@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{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_2019-1,
	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,
	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},
	note = {Section: 177},
	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},
	author = {Kvaalen, Harald and Daehlen, Ola Gram and Rognstad, Anne Tove and Grønstad, Borgny and Egertsdotter, Ulrika},
	month = feb,
	year = {2011},
	note = {Publisher: NRC Research Press Ottawa, Canada},
}

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},
	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},
	note = {Publisher: Oxford Academic},
	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},
	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},
	note = {Publisher: Hindawi},
	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.