varied between 0.15±0.06 and 0.33 ± 0.08 for bud, branch and growth increment traits. Except for relative branch length, all traits showed convariation with the other traits. Levels of heritability and genetic correlation suggest that selection procedures that exploit additive genetic variance and covariance might be practised, provided there would be high juvenile‐mature correlation for this sample of P. contorta subsp. latifolia.},
	number = {1-4},
	urldate = {2026-09-08},
	journal = {Scandinavian Journal of Forest Research},
	publisher = {Taylor \& Francis},
	author = {Wu, Harry X. and Yeh, Francis C. and Pharis, Richard P. and Dancik, Bruce P. and Jiang, Israel B. and Dymock, Ian and Dhir, Narinder K.},
	month = jan,
	year = {1995},
	keywords = {Branch, Pinus contorta subsp. latifolia, bud, coefficient of variation, genetic correlation, growth, heritability, juvenile age},
	pages = {12--21},
}

Stand differentiation, heritabilities and genetic correlations in 16 growth, bud and branch traits in Pinus contorta subsp. latifolia were studied for two growth periods in the greenhouse. Data for analyses were based on 116. open‐pollinated families from 33 stands in one breeding region in central Alberta, Canada. Family effect was significant at the 1% level of probability for all traits. The narrow‐sense heritabilities (h2) from 0.43 + 0.09 to 0.71 + 0.12 for traits of absolute height and diameter were the highest reported for growth traits in this conifer. In contrast, h2 varied between 0.15±0.06 and 0.33 ± 0.08 for bud, branch and growth increment traits. Except for relative branch length, all traits showed convariation with the other traits. Levels of heritability and genetic correlation suggest that selection procedures that exploit additive genetic variance and covariance might be practised, provided there would be high juvenile‐mature correlation for this sample of P. contorta subsp. latifolia.

@article{wu_provenance_1988,
	title = {Provenance variation of photosynthesis and tolerance to water stress in {Platycladus} orientalis {Franco}},
	volume = {24},
	issn = {1001-7488},
	url = {http://www.linyekexue.net/CN/abstract/abstract1121.shtml},
	language = {cn},
	number = {4},
	urldate = {2026-09-08},
	journal = {Scientia Silvae Sinicae},
	author = {Wu, Harry X. and Ji, Ma},
	month = nov,
	year = {1988},
	pages = {448--453},
}

@article{liu_embryogeny_1986,
	title = {The embryogeny of {Cryptomeria} fortunei {L}.},
	volume = {28},
	number = {3},
	journal = {Acta Botanica Sinica},
	author = {Liu, H. E. and Wu, H. X.},
	year = {1986},
	pages = {256--261},
}