@article{berggren_effects_2025,
	title = {Effects of propagation method and methyl jasmonate treatment on stem bark wound healing in {Norway} spruce seedlings},
	issn = {1612-4677},
	url = {https://doi.org/10.1007/s10342-025-01795-0},
	doi = {10.1007/s10342-025-01795-0},
	abstract = {Healing of stem bark wounds is important for minimizing pathogen infection risk, restoring nutrient transport and structural support in trees. Here, we explore how propagation through somatic embryogenesis (SE) and methyl jasmonate (MeJA) treatment affect wound healing ability in Norway spruce (Picea abies) plants. We inflicted a mechanical wound on the lower stem of MeJA- and non-treated plants produced via SE (emblings) or from seeds (seedlings). Visible signs of healing around the wound edges (onset of healing) were recorded 2 weeks post-wounding; wound size (exposed xylem) was measured every other week (June–September) in year 1, and May and September in year 2. Plant height and diameter were also measured. MeJA positively affected healing onset, with 48\% more MeJA- than non-treated plants exhibiting early healing. This resulted in a sharp decrease in wound size for MeJA-treated plants 2–4 weeks post-wounding. However, these benefits only occurred early on, as MeJA reduced the overall healing rate (tissue growth/day) by 9\%. For SE, fewer emblings (70\%) showed early healing signs compared to seedlings (91\%). Yet, non-treated emblings showed the highest healing rate during year 1; in year 2, these effects persisted with all emblings having a 61\% faster healing rate and 68\% more had completely closed their wounds relative to seedlings. Wounding did not affect growth, MeJA negatively affected diameter but not height, and overall emblings grew less than seedlings. We conclude that MeJA may stimulate stem wound healing initiation in Norway spruce, but slow down healing rate and vice versa for SE plants.},
	language = {en},
	urldate = {2025-07-25},
	journal = {European Journal of Forest Research},
	author = {Berggren, Kristina and Tudoran, Amelia and Chen, Yayuan and Tikkinen, Mikko and Bylund, Helena and Björkman, Christer and Egertsdotter, Ulrika and Puentes, Adriana},
	month = jun,
	year = {2025},
	keywords = {Arboriculture, Emblings, Jasmonic acid, Mechanical wounding, Picea abies, Plant regeneration, Plant tolerance, Regeneration, Seedlings, Shoot apical meristem, Somatic embryogenesis, Wound healing rate, Wounding},
}

Healing of stem bark wounds is important for minimizing pathogen infection risk, restoring nutrient transport and structural support in trees. Here, we explore how propagation through somatic embryogenesis (SE) and methyl jasmonate (MeJA) treatment affect wound healing ability in Norway spruce (Picea abies) plants. We inflicted a mechanical wound on the lower stem of MeJA- and non-treated plants produced via SE (emblings) or from seeds (seedlings). Visible signs of healing around the wound edges (onset of healing) were recorded 2 weeks post-wounding; wound size (exposed xylem) was measured every other week (June–September) in year 1, and May and September in year 2. Plant height and diameter were also measured. MeJA positively affected healing onset, with 48% more MeJA- than non-treated plants exhibiting early healing. This resulted in a sharp decrease in wound size for MeJA-treated plants 2–4 weeks post-wounding. However, these benefits only occurred early on, as MeJA reduced the overall healing rate (tissue growth/day) by 9%. For SE, fewer emblings (70%) showed early healing signs compared to seedlings (91%). Yet, non-treated emblings showed the highest healing rate during year 1; in year 2, these effects persisted with all emblings having a 61% faster healing rate and 68% more had completely closed their wounds relative to seedlings. Wounding did not affect growth, MeJA negatively affected diameter but not height, and overall emblings grew less than seedlings. We conclude that MeJA may stimulate stem wound healing initiation in Norway spruce, but slow down healing rate and vice versa for SE plants.

@article{canovi_resource_2024,
	title = {A resource of identified and annotated {lincRNAs} expressed during somatic embryogenesis development in {Norway} spruce},
	volume = {176},
	copyright = {© 2024 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14537},
	doi = {10.1111/ppl.14537},
	abstract = {Long non-coding RNAs (lncRNAs) have emerged as important regulators of many biological processes, although their regulatory roles remain poorly characterized in woody plants, especially in gymnosperms. A major challenge of working with lncRNAs is to assign functional annotations, since they have a low coding potential and low cross-species conservation. We utilised an existing RNA-Sequencing resource and performed short RNA sequencing of somatic embryogenesis developmental stages in Norway spruce (Picea abies L. Karst). We implemented a pipeline to identify lncRNAs located within the intergenic space (lincRNAs) and generated a co-expression network including protein coding, lincRNA and miRNA genes. To assign putative functional annotation, we employed a guilt-by-association approach using the co-expression network and integrated these results with annotation assigned using semantic similarity and co-expression. Moreover, we evaluated the relationship between lincRNAs and miRNAs, and identified which lincRNAs are conserved in other species. We identified lincRNAs with clear evidence of differential expression during somatic embryogenesis and used network connectivity to identify those with the greatest regulatory potential. This work provides the most comprehensive view of lincRNAs in Norway spruce and is the first study to perform global identification of lincRNAs during somatic embryogenesis in conifers. The data have been integrated into the expression visualisation tools at the PlantGenIE.org web resource to enable easy access to the community. This will facilitate the use of the data to address novel questions about the role of lincRNAs in the regulation of embryogenesis and facilitate future comparative genomics studies.},
	language = {en},
	number = {5},
	urldate = {2024-09-27},
	journal = {Physiologia Plantarum},
	author = {Canovi, Camilla and Stojkovič, Katja and Benítez, Aarón Ayllón and Delhomme, Nicolas and Egertsdotter, Ulrika and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14537},
	pages = {e14537},
}

Long non-coding RNAs (lncRNAs) have emerged as important regulators of many biological processes, although their regulatory roles remain poorly characterized in woody plants, especially in gymnosperms. A major challenge of working with lncRNAs is to assign functional annotations, since they have a low coding potential and low cross-species conservation. We utilised an existing RNA-Sequencing resource and performed short RNA sequencing of somatic embryogenesis developmental stages in Norway spruce (Picea abies L. Karst). We implemented a pipeline to identify lncRNAs located within the intergenic space (lincRNAs) and generated a co-expression network including protein coding, lincRNA and miRNA genes. To assign putative functional annotation, we employed a guilt-by-association approach using the co-expression network and integrated these results with annotation assigned using semantic similarity and co-expression. Moreover, we evaluated the relationship between lincRNAs and miRNAs, and identified which lincRNAs are conserved in other species. We identified lincRNAs with clear evidence of differential expression during somatic embryogenesis and used network connectivity to identify those with the greatest regulatory potential. This work provides the most comprehensive view of lincRNAs in Norway spruce and is the first study to perform global identification of lincRNAs during somatic embryogenesis in conifers. The data have been integrated into the expression visualisation tools at the PlantGenIE.org web resource to enable easy access to the community. This will facilitate the use of the data to address novel questions about the role of lincRNAs in the regulation of embryogenesis and facilitate future comparative genomics studies.

@article{stojkovic_transcriptome_2024,
	title = {A transcriptome atlas of zygotic and somatic embryogenesis in {Norway} spruce},
	volume = {120},
	copyright = {© 2024 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.17087},
	doi = {10.1111/tpj.17087},
	abstract = {Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.},
	language = {en},
	number = {5},
	urldate = {2024-12-13},
	journal = {The Plant Journal},
	author = {Stojkovič, Katja and Canovi, Camilla and Le, Kim-Cuong and Ahmad, Iftikhar and Gaboreanu, Ioana and Johansson, Sofie and Delhomme, Nicolas and Egertsdotter, Ulrika and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.17087},
	keywords = {Norway spruce, Picea abies, differential expression, embryo, embryogenesis, transcriptome},
	pages = {2238--2252},
}

Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.

@article{raebild_polyploidy_2024,
	title = {Polyploidy – {A} tool in adapting trees to future climate changes? {A} review of polyploidy in trees},
	volume = {560},
	issn = {0378-1127},
	shorttitle = {Polyploidy – {A} tool in adapting trees to future climate changes?},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112724000793},
	doi = {10.1016/j.foreco.2024.121767},
	abstract = {Polyploidy, or genome doubling, has occurred repeatedly through plant evolution. While polyploid plants are used extensively in agriculture and horticulture, they have so far found limited use in forestry. Here we review the potentials of polyploid trees under climate change, and investigate if there is support for increased use. We find that polyploid trees like other plants have consistent increases in cell sizes compared to diploids, and that leaf-area based rates of photosynthesis tend to increase with increasing levels of ploidy. While no particular trend could be discerned in terms of biomass between trees of different ploidy levels, physiology is affected by polyploidization and several studies point towards a high potential for polyploid trees to adapt to drought stress. The ploidy level of most tree species is unknown, and analysis of geographical patterns in frequencies of polyploid trees are inconclusive. Artificial polyploid trees are often created by colchicine and in a few cases these have been successfully applied in forestry, but the effects of induced polyploidization in many economically important tree species remains untested. Polyploids would also be increasingly useful in tree breeding programs, to create synthetic hybrids or sterile triploids that could control unwanted spreading of germplasm in nature. In conclusion, this review suggests that polyploid trees may be superior under climate change in some cases, but that the potential of polyploids is not yet fully known and should be evaluated on a case-to-case basis for different tree species.},
	urldate = {2024-05-10},
	journal = {Forest Ecology and Management},
	author = {Ræbild, Anders and Anamthawat-Jónsson, Kesara and Egertsdotter, Ulrika and Immanen, Juha and Jensen, Anna Monrad and Koutouleas, Athina and Martens, Helle Jakobe and Nieminen, Kaisa and Olofsson, Jill Katharina and Röper, Anna-Catharina and Salojärvi, Jarkko and Strömvik, Martina and Vatanparast, Mohammad and Vivian-Smith, Adam},
	month = may,
	year = {2024},
	keywords = {Adaptation, Ecophysiology, Fitness, Forestry, Tree breeding, Whole genome duplication (WGD)},
	pages = {121767},
}

Polyploidy, or genome doubling, has occurred repeatedly through plant evolution. While polyploid plants are used extensively in agriculture and horticulture, they have so far found limited use in forestry. Here we review the potentials of polyploid trees under climate change, and investigate if there is support for increased use. We find that polyploid trees like other plants have consistent increases in cell sizes compared to diploids, and that leaf-area based rates of photosynthesis tend to increase with increasing levels of ploidy. While no particular trend could be discerned in terms of biomass between trees of different ploidy levels, physiology is affected by polyploidization and several studies point towards a high potential for polyploid trees to adapt to drought stress. The ploidy level of most tree species is unknown, and analysis of geographical patterns in frequencies of polyploid trees are inconclusive. Artificial polyploid trees are often created by colchicine and in a few cases these have been successfully applied in forestry, but the effects of induced polyploidization in many economically important tree species remains untested. Polyploids would also be increasingly useful in tree breeding programs, to create synthetic hybrids or sterile triploids that could control unwanted spreading of germplasm in nature. In conclusion, this review suggests that polyploid trees may be superior under climate change in some cases, but that the potential of polyploids is not yet fully known and should be evaluated on a case-to-case basis for different tree species.

@article{le_vitro_2023,
	title = {In {Vitro} {Propagation} of the {Blueberry} ‘{Blue} {Suede}™’ ({Vaccinium} hybrid) in {Semi}-{Solid} {Medium} and {Temporary} {Immersion} {Bioreactors}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/12/15/2752},
	doi = {10.3390/plants12152752},
	abstract = {The production of blueberries for fresh and processed consumption is increasing globally and has more than doubled in the last decade. Blueberry is grown commercially across a variety of climates in over 30 countries. The major classes of plants utilized for the planting and breeding of new cultivars are highbush, lowbush, half-high, Rabbiteye, and Southern highbush. Plants can be propagated by cuttings or in vitro micropropagation techniques. In vitro propagation offers advantages for faster generation of a large number of disease-free plants independent of season. Labor costs for in vitro propagation can be reduced using new cultivation technology and automation. Here, we test and demonstrate successful culture conditions and medium compositions for in vitro initiation, multiplication, and rooting of the Southern highbush cultivar ‘Blue Suede™’ (Vaccinium hybrid).},
	language = {en},
	number = {15},
	urldate = {2023-08-21},
	journal = {Plants},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Le, Kim-Cuong and Johnson, Shannon and Aidun, Cyrus K. and Egertsdotter, Ulrika},
	month = jul,
	year = {2023},
	note = {Number: 15},
	keywords = {blueberry, micropropagation, temporary immersion bioreactor, ‘Blue Suede™’ (\textit{Vaccinium} hybrid)},
	pages = {2752},
}

The production of blueberries for fresh and processed consumption is increasing globally and has more than doubled in the last decade. Blueberry is grown commercially across a variety of climates in over 30 countries. The major classes of plants utilized for the planting and breeding of new cultivars are highbush, lowbush, half-high, Rabbiteye, and Southern highbush. Plants can be propagated by cuttings or in vitro micropropagation techniques. In vitro propagation offers advantages for faster generation of a large number of disease-free plants independent of season. Labor costs for in vitro propagation can be reduced using new cultivation technology and automation. Here, we test and demonstrate successful culture conditions and medium compositions for in vitro initiation, multiplication, and rooting of the Southern highbush cultivar ‘Blue Suede™’ (Vaccinium hybrid).

@article{nielsen_accumulated_2022,
	title = {Accumulated effects of factors determining plant development from somatic embryos of {Abies} nordmanniana and {Abies} bornmuelleriana},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.989484},
	abstract = {Despite a much later inception of somatic embryogenesis (SE) propagation protocols for gymnosperms than for angiosperm species, SE is becoming increasingly important due to its applications for commercial forestry. For many conifers, there are however still major bottlenecks in the SE plant production process limiting the use of SE for forestry operations, Christmas tree production and research projects. In the present case study, the effects on plant growth from different cultural factors applied during the SE developmental process were studied in two conifer species of high value for Christmas tree production. Seven clones of Abies nordmanniana and two clones of Abies bornmuelleriana were included in the study. Accumulated effects from cultural treatments were recorded from the start of germination of mature embryos of different quality scores through development into plants in the third growing period. Experimental factors of the cultural treatments included were: germination temperature, germination time, light conditions, survival ex vitro and traits for plant growth and vitality. The results reveal that most of the studied experimental factors influenced plant growth during the first three years however their relative importance was different. Plant survival rate at end of the nursery stage was strongly impacted by germination temperature (p{\textless}0.001), initial embryo score (p=0.007), clone (p{\textless}0.001) and to a lesser extend week of germination (p=0.017). This case-study highlights and quantifies the strong interrelation between the developmental steps of somatic embryogenesis and show the importance of considering all cultural steps when optimizing SE plant production protocols.},
	urldate = {2022-11-03},
	journal = {Frontiers in Plant Science},
	author = {Nielsen, Ulrik Braüner and Hansen, Camilla Bülow and Hansen, Ulrich and Johansen, Vivian Kvist and Egertsdotter, Ulrika},
	month = oct,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Despite a much later inception of somatic embryogenesis (SE) propagation protocols for gymnosperms than for angiosperm species, SE is becoming increasingly important due to its applications for commercial forestry. For many conifers, there are however still major bottlenecks in the SE plant production process limiting the use of SE for forestry operations, Christmas tree production and research projects. In the present case study, the effects on plant growth from different cultural factors applied during the SE developmental process were studied in two conifer species of high value for Christmas tree production. Seven clones of Abies nordmanniana and two clones of Abies bornmuelleriana were included in the study. Accumulated effects from cultural treatments were recorded from the start of germination of mature embryos of different quality scores through development into plants in the third growing period. Experimental factors of the cultural treatments included were: germination temperature, germination time, light conditions, survival ex vitro and traits for plant growth and vitality. The results reveal that most of the studied experimental factors influenced plant growth during the first three years however their relative importance was different. Plant survival rate at end of the nursery stage was strongly impacted by germination temperature (p\textless0.001), initial embryo score (p=0.007), clone (p\textless0.001) and to a lesser extend week of germination (p=0.017). This case-study highlights and quantifies the strong interrelation between the developmental steps of somatic embryogenesis and show the importance of considering all cultural steps when optimizing SE plant production protocols.

@article{aghbolaghi_stipagrostis_2022,
	title = {Stipagrostis pennata ({Trin}.) {De} {Winter} {Artificial} {Seed} {Production} and {Seedlings} {Multiplication} in {Temporary} {Immersion} {Bioreactors}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/22/3122},
	doi = {10.3390/plants11223122},
	abstract = {This study was conducted to develop the protocol for artificial seed production of Stipagrostis pennata (Trin.) De Winter via somatic embryo encapsulation as well as test a temporary bioreactor system for germination and seedling growth. Embryogenic calli were encapsulated using sodium alginate and calcium chloride and then sowed in the Murashige and Skoog (MS) germination medium in in vitro cultures. The experiments were conducted as a factorial based on a completely randomized design with three replications. The treatments include three concentrations of sodium alginate (1.5\%, 2.5\%, and 3.5\%), two ion exchange times (20 and 30 min), and two artificial seed germination media (hormone-free MS and MS supplemented with zeatin riboside and L-proline). Germination percentage and number of days needed until the beginning of germination were studied. The highest percentage of artificial seed germination was obtained when 2.5\% sodium alginate was used for 30 min (ion exchange time) and when the seeds were placed on the MS germination medium supplemented with zeatin riboside and L-proline. The results of the analysis of variance in the temporary immersion bioreactor system showed that the main effects observed on the seedling growth were associated with different growth hormones in culture media and the number of feeding cycles. Experimental results also indicated that the total protein analyses of zygotic seedlings and seedlings originating from the synthetic seeds showed no statistically significant differences between these samples.},
	language = {en},
	number = {22},
	urldate = {2022-12-02},
	journal = {Plants},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Aghbolaghi, Masoumeh Asadi and Dedicova, Beata and Sharifzadeh, Farzad and Omidi, Mansoor and Egertsdotter, Ulrika},
	month = jan,
	year = {2022},
	note = {Number: 22},
	keywords = {in vitro cultures, protein analyses, somatic embryogenesis},
	pages = {3122},
}

This study was conducted to develop the protocol for artificial seed production of Stipagrostis pennata (Trin.) De Winter via somatic embryo encapsulation as well as test a temporary bioreactor system for germination and seedling growth. Embryogenic calli were encapsulated using sodium alginate and calcium chloride and then sowed in the Murashige and Skoog (MS) germination medium in in vitro cultures. The experiments were conducted as a factorial based on a completely randomized design with three replications. The treatments include three concentrations of sodium alginate (1.5%, 2.5%, and 3.5%), two ion exchange times (20 and 30 min), and two artificial seed germination media (hormone-free MS and MS supplemented with zeatin riboside and L-proline). Germination percentage and number of days needed until the beginning of germination were studied. The highest percentage of artificial seed germination was obtained when 2.5% sodium alginate was used for 30 min (ion exchange time) and when the seeds were placed on the MS germination medium supplemented with zeatin riboside and L-proline. The results of the analysis of variance in the temporary immersion bioreactor system showed that the main effects observed on the seedling growth were associated with different growth hormones in culture media and the number of feeding cycles. Experimental results also indicated that the total protein analyses of zygotic seedlings and seedlings originating from the synthetic seeds showed no statistically significant differences between these samples.

@article{ranade_silico_2021,
	title = {In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack {LEC2}, one of the key regulators of initiation of the process},
	volume = {22},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07718-8},
	doi = {10/gkbhh3},
	abstract = {Abstract
            
              Background
              Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation.
            
            
              Results
              
                Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g.
                BBM
                ,
                LEC1
                ,
                LEC1-LIKE, LEC2
                and
                FUSCA3
                , based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from
                Arabidopsis thaliana
                were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus
                Picea
                (
                Picea abies
                ) and
                Pinus
                (
                Pinus taeda
                ), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of
                Arabidopsis thaliana
                proteins and phylogenetic analysis (Phylogeny.fr).
              
            
            
              Conclusions
              
                This in silico analysis suggests absence of
                LEC2
                in
                Picea abies
                and
                Pinus taeda
                , the conifer species whose genomes have been sequenced. Based on available sequence data to date,
                LEC2
                was also not detected in the other conifer species included in the study.
                LEC2
                is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of
                LEC2
                are discussed.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {BMC Genomics},
	author = {Ranade, Sonali Sachin and Egertsdotter, Ulrika},
	month = dec,
	year = {2021},
	pages = {392},
}

Abstract Background Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. Results Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM , LEC1 , LEC1-LIKE, LEC2 and FUSCA3 , based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea ( Picea abies ) and Pinus ( Pinus taeda ), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). Conclusions This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda , the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.

@article{asadi-aghbolaghi_protocol_2021,
	title = {Protocol development for somatic embryogenesis, {SSR} markers and genetic modification of {Stipagrostis} pennata ({Trin}.) {De} {Winter}},
	volume = {17},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-021-00768-9},
	doi = {10.1186/s13007-021-00768-9},
	abstract = {Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Plant Methods},
	author = {Asadi-Aghbolaghi, Masoumeh and Dedicova, Beata and Ranade, Sonali Sachi and Le, Kim-Cuong and Sharifzadeh, Farzad and Omidi, Mansoor and Egertsdotter, Ulrika},
	month = jun,
	year = {2021},
	keywords = {Agrobacterium, Grass, Plant regeneration, SSR markers, Somatic embryogenesis, Stipagrostis pennata (Trin.) De Winter},
	pages = {70},
}

Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources.

@article{edesi_root_2021,
	title = {Root {Rot} {Resistance} {Locus} {PaLAR3} {Is} {Delivered} by {Somatic} {Embryogenesis} ({SE}) {Pipeline} in {Norway} {Spruce} ({Picea} abies ({L}.) {Karst}.)},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/12/2/193},
	doi = {10.3390/f12020193},
	abstract = {Research Highlights: The Norway spruce somatic embryogenesis (SE) pipeline is suitable for multiplication of material with root rot resistance traits. Background and Objectives: Heterobasidion root rot is the economically most severe forest pathogen in Europe, reducing the benefit of planting elite forest material. In this study, the SE-propagation ability of elite Norway spruce material carrying root rot resistance traits was studied. Materials and Methods: We analyzed the presence of the root rot resistance locus PaLAR3B among 80 Finnish progeny-tested Norway spruce plus-trees used for SE-plant production as well as in 241 SE lines (genotypes) derived from them. Seven full-sib families with lines having either AA, AB, or BB genotype for PaLAR3 locus were further studied for their SE-plant propagation ability. Results: The results indicate that 47.5\% of the studied elite trees carry the PaLAR3B allele (45\% are heterozygous and 2.5\% homozygous). The resistance allele was present among the SE lines as expected based on Mendelian segregation and did not interfere with somatic embryo production capacity. All embryos from PaLAR3 genotypes germinated well and emblings were viable in the end of first growing season. However, in three families, PaLAR3B homo- or heterozygotes had 23.2\% to 32.1\% lower viability compared to their respective hetero- or PaLAR3A homozygotes. Conclusions: There is no trade-off between root rot resistance locus PaLAR3B and somatic embryo production ability, but the allele may interfere with Norway spruce embling establishment.},
	language = {en},
	number = {2},
	urldate = {2024-10-16},
	journal = {Forests},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Edesi, Jaanika and Tikkinen, Mikko and Elfstrand, Malin and Olson, Åke and Varis, Saila and Egertsdotter, Ulrika and Aronen, Tuija},
	month = feb,
	year = {2021},
	note = {Number: 2},
	keywords = {genomic selection, root rot resistance, somatic embryogenesis, vegetative propagation},
	pages = {193},
}

Research Highlights: The Norway spruce somatic embryogenesis (SE) pipeline is suitable for multiplication of material with root rot resistance traits. Background and Objectives: Heterobasidion root rot is the economically most severe forest pathogen in Europe, reducing the benefit of planting elite forest material. In this study, the SE-propagation ability of elite Norway spruce material carrying root rot resistance traits was studied. Materials and Methods: We analyzed the presence of the root rot resistance locus PaLAR3B among 80 Finnish progeny-tested Norway spruce plus-trees used for SE-plant production as well as in 241 SE lines (genotypes) derived from them. Seven full-sib families with lines having either AA, AB, or BB genotype for PaLAR3 locus were further studied for their SE-plant propagation ability. Results: The results indicate that 47.5% of the studied elite trees carry the PaLAR3B allele (45% are heterozygous and 2.5% homozygous). The resistance allele was present among the SE lines as expected based on Mendelian segregation and did not interfere with somatic embryo production capacity. All embryos from PaLAR3 genotypes germinated well and emblings were viable in the end of first growing season. However, in three families, PaLAR3B homo- or heterozygotes had 23.2% to 32.1% lower viability compared to their respective hetero- or PaLAR3A homozygotes. Conclusions: There is no trade-off between root rot resistance locus PaLAR3B and somatic embryo production ability, but the allele may interfere with Norway spruce embling establishment.

@article{le_scale-up_2021,
	title = {Scale-up of {Somatic} {Embryogenesis} {Plant} {Production} of {Hybrid} {Larch} ({Larix} x eurolepis) {Using} {Temporary} {Immersion} {Bioreactors}},
	volume = {57},
	issn = {1071-2690},
	language = {English},
	number = {SUPPL 1},
	journal = {In Vitro Cellular \& Developmental Biology-Animal},
	author = {Le, K.-C. and Egertsdotter, U.},
	month = jun,
	year = {2021},
	keywords = {⛔ No DOI found},
	pages = {S38--S39},
}

@article{ahmad_sucrose-dependent_2021,
	title = {Sucrose-dependent production of biomass and low-caloric steviol glycosides in adventitious root cultures of {Stevia} rebaudiana ({Bert}.)},
	volume = {164},
	issn = {09266690},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0926669021001461},
	doi = {10/gj6thz},
	language = {en},
	urldate = {2021-06-03},
	journal = {Industrial Crops and Products},
	author = {Ahmad, Naveed and Rab, Abdur and Sajid, Muhammad and Ahmad, Nisar and Fazal, Hina and Ali, Mohammad and Egertsdotter, Ulrika},
	month = jun,
	year = {2021},
	pages = {113382},
}

@article{le_temporary_2021,
	title = {Temporary immersion bioreactor system for propagation by somatic embryogenesis of hybrid larch ({Larix} × eurolepis {Henry})},
	volume = {32},
	issn = {2215-017X},
	url = {https://www.sciencedirect.com/science/article/pii/S2215017X21001004},
	doi = {10/gnj3pm},
	abstract = {Somatic embryogenesis (SE) has high potential for large-scale clonal propagation of conifers. Different types of bioreactor cultures have been tested for the conifer SE process where the temporary immersion bioreactors (TIBs) have proved to be useful across the different developmental steps of the SE process. In the present study the use of TIBs was tested for hybrid larch (Larix × eurolepis Henry). The results showed two-fold increases in both fresh weight (FW) of pro-embryogenic masses (PEMs) and yield of cotyledonary embryos in the TIBs compared to solid medium in plates. For the germination phase, the highest number of roots per plant, the root length and height of plants were also obtained in the TIBs. The results show that the TIB system can be successfully used to support scale up of plant production in all steps of the SE process from proliferation to germination of hybrid larch (Larix × eurolepis Henry).},
	language = {en},
	urldate = {2021-11-12},
	journal = {Biotechnology Reports},
	author = {Le, Kim-Cuong and Dedicova, Beata and Johansson, Sofie and Lelu-Walter, Marie-Anne and Egertsdotter, Ulrika},
	month = dec,
	year = {2021},
	keywords = {Germination, Horizontal TIB, Larix × eurolepis, Scale up, Somatic embryogenesis, Vertical TIB, ×},
	pages = {e00684},
}

Somatic embryogenesis (SE) has high potential for large-scale clonal propagation of conifers. Different types of bioreactor cultures have been tested for the conifer SE process where the temporary immersion bioreactors (TIBs) have proved to be useful across the different developmental steps of the SE process. In the present study the use of TIBs was tested for hybrid larch (Larix × eurolepis Henry). The results showed two-fold increases in both fresh weight (FW) of pro-embryogenic masses (PEMs) and yield of cotyledonary embryos in the TIBs compared to solid medium in plates. For the germination phase, the highest number of roots per plant, the root length and height of plants were also obtained in the TIBs. The results show that the TIB system can be successfully used to support scale up of plant production in all steps of the SE process from proliferation to germination of hybrid larch (Larix × eurolepis Henry).

@article{egertsdotter_automation_2019,
	title = {Automation and {Scale} {Up} of {Somatic} {Embryogenesis} for {Commercial} {Plant} {Production}, {With} {Emphasis} on {Conifers}},
	volume = {10},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00109/full},
	doi = {10/gjcrmh},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Egertsdotter, Ulrika and Ahmad, Iftikhar and Clapham, David},
	month = feb,
	year = {2019},
	pages = {109},
}

@article{carlsson_nitrogen_2019,
	title = {Nitrogen utilization during germination of somatic embryos of {Norway} spruce: revealing the importance of supplied glutamine for nitrogen metabolism},
	volume = {33},
	issn = {0931-1890, 1432-2285},
	shorttitle = {Nitrogen utilization during germination of somatic embryos of {Norway} spruce},
	url = {http://link.springer.com/10.1007/s00468-018-1784-y},
	doi = {10.1007/s00468-018-1784-y},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Trees},
	author = {Carlsson, Johanna and Egertsdotter, Ulrika and Ganeteg, Ulrika and Svennerstam, Henrik},
	month = apr,
	year = {2019},
	pages = {383--394},
}

@article{egertsdotter_plant_2019,
	title = {Plant physiological and genetical aspects of the somatic embryogenesis process in conifers},
	volume = {34},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2018.1441433},
	doi = {10.1080/02827581.2018.1441433},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Egertsdotter, Ulrika},
	month = jul,
	year = {2019},
	pages = {360--369},
}

@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{dahrendorf_analysis_2018,
	title = {Analysis of {Nitrogen} {Utilization} {Capability} during the {Proliferation} and {Maturation} {Phases} of {Norway} {Spruce} ({Picea} abies ({L}.) {H}.{Karst}.) {Somatic} {Embryogenesis}},
	volume = {9},
	issn = {1999-4907},
	url = {http://www.mdpi.com/1999-4907/9/6/288},
	doi = {10/gdw3gf},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Forests},
	author = {Dahrendorf, Julia and Clapham, David and Egertsdotter, Ulrika},
	month = may,
	year = {2018},
	pages = {288},
}

@article{mamun_improved_2018,
	title = {Improved and synchronized maturation of {Norway} spruce ({Picea} abies ({L}.) {H}.{Karst}.) somatic embryos in temporary immersion bioreactors},
	volume = {54},
	issn = {1054-5476, 1475-2689},
	url = {http://link.springer.com/10.1007/s11627-018-9911-4},
	doi = {10.1007/s11627-018-9911-4},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {In Vitro Cellular \& Developmental Biology - Plant},
	author = {Mamun, Nazmul H. A. and Aidun, Cyrus K. and Egertsdotter, Ulrika},
	month = dec,
	year = {2018},
	pages = {612--620},
}

@article{businge_evaluation_2017,
	title = {Evaluation of a {New} {Temporary} {Immersion} {Bioreactor} {System} for {Micropropagation} of {Cultivars} of {Eucalyptus}, {Birch} and {Fir}},
	volume = {8},
	issn = {1999-4907},
	url = {http://www.mdpi.com/1999-4907/8/6/196},
	doi = {10/gbm5gp},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Forests},
	author = {Businge, Edward and Trifonova, Adelina and Schneider, Carolin and Rödel, Philipp and Egertsdotter, Ulrika},
	month = jun,
	year = {2017},
	pages = {196},
}

@article{dobrowolska_histological_2017,
	title = {Histological analysis reveals the formation of shoots rather than embryos in regenerating cultures of {Eucalyptus} globulus},
	volume = {128},
	issn = {0167-6857, 1573-5044},
	url = {http://link.springer.com/10.1007/s11240-016-1111-5},
	doi = {10/f9szwr},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Cell, Tissue and Organ Culture (PCTOC)},
	author = {Dobrowolska, Izabela and Andrade, Gisele M. and Clapham, David and Egertsdotter, Ulrika},
	month = feb,
	year = {2017},
	pages = {319--326},
}

@article{dobrowolska_metabolome_2017,
	title = {Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in {Norway} spruce ({Picea} abies)},
	volume = {37},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article/37/12/1752/3896382},
	doi = {10/gcwvts},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Dobrowolska, Izabela and Businge, Edward and Abreu, Ilka N and Moritz, Thomas and Egertsdotter, Ulrika},
	month = dec,
	year = {2017},
	pages = {1752--1766},
}

@article{carlsson_nitrogen_2017,
	title = {Nitrogen uptake and assimilation in proliferating embryogenic cultures of {Norway} spruce—{Investigating} the specific role of glutamine},
	volume = {12},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0181785},
	doi = {10/gcjnr5},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Carlsson, Johanna and Svennerstam, Henrik and Moritz, Thomas and Egertsdotter, Ulrika and Ganeteg, Ulrika},
	editor = {Min, Xiang Jia},
	month = aug,
	year = {2017},
	pages = {e0181785},
}

@article{ausin_dna_2016,
	title = {{DNA} methylome of the 20-gigabase {Norway} spruce genome},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1618019113},
	doi = {10.1073/pnas.1618019113},
	abstract = {DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (
              Picea abies
              ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.},
	language = {en},
	number = {50},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Ausin, Israel and Feng, Suhua and Yu, Chaowei and Liu, Wanlu and Kuo, Hsuan Yu and Jacobsen, Elise L. and Zhai, Jixian and Gallego-Bartolome, Javier and Wang, Lin and Egertsdotter, Ulrika and Street, Nathaniel R. and Jacobsen, Steven E. and Wang, Haifeng},
	month = dec,
	year = {2016},
	pages = {E8106--E8113},
}

DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce ( Picea abies ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.

@article{pullman_fraser_2016,
	title = {Fraser fir somatic embryogenesis: high frequency initiation, maintenance, embryo development, germination and cryopreservation},
	volume = {47},
	issn = {0169-4286, 1573-5095},
	shorttitle = {Fraser fir somatic embryogenesis},
	url = {http://link.springer.com/10.1007/s11056-016-9525-9},
	doi = {10.1007/s11056-016-9525-9},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Forests},
	author = {Pullman, Gerald S. and Olson, Katie and Fischer, Taylor and Egertsdotter, Ulrika and Frampton, John and Bucalo, Kylie},
	month = may,
	year = {2016},
	pages = {453--480},
}

@article{mamun_bioreactor_2015,
	chapter = {177},
	title = {Bioreactor technology for clonal propagation of plants and metabolite production},
	volume = {10},
	issn = {1674-7984 1674-7992},
	doi = {10.1007/s11515-015-1355-1},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Frontiers in Biology},
	author = {Mamun, Nazmul H. A. and Egertsdotter, Ulrika and Aidun, Cyrus K.},
	month = apr,
	year = {2015},
	pages = {177--193},
}

@article{businge_possible_2014,
	title = {A possible biochemical basis for fructose-induced inhibition of embryo development in {Norway} spruce ({Picea} abies)},
	volume = {34},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpu053},
	doi = {10/f3m3sv},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Businge, E. and Egertsdotter, U.},
	month = jun,
	year = {2014},
	pages = {657--669},
}

@article{businge_effect_2013,
	title = {The effect of carbohydrates and osmoticum on storage reserve accumulation and germination of {Norway} spruce somatic embryos},
	volume = {149},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12039},
	doi = {10/f2zr7w},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Businge, Edward and Bygdell, Joakim and Wingsle, Gunnar and Moritz, Thomas and Egertsdotter, Ulrika},
	month = oct,
	year = {2013},
	pages = {273--285},
}

@article{lara-chavez_comparison_2012,
	title = {Comparison of gene expression markers during zygotic and somatic embryogenesis in pine},
	volume = {48},
	issn = {1054-5476, 1475-2689},
	url = {http://link.springer.com/10.1007/s11627-012-9440-5},
	doi = {10/f328xq},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {In Vitro Cellular \& Developmental Biology - Plant},
	author = {Lara-Chavez, Alejandra and Egertsdotter, Ulrika and Flinn, Barry S.},
	month = jun,
	year = {2012},
	pages = {341--354},
}

@article{businge_metabolite_2012,
	title = {Metabolite profiling reveals clear metabolic changes during somatic embryo development of {Norway} spruce ({Picea} abies)},
	volume = {32},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpr142},
	doi = {10/f24n88},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Businge, E. and Brackmann, K. and Moritz, T. and Egertsdotter, U.},
	month = feb,
	year = {2012},
	pages = {232--244},
}

@article{lara-chavez_initiation_2011,
	title = {Initiation of somatic embryogenesis from immature zygotic embryos of {Oocarpa} pine ({Pinus} oocarpa {Schiede} ex {Schlectendal})},
	volume = {31},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpr126},
	doi = {10/fjp4pt},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Lara-Chavez, A. and Flinn, B. S. and Egertsdotter, U.},
	month = dec,
	year = {2011},
	pages = {1422--1422},
}

@article{sun_possible_2011,
	title = {Possible {Effect} {From} {Shear} {Stress} on {Maturation} of {Somatic} {Embryos} of {Norway} {Spruce} ({Picea} abies)},
	volume = {108},
	issn = {00063592},
	url = {http://doi.wiley.com/10.1002/bit.23040},
	doi = {10/cpn47k},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Biotechnology and Bioengineering},
	author = {Sun, Hong and Aidun, Cyrus K. and Egertsdotter, Ulrika},
	month = may,
	year = {2011},
	pages = {1089--1099},
}

@article{kvaalen_somatic_2011,
	title = {Somatic embryogenesis for plant production of {Abies} lasiocarpa},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x05-035},
	doi = {10/fqvm8p},
	abstract = {Seeds of Abies lasiocarpa (Hook.) Nutt. (subalpine fir) were dissected, and the different parts were analyzed for elemental composition. The data were used to design a novel growth medium for initi...},
	language = {en},
	urldate = {2021-06-11},
	journal = {Canadian Journal of Forest Research},
	publisher = {NRC Research Press Ottawa, Canada},
	author = {Kvaalen, Harald and Daehlen, Ola Gram and Rognstad, Anne Tove and Grønstad, Borgny and Egertsdotter, Ulrika},
	month = feb,
	year = {2011},
}

Seeds of Abies lasiocarpa (Hook.) Nutt. (subalpine fir) were dissected, and the different parts were analyzed for elemental composition. The data were used to design a novel growth medium for initi...

@article{sun_effects_2010,
	title = {Effects from shear stress on morphology and growth of early stages of {Norway} spruce somatic embryos},
	volume = {105},
	issn = {00063592, 10970290},
	url = {http://doi.wiley.com/10.1002/bit.22554},
	doi = {10/ft23qd},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Biotechnology and Bioengineering},
	author = {Sun, Hong and Aidun, Cyrus K. and Egertsdotter, Ulrika},
	month = feb,
	year = {2010},
	pages = {588--599},
}

@article{wadenback_lignin_2008,
	title = {Lignin biosynthesis in transgenic {Norway} spruce plants harboring an antisense construct for cinnamoyl {CoA} reductase ({CCR})},
	volume = {17},
	issn = {0962-8819, 1573-9368},
	url = {http://link.springer.com/10.1007/s11248-007-9113-z},
	doi = {10/cr7v44},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Transgenic Research},
	author = {Wadenbäck, Johan and von Arnold, Sara and Egertsdotter, Ulrika and Walter, Michael H. and Grima-Pettenati, Jacqueline and Goffner, Deborah and Gellerstedt, Göran and Gullion, Terry and Clapham, David},
	month = jun,
	year = {2008},
	pages = {379--392},
}

@article{wadenback_comparison_2005,
	title = {Comparison of standard exponential and linear techniques to amplify small {cDNA} samples for microarrays},
	volume = {6},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/1471-2164-6-61},
	doi = {10/fmgwt5},
	abstract = {The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Genomics},
	author = {Wadenbäck, Johan and Clapham, David H. and Craig, Deborah and Sederoff, Ronald and Peter, Gary F. and von Arnold, Sara and Egertsdotter, Ulrika},
	month = may,
	year = {2005},
	keywords = {Amplification Method, Linear Amplification, Percentage Unit, Pinus Taeda, Technical Repeat},
	pages = {61},
}

The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.

@article{egertsdotter_gene_2004,
	title = {Gene {Expression} during {Formation} of {Earlywood} and {Latewood} in {Loblolly} {Pine}: {Expression} {Profiles} of 350 {Genes}},
	volume = {6},
	issn = {1438-8677},
	shorttitle = {Gene {Expression} during {Formation} of {Earlywood} and {Latewood} in {Loblolly} {Pine}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1055/s-2004-830383},
	doi = {10/cndbxc},
	abstract = {Abstract: The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy-one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.},
	language = {en},
	number = {6},
	urldate = {2021-06-15},
	journal = {Plant Biology},
	author = {Egertsdotter, U. and Zyl, L. M. van and MacKay, J. and Peter, G. and Kirst, M. and Clark, C. and Whetten, R. and Sederoff, R.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1055/s-2004-830383},
	keywords = {Microarray analysis, Pinus taeda, earlywood, latewood, transcript abundance},
	pages = {654--663},
}

Abstract: The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy-one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.

@article{stasolla_variation_2004,
	title = {Variation in transcript abundance during somatic embryogenesis in gymnosperms},
	volume = {24},
	issn = {0829-318X},
	url = {https://academic.oup.com/treephys/article/24/10/1073/1646975},
	doi = {10/fxjbcn},
	abstract = {Abstract. Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development becaus},
	language = {en},
	number = {10},
	urldate = {2021-06-15},
	journal = {Tree Physiology},
	publisher = {Oxford Academic},
	author = {Stasolla, Claudio and Bozhkov, Peter V. and Chu, Tzu-Ming and van Zyl, Leonel and Egertsdotter, Ulrika and Suarez, Maria F. and Craig, Deborah and Wolfinger, Russ D. and Von Arnold, Sara and Sederoff, Ronald R.},
	month = oct,
	year = {2004},
	pages = {1073--1085},
}

Abstract. Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development becaus

@article{stasolla_analysis_2003,
	title = {Analysis of lignin produced by cinnamyl alcohol dehydrogenase-deficient {Pinus} taeda cultured cells},
	volume = {41},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942803000512},
	doi = {10/bkcwgq},
	abstract = {Comparative studies were conducted on composition of lignin produced both in vivo and in vitro by cinnamyl alcohol dehydrogenase (CAD)-deficient mutant loblolly pine (Pinus taeda L.). In vivo studies were performed using differentiating xylem obtained from two genotypes of heterozygous (CAD/cad) and two genotypes of homozygous (cad/cad) CAD-deficient mutant trees. In vitro studies were performed using a culture system in which cells, generated from the same genotypes, were induced to produce lignin in culture. Steady state RNA levels and enzyme activity of CAD were dramatically reduced in both xylem and cultured cells obtained from homozygous mutant trees, compared to their heterozygous counterparts. Light microscopic studies showed pronounced differences during the lignin formation between homozygous and heterozygous cells. Phenolic compounds in the heterozygous (CAD/cad) cells were deposited around the cell wall, accumulated preferentially in vacuoles of the homozygous (cad/cad) cells. Differences in lignin composition as revealed by thioacidolysis were also observed. Lignin of both xylem tissue and cultured cells obtained from CAD-deficient homozygotes showed lower levels of coniferyl alcohols and significant enrichments in dihydroconiferyl alcohol (DHCA) and coniferyl aldehyde, compared to their heterozygous counterparts. The striking similarities in lignin composition observed both in vivo and in vitro, open new possibilities for the use of culture systems aimed at revealing the mechanisms controlling lignin biosynthesis, and the formation of DHCA subunits.},
	language = {en},
	number = {5},
	urldate = {2021-07-05},
	journal = {Plant Physiology and Biochemistry},
	author = {Stasolla, Claudio and Scott, Jay and Egertsdotter, Ulrika and Kadla, John and O’ Malley, David and Sederoff, Ronald and van Zyl, Leonel},
	month = may,
	year = {2003},
	keywords = {Cinnamyl alcohol dehydrogenase, Cultured cells, Dihydroconiferyl alcohol, Lignin, Xylem},
	pages = {439--445},
}

Comparative studies were conducted on composition of lignin produced both in vivo and in vitro by cinnamyl alcohol dehydrogenase (CAD)-deficient mutant loblolly pine (Pinus taeda L.). In vivo studies were performed using differentiating xylem obtained from two genotypes of heterozygous (CAD/cad) and two genotypes of homozygous (cad/cad) CAD-deficient mutant trees. In vitro studies were performed using a culture system in which cells, generated from the same genotypes, were induced to produce lignin in culture. Steady state RNA levels and enzyme activity of CAD were dramatically reduced in both xylem and cultured cells obtained from homozygous mutant trees, compared to their heterozygous counterparts. Light microscopic studies showed pronounced differences during the lignin formation between homozygous and heterozygous cells. Phenolic compounds in the heterozygous (CAD/cad) cells were deposited around the cell wall, accumulated preferentially in vacuoles of the homozygous (cad/cad) cells. Differences in lignin composition as revealed by thioacidolysis were also observed. Lignin of both xylem tissue and cultured cells obtained from CAD-deficient homozygotes showed lower levels of coniferyl alcohols and significant enrichments in dihydroconiferyl alcohol (DHCA) and coniferyl aldehyde, compared to their heterozygous counterparts. The striking similarities in lignin composition observed both in vivo and in vitro, open new possibilities for the use of culture systems aimed at revealing the mechanisms controlling lignin biosynthesis, and the formation of DHCA subunits.

@article{watkinson_photosynthetic_2003,
	title = {Photosynthetic {Acclimation} {Is} {Reflected} in {Specific} {Patterns} of {Gene} {Expression} in {Drought}-{Stressed} {Loblolly} {Pine}},
	volume = {133},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.103.026914},
	doi = {10.1104/pp.103.026914},
	abstract = {Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of -1 MPa for mild stress and -1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2,173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.},
	number = {4},
	urldate = {2021-07-05},
	journal = {Plant Physiology},
	author = {Watkinson, Jonathan I. and Sioson, Allan A. and Vasquez-Robinet, Cecilia and Shukla, Maulik and Kumar, Deept and Ellis, Margaret and Heath, Lenwood S. and Ramakrishnan, Naren and Chevone, Boris and Watson, Layne T. and van Zyl, Leonel and Egertsdotter, Ulrika and Sederoff, Ronald R. and Grene, Ruth},
	month = dec,
	year = {2003},
	pages = {1702--1716},
}

Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of -1 MPa for mild stress and -1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2,173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.

@article{stasolla_effects_2003,
	title = {The {Effects} of {Polyethylene} {Glycol} on {Gene} {Expression} of {Developing} {White} {Spruce} {Somatic} {Embryos}},
	volume = {131},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.015214},
	doi = {10/b6z454},
	abstract = {Somatic embryogenic cultures of white spruce (Picea glauca) represent a valuable system to study molecular mechanisms regulating embryo development because many embryos of defined developmental stages can be generated. The inclusion of polyethylene glycol (PEG) in the maturation medium can improve the number and quality of embryos produced. To learn more about the mechanism of action of PEG, we analyzed transcript profiles of stage-specific embryos matured without (control) or with (PEG treated) PEG. RNA extracted from maturing spruce embryos was analyzed on DNA microarrays containing 2,178 cDNAs from loblolly pine (Pinus taeda). The efficiency of heterologous hybridization between spruce and pine species on microarrays has been documented previously (L. van Zyl, S. von Arnold, P. Bozhkov, Y. Chen, U. Egertsdotter, J. MacKay, R. Sederoff, J. Shen, L. Zelena, D. Clapham [2002] Comp Funct Genomics 3: 306–318). Several pine genes, including the apparent homologs to the Arabidopsis genes ZWILLE, FIDDLEHEAD, FUSCA, and SCARECROW, increased in expression after PEG treatments. These genes are known to be involved in the formation of the embryo body plan and in the control of the shoot and root apical meristems. The increased transcript levels of these genes in immature PEG-treated embryos suggest that PEG may improve the quality of spruce somatic embryos by promoting normal differentiation of the embryonic shoot and root. Changes in the transcript levels of many genes involved in sucrose catabolism and nitrogen assimilation and utilization were also observed between control and PEG-treated embryos.},
	number = {1},
	urldate = {2021-07-05},
	journal = {Plant Physiology},
	author = {Stasolla, Claudio and van Zyl, Leonel and Egertsdotter, Ulrika and Craig, Deborah and Liu, Wenbin and Sederoff, Ron R.},
	month = jan,
	year = {2003},
	pages = {49--60},
}

Somatic embryogenic cultures of white spruce (Picea glauca) represent a valuable system to study molecular mechanisms regulating embryo development because many embryos of defined developmental stages can be generated. The inclusion of polyethylene glycol (PEG) in the maturation medium can improve the number and quality of embryos produced. To learn more about the mechanism of action of PEG, we analyzed transcript profiles of stage-specific embryos matured without (control) or with (PEG treated) PEG. RNA extracted from maturing spruce embryos was analyzed on DNA microarrays containing 2,178 cDNAs from loblolly pine (Pinus taeda). The efficiency of heterologous hybridization between spruce and pine species on microarrays has been documented previously (L. van Zyl, S. von Arnold, P. Bozhkov, Y. Chen, U. Egertsdotter, J. MacKay, R. Sederoff, J. Shen, L. Zelena, D. Clapham [2002] Comp Funct Genomics 3: 306–318). Several pine genes, including the apparent homologs to the Arabidopsis genes ZWILLE, FIDDLEHEAD, FUSCA, and SCARECROW, increased in expression after PEG treatments. These genes are known to be involved in the formation of the embryo body plan and in the control of the shoot and root apical meristems. The increased transcript levels of these genes in immature PEG-treated embryos suggest that PEG may improve the quality of spruce somatic embryos by promoting normal differentiation of the embryonic shoot and root. Changes in the transcript levels of many genes involved in sucrose catabolism and nitrogen assimilation and utilization were also observed between control and PEG-treated embryos.

@article{stasolla_transcript_2003,
	title = {Transcript profiles of stress-related genes in developing white spruce ({Picea} glauca) somatic embryos cultured with polyethylene glycol},
	volume = {165},
	issn = {0168-9452},
	url = {https://www.sciencedirect.com/science/article/pii/S0168945203002280},
	doi = {10/fk3m4b},
	abstract = {The effect of polyethylene glycol (PEG) on the transcript level of 512 stress-related genes was analyzed by cDNA microarray. Major changes in gene expression between control and PEG-treated embryos were observed during the initial stages of development, upon transfer of the embryogenic tissue on maturation medium, and during the late phases of development, culminating with the generation of cotyledonary embryos. Only small changes in gene expression were observed during the intermediate phases of embryo development. The transcript levels of several genes involved in cell aging and detoxification mechanisms, including peroxidases and chitinases, were developmentally regulated during the embryogenic process. Major differences in the expression of these genes were observed between control and PEG-treated embryos. Based on their expression profiles, four different clusters of genes involved in stress response mechanisms were identified. The first group of genes, which included several heat shock proteins, was up-regulated in PEG-treated immature embryos. An opposite tendency was observed for a second cluster of genes, which included a glutathione-S-transferase, and a cysteine protease. The third class included genes repressed by PEG in fully developed embryos, whereas a fourth group of genes, which included several heat shock proteins and ubiquitin, was induced in PEG-treated embryos at the end of the culture period. Difference in transcript levels and profiles of several genes involved in cell wall and lignin biosynthesis were also observed between control and PEG-treated embryos.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Plant Science},
	author = {Stasolla, Claudio and van Zyl, Leonel and Egertsdotter, Ulrika and Craig, Deborah and Liu, Wenbin and Sederoff, Ronald R.},
	month = oct,
	year = {2003},
	keywords = {Microarray, Polyethylene glycol, Transcript levels, White spruce},
	pages = {719--729},
}

The effect of polyethylene glycol (PEG) on the transcript level of 512 stress-related genes was analyzed by cDNA microarray. Major changes in gene expression between control and PEG-treated embryos were observed during the initial stages of development, upon transfer of the embryogenic tissue on maturation medium, and during the late phases of development, culminating with the generation of cotyledonary embryos. Only small changes in gene expression were observed during the intermediate phases of embryo development. The transcript levels of several genes involved in cell aging and detoxification mechanisms, including peroxidases and chitinases, were developmentally regulated during the embryogenic process. Major differences in the expression of these genes were observed between control and PEG-treated embryos. Based on their expression profiles, four different clusters of genes involved in stress response mechanisms were identified. The first group of genes, which included several heat shock proteins, was up-regulated in PEG-treated immature embryos. An opposite tendency was observed for a second cluster of genes, which included a glutathione-S-transferase, and a cysteine protease. The third class included genes repressed by PEG in fully developed embryos, whereas a fourth group of genes, which included several heat shock proteins and ubiquitin, was induced in PEG-treated embryos at the end of the culture period. Difference in transcript levels and profiles of several genes involved in cell wall and lignin biosynthesis were also observed between control and PEG-treated embryos.

@article{ciavatta_promoter_2002,
	title = {A promoter from the loblolly pine {PtNIP1};1 gene directs expression in an early-embryogenesis and suspensor-specific fashion},
	volume = {215},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-002-0822-5},
	doi = {10/b3zcr8},
	abstract = {The PtNIP1;1 gene encodes an aquaglyceroporin that is expressed early in embryogenesis and appears to be expressed preferentially in the suspensor [V.T. Ciavatta et al. (2001) Plant Physiol 127:211–224]. An 899-bp fragment 5′ to the PtNIP1;1 open reading frame (NIP-899) was cloned from loblolly pine (Pinus taeda L.) genomic DNA and fused to the β-glucuronidase (GUS) reporter gene. The resulting plasmid, pNIP-GUS, was transformed into Norway spruce (Picea abies L.) embryogenic cultures by co-bombarding with a plasmid containing a bar gene construct as a selectable marker. The identity of lines selected on medium containing the herbicide Basta and showing β-glucuronidase activity was confirmed by polymerase chain reaction as harboring GUS. Histochemical GUS assays of these lines revealed GUS activity in all cells of proembryogenic masses. During early embryogeny, GUS staining was intense in the suspensor region but not detectable in embryonal masses. GUS staining was absent by mid-embryogeny. By contrast, a control transgenic line, transformed with EuCAD-GUS, expressed GUS throughout embryo development. These results suggest that NIP-899 contains elements that drive early embryogenesis-specific expression and suspensor-specific expression. This is the first example of a suspensor-specific promoter in conifers.},
	language = {en},
	number = {4},
	urldate = {2021-08-26},
	journal = {Planta},
	author = {Ciavatta, Vincent T. and Egertsdotter, Ulrika and Clapham, David and von Arnold, Sara and Cairney, John},
	month = aug,
	year = {2002},
	pages = {694--698},
}

The PtNIP1;1 gene encodes an aquaglyceroporin that is expressed early in embryogenesis and appears to be expressed preferentially in the suspensor [V.T. Ciavatta et al. (2001) Plant Physiol 127:211–224]. An 899-bp fragment 5′ to the PtNIP1;1 open reading frame (NIP-899) was cloned from loblolly pine (Pinus taeda L.) genomic DNA and fused to the β-glucuronidase (GUS) reporter gene. The resulting plasmid, pNIP-GUS, was transformed into Norway spruce (Picea abies L.) embryogenic cultures by co-bombarding with a plasmid containing a bar gene construct as a selectable marker. The identity of lines selected on medium containing the herbicide Basta and showing β-glucuronidase activity was confirmed by polymerase chain reaction as harboring GUS. Histochemical GUS assays of these lines revealed GUS activity in all cells of proembryogenic masses. During early embryogeny, GUS staining was intense in the suspensor region but not detectable in embryonal masses. GUS staining was absent by mid-embryogeny. By contrast, a control transgenic line, transformed with EuCAD-GUS, expressed GUS throughout embryo development. These results suggest that NIP-899 contains elements that drive early embryogenesis-specific expression and suspensor-specific expression. This is the first example of a suspensor-specific promoter in conifers.

@article{van_zyl_heterologous_2002,
	title = {Heterologous {Array} {Analysis} in {Pinaceae}: {Hybridization} of {Pinus} taeda {cDNA} {Arrays} with {cDNA} from {Needles} and {Embryogenic} {Cultures} of {P}. taeda, {P}. sylvestris or {Picea} abies},
	volume = {3},
	issn = {2314-436X},
	shorttitle = {Heterologous {Array} {Analysis} in {Pinaceae}},
	url = {https://www.hindawi.com/journals/ijg/2002/186124/},
	doi = {10.1002/cfg.199},
	abstract = {Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Comparative and Functional Genomics},
	publisher = {Hindawi},
	author = {van Zyl, Leonel and von Arnold, Sara and Bozhkov, Peter and Chen, Yongzhong and Egertsdotter, Ulrika and MacKay, John and Sederoff, Ronald R. and Shen, Jing and Zelena, Lyubov and Clapham, David H.},
	year = {2002},
	pages = {306--318},
}

Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.