Nilsson, Ove - Control of Flowering Time and Tree Phenology

@article{liao_age-dependent_2023,
	title = {Age-dependent seasonal growth cessation in {Populus}},
	volume = {120},
	url = {https://www.pnas.org/doi/10.1073/pnas.2311226120},
	doi = {10.1073/pnas.2311226120},
	abstract = {In temperate and boreal regions, perennial plants adapt their annual growth cycle to the change of seasons. In natural forests, juvenile seedlings usually display longer growth seasons compared to adult trees to ensure their establishment and survival under canopy shade. However, how trees adjust their annual growth according to their age is not known. In this study, we show that age-dependent seasonal growth cessation is genetically controlled and found that the miR156-SPL3/5 module, a key regulon of vegetative phase change (VPC), also triggers age-dependent growth cessation in Populus trees. We show that miR156 promotes shoot elongation during vegetative growth, and its targets SPL3/5s function in the same pathway but as repressors. We find that the miR156-SPL3/5s regulon controls growth cessation in both leaves and shoot apices and through multiple pathways, but with a different mechanism compared to how the miR156-SPL regulon controls VPC in annual plants. Taken together, our results reveal an age-dependent genetic network in mediating seasonal growth cessation, a key phenological process in the climate adaptation of perennial trees.},
	number = {48},
	urldate = {2023-11-24},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Liao, Xiaoli and Su, Yunjie and Klintenäs, Maria and Li, Yue and Sane, Shashank and Wu, Zhihao and Chen, Qihui and Zhang, Bo and Nilsson, Ove and Ding, Jihua},
	month = nov,
	year = {2023},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2311226120},
}

In temperate and boreal regions, perennial plants adapt their annual growth cycle to the change of seasons. In natural forests, juvenile seedlings usually display longer growth seasons compared to adult trees to ensure their establishment and survival under canopy shade. However, how trees adjust their annual growth according to their age is not known. In this study, we show that age-dependent seasonal growth cessation is genetically controlled and found that the miR156-SPL3/5 module, a key regulon of vegetative phase change (VPC), also triggers age-dependent growth cessation in Populus trees. We show that miR156 promotes shoot elongation during vegetative growth, and its targets SPL3/5s function in the same pathway but as repressors. We find that the miR156-SPL3/5s regulon controls growth cessation in both leaves and shoot apices and through multiple pathways, but with a different mechanism compared to how the miR156-SPL regulon controls VPC in annual plants. Taken together, our results reveal an age-dependent genetic network in mediating seasonal growth cessation, a key phenological process in the climate adaptation of perennial trees.

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

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

@article{akhter_cone-setting_2022,
	title = {Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway},
	volume = {236},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18449},
	doi = {10.1111/nph.18449},
	abstract = {Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.},
	language = {en},
	number = {5},
	urldate = {2022-11-10},
	journal = {New Phytologist},
	author = {Akhter, Shirin and Westrin, Karl Johan and Zivi, Nathan and Nordal, Veronika and Kretzschmar, Warren W. and Delhomme, Nicolas and Street, Nathaniel R. and Nilsson, Ove and Emanuelsson, Olof and Sundström, Jens F.},
	month = dec,
	year = {2022},
	keywords = {Cone-setting, Flowering, Gymnosperm, Picea abies, Reproductive development, SPL-gene family, Transcriptome, cone-setting, flowering, gymnosperm, reproductive development, transcriptome},
	pages = {1951--1963},
}

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

@article{andre_flowering_2022,
	title = {{FLOWERING} {LOCUS} {T} paralogs control the annual growth cycle in {Populus} trees},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(22)00782-5},
	doi = {10.1016/j.cub.2022.05.023},
	abstract = {In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1, 2, 3, 4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.},
	language = {English},
	number = {13},
	urldate = {2022-08-12},
	journal = {Current Biology},
	author = {André, Domenique and Marcon, Alice and Lee, Keh Chien and Goretti, Daniela and Zhang, Bo and Delhomme, Nicolas and Schmid, Markus and Nilsson, Ove},
	month = jul,
	year = {2022},
	pmid = {35660141},
	note = {Publisher: Elsevier},
	keywords = {FLOWERING LOCUS T, Populus, annual growth cycle, bud flush, dormancy, paralogs},
	pages = {2988--2996.e4},
}

In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1, 2, 3, 4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.

@article{curci_identification_2022,
	title = {Identification of growth regulators using cross-species network analysis in plants},
	volume = {190},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac374},
	doi = {10.1093/plphys/kiac374},
	abstract = {With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.},
	number = {4},
	urldate = {2022-12-02},
	journal = {Plant Physiology},
	author = {Curci, Pasquale Luca and Zhang, Jie and Mähler, Niklas and Seyfferth, Carolin and Mannapperuma, Chanaka and Diels, Tim and Van Hautegem, Tom and Jonsen, David and Street, Nathaniel and Hvidsten, Torgeir R and Hertzberg, Magnus and Nilsson, Ove and Inzé, Dirk and Nelissen, Hilde and Vandepoele, Klaas},
	month = dec,
	year = {2022},
	pages = {2350--2365},
}

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

@article{andre_populus_2022,
	title = {Populus {SVL} {Acts} in {Leaves} to {Modulate} the {Timing} of {Growth} {Cessation} and {Bud} {Set}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.823019},
	doi = {10.3389/fpls.2022.823019},
	abstract = {SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.},
	urldate = {2022-02-17},
	journal = {Frontiers in Plant Science},
	author = {André, Domenique and Zambrano, José Alfredo and Zhang, Bo and Lee, Keh Chien and Rühl, Mark and Marcon, Alice and Nilsson, Ove},
	month = feb,
	year = {2022},
}

SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.

@article{nilsson_winter_2022,
	title = {Winter dormancy in trees},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222005802},
	doi = {10.1016/j.cub.2022.04.011},
	abstract = {Plants growing in temperate and boreal regions of the world have to face strikingly different environmental conditions during summer and winter. Being sessile organisms, plants have had to develop various strategies to adapt to these changes in light, temperature, and water availability, thereby optimizing their ‘economy of growth’. While annual plants can endure unfavorable winter conditions in the form of a seed, or under a protective cover of thick snow, perennial plants such as trees adapt by going into a stage of deep sleep called winter dormancy. To enter dormancy, vegetative growth is stopped in the late summer or early autumn and the shoots are converted into buds, where the shoot apical meristems are protected by tightly closed and hardened bud scales (Figures 1 and 2). At the same time, cold hardiness develops and the need for water and nutrient uptake is drastically reduced. Deciduous trees also go through leaf senescence whereby the leaves develop their autumn colors and are shed (Figure 1A). The trees then spend the beginning of the winter in a state of deep sleep in which they are completely unreceptive to any environmental signals telling them to wake up. However, as winter progresses, the trees are gradually released from this slumber and will eventually flush their buds in the spring. Vegetative growth then resumes with the formation of new leaves and shoots during summer until the trees again go into growth cessation and the cycle is closed (Figures 1 and 2). This cycle of growth and dormancy is central for the ability of trees to adapt to growth at different latitudes and elevations. The further north, or the higher the elevation at which the trees grow, the earlier in the season the trees enter growth cessation and the later they flush their buds in the spring. This is because meteorological winter arrives earlier in the season and lasts longer into the spring. The trees therefore have to stop growth earlier in the season to ensure that they have enough time to complete bud formation and to develop cold hardiness and dormancy. They also have to be sure that winter is really over before flushing their buds. Winter dormancy is therefore a clear case of a trade-off between the length of the growing season and the protection against winter damage — a nice example of ‘economy in biology’, the theme of this special issue. This primer will briefly summarize what we know about the environmental signals that influence the annual growth cycle in trees, as well as our current understanding of the genetic pathways and molecular mechanisms regulated by these signals.},
	language = {en},
	number = {12},
	urldate = {2022-06-21},
	journal = {Current Biology},
	author = {Nilsson, Ove},
	month = jun,
	year = {2022},
	pages = {R630--R634},
}

Plants growing in temperate and boreal regions of the world have to face strikingly different environmental conditions during summer and winter. Being sessile organisms, plants have had to develop various strategies to adapt to these changes in light, temperature, and water availability, thereby optimizing their ‘economy of growth’. While annual plants can endure unfavorable winter conditions in the form of a seed, or under a protective cover of thick snow, perennial plants such as trees adapt by going into a stage of deep sleep called winter dormancy. To enter dormancy, vegetative growth is stopped in the late summer or early autumn and the shoots are converted into buds, where the shoot apical meristems are protected by tightly closed and hardened bud scales (Figures 1 and 2). At the same time, cold hardiness develops and the need for water and nutrient uptake is drastically reduced. Deciduous trees also go through leaf senescence whereby the leaves develop their autumn colors and are shed (Figure 1A). The trees then spend the beginning of the winter in a state of deep sleep in which they are completely unreceptive to any environmental signals telling them to wake up. However, as winter progresses, the trees are gradually released from this slumber and will eventually flush their buds in the spring. Vegetative growth then resumes with the formation of new leaves and shoots during summer until the trees again go into growth cessation and the cycle is closed (Figures 1 and 2). This cycle of growth and dormancy is central for the ability of trees to adapt to growth at different latitudes and elevations. The further north, or the higher the elevation at which the trees grow, the earlier in the season the trees enter growth cessation and the later they flush their buds in the spring. This is because meteorological winter arrives earlier in the season and lasts longer into the spring. The trees therefore have to stop growth earlier in the season to ensure that they have enough time to complete bud formation and to develop cold hardiness and dormancy. They also have to be sure that winter is really over before flushing their buds. Winter dormancy is therefore a clear case of a trade-off between the length of the growing season and the protection against winter damage — a nice example of ‘economy in biology’, the theme of this special issue. This primer will briefly summarize what we know about the environmental signals that influence the annual growth cycle in trees, as well as our current understanding of the genetic pathways and molecular mechanisms regulated by these signals.

@article{fataftah_gigantea_2021,
	title = {{GIGANTEA} influences leaf senescence in trees in two different ways},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab439},
	doi = {10/gnxfqw},
	abstract = {GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.},
	number = {4},
	urldate = {2021-10-15},
	journal = {Plant Physiology},
	author = {Fataftah, Nazeer and Bag, Pushan and André, Domenique and Lihavainen, Jenna and Zhang, Bo and Ingvarsson, Pär K and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	pages = {2435--2450},
}

GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.

@article{ding_phytochrome_2021,
	title = {Phytochrome {B} and {PHYTOCHROME} {INTERACTING} {FACTOR8} modulate seasonal growth in trees},
	volume = {232},
	copyright = {© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17350},
	doi = {10.1111/nph.17350},
	abstract = {The seasonally synchronized annual growth cycle that is regulated mainly by photoperiod and temperature cues is a crucial adaptive strategy for perennial plants in boreal and temperate ecosystems. Phytochrome B (phyB), as a light and thermal sensor, has been extensively studied in Arabidopsis. However, the specific mechanisms for how the phytochrome photoreceptors control the phenology in tree species remain poorly understood. We characterized the functions of PHYB genes and their downstream PHYTOCHROME INTERACTING FACTOR (PIF) targets in the regulation of shade avoidance and seasonal growth in hybrid aspen trees. We show that while phyB1 and phyB2, as phyB in other plants, act as suppressors of shoot elongation during vegetative growth, they act as promoters of tree seasonal growth. Furthermore, while the Populus homologs of both PIF4 and PIF8 are involved in the shade avoidance syndrome (SAS), only PIF8 plays a major role as a suppressor of seasonal growth. Our data suggest that the PHYB-PIF8 regulon controls seasonal growth through the regulation of FT and CENL1 expression while a genome-wide transcriptome analysis suggests how, in Populus trees, phyB coordinately regulates SAS responses and seasonal growth cessation.},
	language = {en},
	number = {6},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Ding, Jihua and Zhang, Bo and Li, Yue and André, Domenique and Nilsson, Ove},
	month = mar,
	year = {2021},
	keywords = {PHYTOCHROME B, PHYTOCHROME INTERACTING FACTOR8, Populus, bud break, growth cessation, shade avoidance},
	pages = {2339--2352},
}

The seasonally synchronized annual growth cycle that is regulated mainly by photoperiod and temperature cues is a crucial adaptive strategy for perennial plants in boreal and temperate ecosystems. Phytochrome B (phyB), as a light and thermal sensor, has been extensively studied in Arabidopsis. However, the specific mechanisms for how the phytochrome photoreceptors control the phenology in tree species remain poorly understood. We characterized the functions of PHYB genes and their downstream PHYTOCHROME INTERACTING FACTOR (PIF) targets in the regulation of shade avoidance and seasonal growth in hybrid aspen trees. We show that while phyB1 and phyB2, as phyB in other plants, act as suppressors of shoot elongation during vegetative growth, they act as promoters of tree seasonal growth. Furthermore, while the Populus homologs of both PIF4 and PIF8 are involved in the shade avoidance syndrome (SAS), only PIF8 plays a major role as a suppressor of seasonal growth. Our data suggest that the PHYB-PIF8 regulon controls seasonal growth through the regulation of FT and CENL1 expression while a genome-wide transcriptome analysis suggests how, in Populus trees, phyB coordinately regulates SAS responses and seasonal growth cessation.

@article{robinson_variation_2021,
	title = {Variation in non-target traits in genetically modified hybrid aspens does not exceed natural variation},
	volume = {64},
	issn = {1871-6784},
	url = {https://www.sciencedirect.com/science/article/pii/S1871678421000625},
	doi = {10.1016/j.nbt.2021.05.005},
	abstract = {Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.},
	language = {en},
	urldate = {2021-09-21},
	journal = {New Biotechnology},
	author = {Robinson, Kathryn M. and Möller, Linus and Bhalerao, Rishikesh P. and Hertzberg, Magnus and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	keywords = {European aspen, Field experiment, Genetically modified, Hybrid aspen, Natural variation, Non-target traits},
	pages = {27--36},
}

Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.

@article{kucukoglu_peptide_2020,
	title = {Peptide encoding \textit{{Populus} {CLV3}/{ESR}‐{RELATED} 47} ( \textit{{PttCLE47}} ) promotes cambial development and secondary xylem formation in hybrid aspen},
	volume = {226},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16331},
	doi = {10.1111/nph.16331},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Kucukoglu, Melis and Chaabouni, Salma and Zheng, Bo and Mähönen, Ari Pekka and Helariutta, Ykä and Nilsson, Ove},
	month = apr,
	year = {2020},
	pages = {75--85},
}

@article{strauss_certification_2019,
	title = {Certification for gene-edited forests},
	volume = {365},
	copyright = {Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. http://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/365/6455/767.2},
	doi = {10/gjcsp9},
	abstract = {Forest certification bodies were established to provide consumers with confidence that they are purchasing sustainably sourced wood products. Over 500 million hectares of forests, or about 13\% of global forest area, are certified under the largest certification systems ([ 1 ][1]–[ 3 ][2]). However, certification bodies have consistently excluded all genetically engineered or gene-edited (GE) trees from certification, including from field research on certified lands that is essential for understanding local benefits and impacts ([ 4 ][3]). We, leading forest biotechnology scientists from around the world, with the support of more than 1000 globally diverse signatories to a recent detailed petition ([ 5 ][4]), call for all forest certification systems to promptly examine and modify these policies.

Forests face mounting stresses posed by invasive pests and climate change ([ 6 ][5]). Given the growing need for sustainable and renewable forest products and the increasing precision and safety record of biotechnologies, we believe that GE trees can make a substantial contribution to management of certified forests. To face the challenges of forest health, carbon sequestration, and maintenance of other ecological services, we must use all available tools. GE tree research should be allowed immediately on certified land, and GE trees proven by research to provide value should eventually be allowed in certified forests.

A variety of current biotechnologies—including grafting, in vitro propagation, breeding, hybridization, and cloning—have made tremendous impacts on tree health and productivity ([ 7 ][6]). Newer forms of biotechnology, specifically gene editing, can make substantial further contributions to forest management. Traits that have shown great promise based on field trials of GE trees are highly diverse and include those related to productivity, wood quality, pest and stress resistance, protection of endangered species, and reproductive control ([ 8 ][7]). Research results also suggest that there are no hazards unique to GE methods compared with conventional breeding; rather, it is the value and novelty of the specific traits imparted and how they interact with conventional breeding that are germane to safety and economic assessments ([ 9 ][8], [ 10 ][9]). Instead of categorically excluding GE methods, each application of GE technology should be evaluated on its individual merits based on the trait and its mechanism.

Democratic and stakeholder-driven processes generally govern certification agencies in sustainable forest management systems. However, the Programme for the Endorsement of Forest Certification (PEFC) recently extended the GE tree ban through 2022 via editorial updates ([ 11 ][10]), an internal procedure that did not meet the standards of a rigorous, science-based, democratic, and transparent process. We urge in-depth discussion and decisions on this issue at the PEFC annual stakeholder meeting on 3 October and at the Forest Stewardship Council general assembly on 8 October.

The National Academies of Sciences, Engineering, and Medicine recently completed an in-depth study on forest health and biotechnology, concluding that the potential benefits are numerous and rapidly increasing ([ 12 ][11]). Our forests are in dire need of assistance, and GE trees hold tremendous potential as a safe and powerful tool for promoting forest resilience and sustainability.



1.  [↵][12]FAO, Global Forest Resources Assessment 2015 (2015); [www.fao.org/3/a-i4793e.pdf][13].
2.  PEFC ({\textless}https://pefc.org/{\textgreater}).
3.  [↵][14]Forest Stewardship Council, Facts and Figures ({\textless}https://fsc.org/en/page/facts-figures{\textgreater}).
4.  [↵][15]1.   S. H. Strauss, 
    2.   A. Costanza, 
    3.   A. Séguin
    
    , Science 349, 794 (2015).
    
    [OpenUrl][16]

5.  [↵][17]Committee of Scientists, Petition in Support of Forest Biotechnology Research (2019); {\textless}http://biotechtrees.forestry.oregonstate.edu/petition{\textgreater}.
6.  [↵][18]1.   S. Trumbore, 
    2.   P. Brando, 
    3.   H. Hartmann
    
    , Science 349, 814 (2015).
    
    [OpenUrl][19]

7.  [↵][20]1.   T. L. White, 
    2.   W. T. Adams, 
    3.   D. B. Neale
    
    , Forest Genetics (Cabi International, 2007).
    
    

8.  [↵][21]1.   S. Chang et al
    
    ., In Vitro Cell. Dev. Biol. Plant. 54, 341 (2018).
    
    [OpenUrl][22]

9.  [↵][23]1.   C. Walter, 
    2.   M. Fladung, 
    3.   W. Boerjan
    
    , Nat. Biotechnol. 28, 656 (2010).
    
    [OpenUrl][24][CrossRef][25][PubMed][26]

10. [↵][27]1.   V. Viswanath, 
    2.   B. R. Albrectsen, 
    3.   S. H. Strauss
    
    , Tree Genet. Genomes 8, 221 (2012).
    
    [OpenUrl][28]

11. [↵][29]PEFC, “Editorial updates to chain of custody standard (PEFC ST 2002:2013)” (2016); [www.pefc.co.uk/news\_articles/editorial-updates-to-chain-of-custody-standard-pefc-st-2002-2013][30].
12. [↵][31]National Academies of Sciences, Engineering, and Medicine, Forest Health and Biotechnology: Possibilities and Considerations (2019); [www.nap.edu/catalog/25221/forest-health-and-biotechnology-possibilities-and-considerations][32].

 [1]: \#ref-1
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 [3]: \#ref-4
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 [28]: \{openurl\}?query=rft.jtitle\%253DTree\%2BGenet.\%2BGenomes\%26rft.volume\%253D8\%26rft.spage\%253D221\%26rft.genre\%253Darticle\%26rft\_val\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Ajournal\%26ctx\_ver\%253DZ39.88-2004\%26url\_ver\%253DZ39.88-2004\%26url\_ctx\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Actx
 [29]: \#xref-ref-11-1 "View reference 11 in text"
 [30]: http://www.pefc.co.uk/news\_articles/editorial-updates-to-chain-of-custody-standard-pefc-st-2002-2013
 [31]: \#xref-ref-12-1 "View reference 12 in text"
 [32]: http://www.nap.edu/catalog/25221/forest-health-and-biotechnology-possibilities-and-considerations},
	language = {en},
	number = {6455},
	urldate = {2021-06-07},
	journal = {Science},
	author = {Strauss, Steven H. and Boerjan, Wout and Chiang, Vincent and Costanza, Adam and Coleman, Heather and Davis, John M. and Lu, Meng-Zhu and Mansfield, Shawn D. and Merkle, Scott and Myburg, Alexander and Nilsson, Ove and Pilate, Gilles and Powell, William and Seguin, Armand and Valenzuela, Sofia},
	month = aug,
	year = {2019},
	pmid = {31439790},
	note = {Publisher: American Association for the Advancement of Science
Section: Letters},
	pages = {767--768},
}

Forest certification bodies were established to provide consumers with confidence that they are purchasing sustainably sourced wood products. Over 500 million hectares of forests, or about 13% of global forest area, are certified under the largest certification systems ([ 1 ][1]–[ 3 ][2]). However, certification bodies have consistently excluded all genetically engineered or gene-edited (GE) trees from certification, including from field research on certified lands that is essential for understanding local benefits and impacts ([ 4 ][3]). We, leading forest biotechnology scientists from around the world, with the support of more than 1000 globally diverse signatories to a recent detailed petition ([ 5 ][4]), call for all forest certification systems to promptly examine and modify these policies. Forests face mounting stresses posed by invasive pests and climate change ([ 6 ][5]). Given the growing need for sustainable and renewable forest products and the increasing precision and safety record of biotechnologies, we believe that GE trees can make a substantial contribution to management of certified forests. To face the challenges of forest health, carbon sequestration, and maintenance of other ecological services, we must use all available tools. GE tree research should be allowed immediately on certified land, and GE trees proven by research to provide value should eventually be allowed in certified forests. A variety of current biotechnologies—including grafting, in vitro propagation, breeding, hybridization, and cloning—have made tremendous impacts on tree health and productivity ([ 7 ][6]). Newer forms of biotechnology, specifically gene editing, can make substantial further contributions to forest management. Traits that have shown great promise based on field trials of GE trees are highly diverse and include those related to productivity, wood quality, pest and stress resistance, protection of endangered species, and reproductive control ([ 8 ][7]). Research results also suggest that there are no hazards unique to GE methods compared with conventional breeding; rather, it is the value and novelty of the specific traits imparted and how they interact with conventional breeding that are germane to safety and economic assessments ([ 9 ][8], [ 10 ][9]). Instead of categorically excluding GE methods, each application of GE technology should be evaluated on its individual merits based on the trait and its mechanism. Democratic and stakeholder-driven processes generally govern certification agencies in sustainable forest management systems. However, the Programme for the Endorsement of Forest Certification (PEFC) recently extended the GE tree ban through 2022 via editorial updates ([ 11 ][10]), an internal procedure that did not meet the standards of a rigorous, science-based, democratic, and transparent process. We urge in-depth discussion and decisions on this issue at the PEFC annual stakeholder meeting on 3 October and at the Forest Stewardship Council general assembly on 8 October. The National Academies of Sciences, Engineering, and Medicine recently completed an in-depth study on forest health and biotechnology, concluding that the potential benefits are numerous and rapidly increasing ([ 12 ][11]). Our forests are in dire need of assistance, and GE trees hold tremendous potential as a safe and powerful tool for promoting forest resilience and sustainability. 1. [↵][12]FAO, Global Forest Resources Assessment 2015 (2015); [www.fao.org/3/a-i4793e.pdf][13]. 2. PEFC (\textlesshttps://pefc.org/\textgreater). 3. [↵][14]Forest Stewardship Council, Facts and Figures (\textlesshttps://fsc.org/en/page/facts-figures\textgreater). 4. [↵][15]1. S. H. Strauss, 2. A. Costanza, 3. A. Séguin , Science 349, 794 (2015). [OpenUrl][16] 5. [↵][17]Committee of Scientists, Petition in Support of Forest Biotechnology Research (2019); \textlesshttp://biotechtrees.forestry.oregonstate.edu/petition\textgreater. 6. [↵][18]1. S. Trumbore, 2. P. Brando, 3. H. Hartmann , Science 349, 814 (2015). [OpenUrl][19] 7. [↵][20]1. T. L. White, 2. W. T. Adams, 3. D. B. Neale , Forest Genetics (Cabi International, 2007). 8. [↵][21]1. S. Chang et al ., In Vitro Cell. Dev. Biol. Plant. 54, 341 (2018). [OpenUrl][22] 9. [↵][23]1. C. Walter, 2. M. Fladung, 3. W. Boerjan , Nat. Biotechnol. 28, 656 (2010). [OpenUrl][24][CrossRef][25][PubMed][26] 10. [↵][27]1. V. Viswanath, 2. B. R. Albrectsen, 3. S. H. Strauss , Tree Genet. Genomes 8, 221 (2012). [OpenUrl][28] 11. [↵][29]PEFC, “Editorial updates to chain of custody standard (PEFC ST 2002:2013)” (2016); [www.pefc.co.uk/news_articles/editorial-updates-to-chain-of-custody-standard-pefc-st-2002-2013][30]. 12. [↵][31]National Academies of Sciences, Engineering, and Medicine, Forest Health and Biotechnology: Possibilities and Considerations (2019); [www.nap.edu/catalog/25221/forest-health-and-biotechnology-possibilities-and-considerations][32]. [1]: #ref-1 [2]: #ref-3 [3]: #ref-4 [4]: #ref-5 [5]: #ref-6 [6]: #ref-7 [7]: #ref-8 [8]: #ref-9 [9]: #ref-10 [10]: #ref-11 [11]: #ref-12 [12]: #xref-ref-1-1 "View reference 1 in text" [13]: http://www.fao.org/3/a-i4793e.pdf [14]: #xref-ref-3-1 "View reference 3 in text" [15]: #xref-ref-4-1 "View reference 4 in text" [16]: \openurl\?query=rft.jtitle%253DScience%26rft.volume%253D54%26rft.spage%253D341%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [17]: #xref-ref-5-1 "View reference 5 in text" [18]: #xref-ref-6-1 "View reference 6 in text" [19]: \openurl\?query=rft.jtitle%253DScience%26rft.volume%253D8%26rft.spage%253D221%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [20]: #xref-ref-7-1 "View reference 7 in text" [21]: #xref-ref-8-1 "View reference 8 in text" [22]: \openurl\?query=rft.jtitle%253DIn%2BVitro%2BCell.%2BDev.%2BBiol.%2BPlant.%26rft.volume%253D54%26rft.spage%253D341%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [23]: #xref-ref-9-1 "View reference 9 in text" [24]: \openurl\?query=rft.jtitle%253DNature%2Bbiotechnology%26rft.stitle%253DNat%2BBiotechnol%26rft.aulast%253DWalter%26rft.auinit1%253DC.%26rft.volume%253D28%26rft.issue%253D7%26rft.spage%253D656%26rft.epage%253D658%26rft.atitle%253DThe%2B20-year%2Benvironmental%2Bsafety%2Brecord%2Bof%2BGM%2Btrees.%26rft_id%253Dinfo%253Adoi%252F10.1038%252Fnbt0710-656%26rft_id%253Dinfo%253Apmid%252F20622831%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [25]: /lookup/external-ref?access_num=10.1038/nbt0710-656&link_type=DOI [26]: /lookup/external-ref?access_num=20622831&link_type=MED&atom=%2Fsci%2F365%2F6455%2F767.2.atom [27]: #xref-ref-10-1 "View reference 10 in text" [28]: \openurl\?query=rft.jtitle%253DTree%2BGenet.%2BGenomes%26rft.volume%253D8%26rft.spage%253D221%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [29]: #xref-ref-11-1 "View reference 11 in text" [30]: http://www.pefc.co.uk/news_articles/editorial-updates-to-chain-of-custody-standard-pefc-st-2002-2013 [31]: #xref-ref-12-1 "View reference 12 in text" [32]: http://www.nap.edu/catalog/25221/forest-health-and-biotechnology-possibilities-and-considerations

@article{wang_major_2018,
	title = {A major locus controls local adaptation and adaptive life history variation in a perennial plant},
	volume = {19},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1444-y},
	doi = {10.1186/s13059-018-1444-y},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Genome Biology},
	author = {Wang, Jing and Ding, Jihua and Tan, Biyue and Robinson, Kathryn M. and Michelson, Ingrid H. and Johansson, Anna and Nystedt, Björn and Scofield, Douglas G. and Nilsson, Ove and Jansson, Stefan and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = dec,
	year = {2018},
	pages = {72},
}

@article{michelson_autumn_2018,
	title = {Autumn senescence in aspen is not triggered by day length},
	volume = {162},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12593},
	doi = {10.1111/ppl.12593},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Michelson, Ingrid H. and Ingvarsson, Pär K. and Robinson, Kathryn M. and Edlund, Erik and Eriksson, Maria E. and Nilsson, Ove and Jansson, Stefan},
	month = jan,
	year = {2018},
	pages = {123--134},
}

@article{ding_gigantea-like_2018,
	title = {{GIGANTEA}-like genes control seasonal growth cessation in {Populus}},
	volume = {218},
	copyright = {© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15087},
	doi = {10/gdt24k},
	abstract = {Survival of trees growing in temperate zones requires cycling between active growth and dormancy. This involves growth cessation in the autumn triggered by a photoperiod shorter than the critical day length. Variations in GIGANTEA (GI)-like genes have been associated with phenology in a range of different tree species, but characterization of the functions of these genes in the process is still lacking. We describe the identification of the Populus orthologs of GI and their critical role in short-day-induced growth cessation. Using ectopic expression and silencing, gene expression analysis, protein interaction and chromatin immunoprecipitation experiments, we show that PttGIs are likely to act in a complex with PttFKF1s (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) and PttCDFs (CYCLING DOF FACTOR) to control the expression of PttFT2, the key gene regulating short-day-induced growth cessation in Populus. In contrast to Arabidopsis, in which the GI-CONSTANS (CO)-FLOWERING LOCUS T (FT) regulon is a crucial day-length sensor for flowering time, our study suggests that, in Populus, PttCO-independent regulation of PttFT2 by PttGI is more important in the photoperiodic control of growth cessation and bud set.},
	language = {en},
	number = {4},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Ding, Jihua and Böhlenius, Henrik and Rühl, Mark Georg and Chen, Peng and Sane, Shashank and Zambrano, Jose A. and Zheng, Bo and Eriksson, Maria E. and Nilsson, Ove},
	year = {2018},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15087},
	keywords = {FLOWERING LOCUS (FT), GIGANTEA (GI), Populus, growth cessation, photoperiod},
	pages = {1491--1503},
}

Survival of trees growing in temperate zones requires cycling between active growth and dormancy. This involves growth cessation in the autumn triggered by a photoperiod shorter than the critical day length. Variations in GIGANTEA (GI)-like genes have been associated with phenology in a range of different tree species, but characterization of the functions of these genes in the process is still lacking. We describe the identification of the Populus orthologs of GI and their critical role in short-day-induced growth cessation. Using ectopic expression and silencing, gene expression analysis, protein interaction and chromatin immunoprecipitation experiments, we show that PttGIs are likely to act in a complex with PttFKF1s (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) and PttCDFs (CYCLING DOF FACTOR) to control the expression of PttFT2, the key gene regulating short-day-induced growth cessation in Populus. In contrast to Arabidopsis, in which the GI-CONSTANS (CO)-FLOWERING LOCUS T (FT) regulon is a crucial day-length sensor for flowering time, our study suggests that, in Populus, PttCO-independent regulation of PttFT2 by PttGI is more important in the photoperiodic control of growth cessation and bud set.

@article{akhter_integrative_2018,
	title = {Integrative {Analysis} of {Three} {RNA} {Sequencing} {Methods} {Identifies} {Mutually} {Exclusive} {Exons} of {MADS}-{Box} {Isoforms} {During} {Early} {Bud} {Development} in {Picea} abies},
	volume = {9},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.01625/full},
	doi = {10/gh967n},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Akhter, Shirin and Kretzschmar, Warren W. and Nordal, Veronika and Delhomme, Nicolas and Street, Nathaniel R. and Nilsson, Ove and Emanuelsson, Olof and Sundström, Jens F.},
	month = nov,
	year = {2018},
	pages = {1625},
}

@article{chahtane_leafy_2018,
	title = {{LEAFY} activity is post-transcriptionally regulated by {BLADE} {ON} {PETIOLE2} and {CULLIN3} in {Arabidopsis}},
	volume = {220},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15329},
	doi = {10/gfcdwc},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Chahtane, Hicham and Zhang, Bo and Norberg, Mikael and LeMasson, Marie and Thévenon, Emmanuel and Bakó, László and Benlloch, Reyes and Holmlund, Mattias and Parcy, François and Nilsson, Ove and Vachon, Gilles},
	month = oct,
	year = {2018},
	pages = {579--592},
}

@article{jokipii-lukkari_transcriptional_2018,
	title = {Transcriptional {Roadmap} to {Seasonal} {Variation} in {Wood} {Formation} of {Norway} {Spruce}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/4/2851-2870/6117009},
	doi = {10.1104/pp.17.01590},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Jokipii-Lukkari, Soile and Delhomme, Nicolas and Schiffthaler, Bastian and Mannapperuma, Chanaka and Prestele, Jakob and Nilsson, Ove and Street, Nathaniel R. and Tuominen, Hannele},
	month = apr,
	year = {2018},
	pages = {2851--2870},
}

@article{reza_transcriptome_2018,
	title = {Transcriptome analysis of embryonic domains in {Norway} spruce reveals potential regulators of suspensor cell death},
	volume = {13},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0192945},
	doi = {10/gc8wb4},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Reza, Salim H. and Delhomme, Nicolas and Street, Nathaniel R. and Ramachandran, Prashanth and Dalman, Kerstin and Nilsson, Ove and Minina, Elena A. and Bozhkov, Peter V.},
	editor = {Sun, Meng-xiang},
	month = mar,
	year = {2018},
	pages = {e0192945},
}

@article{sundell_aspwood_2017,
	title = {{AspWood}: {High}-{Spatial}-{Resolution} {Transcriptome} {Profiles} {Reveal} {Uncharacterized} {Modularity} of {Wood} {Formation} in {Populus} tremula},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	shorttitle = {{AspWood}},
	url = {https://academic.oup.com/plcell/article/29/7/1585-1604/6099151},
	doi = {10/gbshnb},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Sundell, David and Street, Nathaniel R. and Kumar, Manoj and Mellerowicz, Ewa J. and Kucukoglu, Melis and Johnsson, Christoffer and Kumar, Vikash and Mannapperuma, Chanaka and Delhomme, Nicolas and Nilsson, Ove and Tuominen, Hannele and Pesquet, Edouard and Fischer, Urs and Niittylä, Totte and Sundberg, Björn and Hvidsten, Torgeir R.},
	month = jul,
	year = {2017},
	pages = {1585--1604},
}

@article{zhang_blade--petiole_2017,
	title = {{BLADE}-{ON}-{PETIOLE} proteins act in an {E3} ubiquitin ligase complex to regulate {PHYTOCHROME} {INTERACTING} {FACTOR} 4 abundance},
	volume = {6},
	issn = {2050-084X},
	url = {https://elifesciences.org/articles/26759},
	doi = {10/gb2fm5},
	abstract = {Both light and temperature have dramatic effects on plant development. Phytochrome photoreceptors regulate plant responses to the environment in large part by controlling the abundance of PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. However, the molecular determinants of this essential signaling mechanism still remain largely unknown. Here, we present evidence that the BLADE-ON-PETIOLE (BOP) genes, which have previously been shown to control leaf and flower development in Arabidopsis, are involved in controlling the abundance of PIF4. Genetic analysis shows that BOP2 promotes photo-morphogenesis and modulates thermomorphogenesis by suppressing PIF4 activity, through a reduction in PIF4 protein level. In red-light-grown seedlings PIF4 ubiquitination was reduced in the bop2 mutant. Moreover, we found that BOP proteins physically interact with both PIF4 and CULLIN3A and that a CULLIN3-BOP2 complex ubiquitinates PIF4 in vitro. This shows that BOP proteins act as substrate adaptors in a CUL3BOP1/BOP2 E3 ubiquitin ligase complex, targeting PIF4 proteins for ubiquitination and subsequent degradation.},
	language = {en},
	urldate = {2021-06-07},
	journal = {eLife},
	author = {Zhang, Bo and Holmlund, Mattias and Lorrain, Severine and Norberg, Mikael and Bakó, László and Fankhauser, Christian and Nilsson, Ove},
	month = aug,
	year = {2017},
	pages = {e26759},
}

Both light and temperature have dramatic effects on plant development. Phytochrome photoreceptors regulate plant responses to the environment in large part by controlling the abundance of PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. However, the molecular determinants of this essential signaling mechanism still remain largely unknown. Here, we present evidence that the BLADE-ON-PETIOLE (BOP) genes, which have previously been shown to control leaf and flower development in Arabidopsis, are involved in controlling the abundance of PIF4. Genetic analysis shows that BOP2 promotes photo-morphogenesis and modulates thermomorphogenesis by suppressing PIF4 activity, through a reduction in PIF4 protein level. In red-light-grown seedlings PIF4 ubiquitination was reduced in the bop2 mutant. Moreover, we found that BOP proteins physically interact with both PIF4 and CULLIN3A and that a CULLIN3-BOP2 complex ubiquitinates PIF4 in vitro. This shows that BOP proteins act as substrate adaptors in a CUL3BOP1/BOP2 E3 ubiquitin ligase complex, targeting PIF4 proteins for ubiquitination and subsequent degradation.

@article{davoine_functional_2017,
	title = {Functional metabolomics as a tool to analyze {Mediator} function and structure in plants},
	volume = {12},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0179640},
	doi = {10/gcjk93},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Davoine, Celine and Abreu, Ilka N. and Khajeh, Khalil and Blomberg, Jeanette and Kidd, Brendan N. and Kazan, Kemal and Schenk, Peer M. and Gerber, Lorenz and Nilsson, Ove and Moritz, Thomas and Björklund, Stefan},
	editor = {Mantovani, Roberto},
	month = jun,
	year = {2017},
	pages = {e0179640},
}

@article{jokipiilukkari_norwood_2017,
	title = {{NorWood}: a gene expression resource for evo‐devo studies of conifer wood development},
	volume = {216},
	issn = {0028-646X, 1469-8137},
	shorttitle = {{NorWood}},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14458},
	doi = {10.1111/nph.14458},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Jokipii‐Lukkari, Soile and Sundell, David and Nilsson, Ove and Hvidsten, Torgeir R. and Street, Nathaniel R. and Tuominen, Hannele},
	month = oct,
	year = {2017},
	pages = {482--494},
}

@article{kucukoglu_wuschel-related_2017,
	title = {{WUSCHEL}-{RELATED} {HOMEOBOX4} ({WOX4})-like genes regulate cambial cell division activity and secondary growth in {Populus} trees},
	volume = {215},
	copyright = {© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.14631},
	doi = {10/gbjxjh},
	abstract = {Plant secondary growth derives from the meristematic activity of the vascular cambium. In Arabidopsis thaliana, cell divisions in the cambium are regulated by the transcription factor WOX4, a key target of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED 41 (CLE41) signaling pathway. However, function of the WOX4-like genes in plants that are dependent on a much more prolific secondary growth, such as trees, remains unclear. Here, we investigate the role of WOX4 and CLE41 homologs for stem secondary growth in Populus trees. In Populus, PttWOX4 genes are specifically expressed in the cambial region during vegetative growth, but not after growth cessation and during dormancy, possibly involving a regulation by auxin. In PttWOX4a/b RNAi trees, primary growth was not affected whereas the width of the vascular cambium was severely reduced and secondary growth was greatly diminished. Our data show that in Populus trees, PttWOX4 genes control cell division activity in the vascular cambium, and hence growth in stem girth. This activity involves the positive regulation of PttWOX4a/b through PttCLE41-related genes. Finally, expression profiling suggests that the CLE41 signaling pathway is an evolutionarily conserved program for the regulation of vascular cambium activity between angiosperm and gymnosperm tree species.},
	language = {en},
	number = {2},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Kucukoglu, Melis and Nilsson, Jeanette and Zheng, Bo and Chaabouni, Salma and Nilsson, Ove},
	year = {2017},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14631},
	keywords = {Populus, PttCLE41, PttWOX4, hybrid aspen, secondary development, vascular cambium},
	pages = {642--657},
}

Plant secondary growth derives from the meristematic activity of the vascular cambium. In Arabidopsis thaliana, cell divisions in the cambium are regulated by the transcription factor WOX4, a key target of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED 41 (CLE41) signaling pathway. However, function of the WOX4-like genes in plants that are dependent on a much more prolific secondary growth, such as trees, remains unclear. Here, we investigate the role of WOX4 and CLE41 homologs for stem secondary growth in Populus trees. In Populus, PttWOX4 genes are specifically expressed in the cambial region during vegetative growth, but not after growth cessation and during dormancy, possibly involving a regulation by auxin. In PttWOX4a/b RNAi trees, primary growth was not affected whereas the width of the vascular cambium was severely reduced and secondary growth was greatly diminished. Our data show that in Populus trees, PttWOX4 genes control cell division activity in the vascular cambium, and hence growth in stem girth. This activity involves the positive regulation of PttWOX4a/b through PttCLE41-related genes. Finally, expression profiling suggests that the CLE41 signaling pathway is an evolutionarily conserved program for the regulation of vascular cambium activity between angiosperm and gymnosperm tree species.

@article{custers_eu_2016,
	title = {{EU} {Regulations} {Impede} {Market} {Introduction} of {GM} {Forest} {Trees}},
	volume = {21},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138516000315},
	doi = {10.1016/j.tplants.2016.01.015},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Trends in Plant Science},
	author = {Custers, René and Bartsch, Detlef and Fladung, Matthias and Nilsson, Ove and Pilate, Gilles and Sweet, Jeremy and Boerjan, Wout},
	month = apr,
	year = {2016},
	pages = {283--285},
}

@article{klocko_ft_2016,
	title = {{FT} overexpression induces precocious flowering and normal reproductive development in {Eucalyptus}},
	volume = {14},
	copyright = {© 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley \& Sons Ltd},
	issn = {1467-7652},
	url = {https://www.onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12431},
	doi = {10/f78rxh},
	abstract = {Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1–5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.},
	language = {en},
	number = {2},
	urldate = {2021-06-21},
	journal = {Plant Biotechnology Journal},
	author = {Klocko, Amy L. and Ma, Cathleen and Robertson, Sarah and Esfandiari, Elahe and Nilsson, Ove and Strauss, Steven H.},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.12431},
	keywords = {Eucalypts, Flowering Locus T, breeding, forest biotechnology, genetic engineering, transgenic},
	pages = {808--819},
}

Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1–5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.

@article{hoenicka_low_2016,
	title = {Low temperatures are required to induce the development of fertile flowers in transgenic male and female early flowering poplar ( \textit{{Populus} tremula} {L}.)},
	volume = {36},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpw015},
	doi = {10.1093/treephys/tpw015},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Hoenicka, Hans and Lehnhardt, Denise and Briones, Valentina and Nilsson, Ove and Fladung, Matthias},
	editor = {Schnitzler, Jörg-Peter},
	month = may,
	year = {2016},
	pages = {667--677},
}

@article{ding_molecular_2016,
	title = {Molecular regulation of phenology in trees — because the seasons they are a-changin’},
	volume = {29},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526615001831},
	doi = {10.1016/j.pbi.2015.11.007},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Ding, Jihua and Nilsson, Ove},
	month = feb,
	year = {2016},
	pages = {73--79},
}

@article{kucukoglu_cle_2015,
	title = {{CLE} peptide signaling in plants - the power of moving around},
	volume = {155},
	issn = {1399-3054 (Electronic) 0031-9317 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26096704},
	doi = {10.1111/ppl.12358},
	abstract = {The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED (CLE) gene family encodes small secreted peptide ligands in plants. These peptides function non-cell autonomously through interactions with plasma membrane-associated LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASEs (LRR-RLKs). These interactions are critical for cell-to-cell communications and control a variety of developmental and physiological processes in plants, such as regulation of stem cell proliferation and differentiation in the meristems, embryo and endosperm development, vascular development and autoregulation of nodulation. Here, we review the current knowledge in the field of CLE polypeptide signaling.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiol Plant},
	author = {Kucukoglu, M. and Nilsson, O.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/06/23},
	keywords = {*Gene Expression Profiling, Arabidopsis Proteins/classification/*genetics, Arabidopsis/cytology/*genetics/growth \& development, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Meristem/cytology/genetics/growth \& development, Phylogeny, Protein Sorting Signals/*genetics, Signal Transduction/*genetics, Stem Cells/cytology/metabolism},
	pages = {74--87},
}

The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED (CLE) gene family encodes small secreted peptide ligands in plants. These peptides function non-cell autonomously through interactions with plasma membrane-associated LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASEs (LRR-RLKs). These interactions are critical for cell-to-cell communications and control a variety of developmental and physiological processes in plants, such as regulation of stem cell proliferation and differentiation in the meristems, embryo and endosperm development, vascular development and autoregulation of nodulation. Here, we review the current knowledge in the field of CLE polypeptide signaling.

@article{stavrinidou_electronic_2015,
	title = {Electronic plants},
	volume = {1},
	issn = {2375-2548},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1501136},
	doi = {10.1126/sciadv.1501136},
	abstract = {The roots, stems, leaves, and vascular circuitry of higher plants are responsible for conveying the chemical signals that regulate growth and functions. From a certain perspective, these features are analogous to the contacts, interconnections, devices, and wires of discrete and integrated electronic circuits. Although many attempts have been made to augment plant function with electroactive materials, plants’ “circuitry” has never been directly merged with electronics. We report analog and digital organic electronic circuits and devices manufactured in living plants. The four key components of a circuit have been achieved using the xylem, leaves, veins, and signals of the plant as the template and integral part of the circuit elements and functions. With integrated and distributed electronics in plants, one can envisage a range of applications including precision recording and regulation of physiology, energy harvesting from photosynthesis, and alternatives to genetic modification for plant optimization.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Science Advances},
	author = {Stavrinidou, Eleni and Gabrielsson, Roger and Gomez, Eliot and Crispin, Xavier and Nilsson, Ove and Simon, Daniel T. and Berggren, Magnus},
	month = nov,
	year = {2015},
	keywords = {conducting polymers, organic bioelectronics, plants},
	pages = {e1501136},
}

The roots, stems, leaves, and vascular circuitry of higher plants are responsible for conveying the chemical signals that regulate growth and functions. From a certain perspective, these features are analogous to the contacts, interconnections, devices, and wires of discrete and integrated electronic circuits. Although many attempts have been made to augment plant function with electroactive materials, plants’ “circuitry” has never been directly merged with electronics. We report analog and digital organic electronic circuits and devices manufactured in living plants. The four key components of a circuit have been achieved using the xylem, leaves, veins, and signals of the plant as the template and integral part of the circuit elements and functions. With integrated and distributed electronics in plants, one can envisage a range of applications including precision recording and regulation of physiology, energy harvesting from photosynthesis, and alternatives to genetic modification for plant optimization.

@article{liebsch_class_2014,
	title = {Class {I} {KNOX} transcription factors promote differentiation of cambial derivatives into xylem fibers in the \textit{{Arabidopsis}} hypocotyl},
	volume = {141},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/141/22/4311/46487/Class-I-KNOX-transcription-factors-promote},
	doi = {10/f3p5d6},
	abstract = {The class I KNOX transcription factors SHOOT MERISTEMLESS (STM) and KNAT1 are important regulators of meristem maintenance in shoot apices, with a dual role of promoting cell proliferation and inhibiting differentiation. We examined whether they control stem cell maintenance in the cambium of Arabidopsis hypocotyls, a wood-forming lateral meristem, in a similar fashion as in the shoot apical meristem. Weak loss-of-function alleles of KNAT1 and STM led to reduced formation of xylem fibers – highly differentiated cambial derivatives – whereas cell proliferation in the cambium was only mildly affected. In a knat1;stm double mutant, xylem fiber differentiation was completely abolished, but residual cambial activity was maintained. Expression of early and late markers of xylary cell differentiation was globally reduced in the knat1;stm double mutant. KNAT1 and STM were found to act through transcriptional repression of the meristem boundary genes BLADE-ON-PETIOLE 1 (BOP1) and BOP2 on xylem fiber differentiation. Together, these data indicate that, in the cambium, KNAT1 and STM, contrary to their function in the shoot apical meristem, promote cell differentiation through repression of BOP genes.},
	language = {en},
	number = {22},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Liebsch, Daniela and Sunaryo, Widi and Holmlund, Mattias and Norberg, Mikael and Zhang, Jing and Hall, Hardy C. and Helizon, Hanna and Jin, Xu and Helariutta, Ykä and Nilsson, Ove and Polle, Andrea and Fischer, Urs},
	month = nov,
	year = {2014},
	pages = {4311--4319},
}

The class I KNOX transcription factors SHOOT MERISTEMLESS (STM) and KNAT1 are important regulators of meristem maintenance in shoot apices, with a dual role of promoting cell proliferation and inhibiting differentiation. We examined whether they control stem cell maintenance in the cambium of Arabidopsis hypocotyls, a wood-forming lateral meristem, in a similar fashion as in the shoot apical meristem. Weak loss-of-function alleles of KNAT1 and STM led to reduced formation of xylem fibers – highly differentiated cambial derivatives – whereas cell proliferation in the cambium was only mildly affected. In a knat1;stm double mutant, xylem fiber differentiation was completely abolished, but residual cambial activity was maintained. Expression of early and late markers of xylary cell differentiation was globally reduced in the knat1;stm double mutant. KNAT1 and STM were found to act through transcriptional repression of the meristem boundary genes BLADE-ON-PETIOLE 1 (BOP1) and BOP2 on xylem fiber differentiation. Together, these data indicate that, in the cambium, KNAT1 and STM, contrary to their function in the shoot apical meristem, promote cell differentiation through repression of BOP genes.

@article{de_la_torre_insights_2014,
	title = {Insights into {Conifer} {Giga}-{Genomes}},
	volume = {166},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/166/4/1724-1732/6113514},
	doi = {10/f25hfn},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {De La Torre, Amanda R. and Birol, Inanc and Bousquet, Jean and Ingvarsson, Pär K. and Jansson, Stefan and Jones, Steven J.M. and Keeling, Christopher I. and MacKay, John and Nilsson, Ove and Ritland, Kermit and Street, Nathaniel and Yanchuk, Alvin and Zerbe, Philipp and Bohlmann, Jörg},
	month = dec,
	year = {2014},
	pages = {1724--1732},
}

@article{hoenicka_successful_2014,
	title = {Successful crossings with early flowering transgenic poplar: interspecific crossings, but not transgenesis, promoted aberrant phenotypes in offspring},
	volume = {12},
	issn = {14677644},
	shorttitle = {Successful crossings with early flowering transgenic poplar},
	url = {http://doi.wiley.com/10.1111/pbi.12213},
	doi = {10/f3p652},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Plant Biotechnology Journal},
	author = {Hoenicka, Hans and Lehnhardt, Denise and Nilsson, Ove and Hanelt, Dieter and Fladung, Matthias},
	month = oct,
	year = {2014},
	pages = {1066--1074},
}

@article{wang_arabidopsis_2013,
	title = {The {Arabidopsis} {LRR}-{RLK}, {PXC1}, is a regulator of secondary wall formation correlated with the {TDIF}-{PXY}/{TDR}-{WOX4} signaling pathway},
	volume = {13},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-13-94},
	doi = {10/f225hg},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Wang, Jiehua and Kucukoglu, Melis and Zhang, Linbin and Chen, Peng and Decker, Daniel and Nilsson, Ove and Jones, Brian and Sandberg, Göran and Zheng, Bo},
	year = {2013},
	pages = {94},
}

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{klintenas_analysis_2012,
	title = {Analysis of conifer \textit{{FLOWERING} {LOCUS} {T}} / \textit{{TERMINAL} {FLOWER1}} ‐like genes provides evidence for dramatic biochemical evolution in the angiosperm {\textless}span style="font-variant:small-caps;"{\textgreater} \textit{{FT}} {\textless}/span{\textgreater} lineage},
	volume = {196},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Analysis of conifer \textit{{FLOWERING} {LOCUS} {T}} / \textit{{TERMINAL} {FLOWER1}} ‐like genes provides evidence for dramatic biochemical evolution in the angiosperm {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04332.x},
	doi = {10/f23gx2},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Klintenäs, Maria and Pin, Pierre A. and Benlloch, Reyes and Ingvarsson, Pär K. and Nilsson, Ove},
	month = dec,
	year = {2012},
	pages = {1260--1273},
}

@article{plackett_analysis_2012,
	title = {Analysis of the {Developmental} {Roles} of the {Arabidopsis} {Gibberellin} 20-{Oxidases} {Demonstrates} {That} {GA20ox1} , -2 , and -3 {Are} the {Dominant} {Paralogs}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/3/941-960/6097253},
	doi = {10/f238b4},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Plackett, Andrew R.G. and Powers, Stephen J. and Fernandez-Garcia, Nieves and Urbanova, Terezie and Takebayashi, Yumiko and Seo, Mitsunori and Jikumaru, Yusuke and Benlloch, Reyes and Nilsson, Ove and Ruiz-Rivero, Omar and Phillips, Andrew L. and Wilson, Zoe A. and Thomas, Stephen G. and Hedden, Peter},
	month = mar,
	year = {2012},
	pages = {941--960},
}

@article{pin_role_2012,
	title = {The {Role} of a {Pseudo}-{Response} {Regulator} {Gene} in {Life} {Cycle} {Adaptation} and {Domestication} of {Beet}},
	volume = {22},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982212003946},
	doi = {10/f233wd},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Pin, Pierre A. and Zhang, Wenying and Vogt, Sebastian H. and Dally, Nadine and Büttner, Bianca and Schulze-Buxloh, Gretel and Jelly, Noémie S. and Chia, Tansy Y.P. and Mutasa-Göttgens, Effie S. and Dohm, Juliane C. and Himmelbauer, Heinz and Weisshaar, Bernd and Kraus, Josef and Gielen, Jan J.L. and Lommel, Murielle and Weyens, Guy and Wahl, Bettina and Schechert, Axel and Nilsson, Ove and Jung, Christian and Kraft, Thomas and Müller, Andreas E.},
	month = jun,
	year = {2012},
	pages = {1095--1101},
}

@article{pin_multifaceted_2012,
	title = {The multifaceted roles of {FLOWERING} {LOCUS} {T} in plant development: {FT}, a multifunctional protein},
	volume = {35},
	issn = {01407791},
	shorttitle = {The multifaceted roles of {FLOWERING} {LOCUS} {T} in plant development},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2012.02558.x},
	doi = {10/f23ndf},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Pin, P. A. and Nilsson, O.},
	month = oct,
	year = {2012},
	pages = {1742--1755},
}

@article{elfving_arabidopsis_2011,
	title = {The {Arabidopsis} thaliana {Med25} mediator subunit integrates environmental cues to control plant development},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/20/8245},
	doi = {10.1073/pnas.1002981108},
	abstract = {Development in plants is controlled by abiotic environmental cues such as day length, light quality, temperature, drought, and salinity. These signals are sensed by a variety of systems and transmitted by different signal transduction pathways. Ultimately, these pathways are integrated to control expression of specific target genes, which encode proteins that regulate development and differentiation. The molecular mechanisms for such integration have remained elusive. We here show that a linear 130-amino-acids-long sequence in the Med25 subunit of the Arabidopsis thaliana Mediator is a common target for the drought response element binding protein 2A, zinc finger homeodomain 1, and Myb-like transcription factors which are involved in different stress response pathways. In addition, our results show that Med25 together with drought response element binding protein 2A also function in repression of PhyB-mediated light signaling and thus integrate signals from different regulatory pathways.},
	language = {en},
	number = {20},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Elfving, Nils and Davoine, Céline and Benlloch, Reyes and Blomberg, Jeanette and Brännström, Kristoffer and Müller, Dörte and Nilsson, Anders and Ulfstedt, Mikael and Ronne, Hans and Wingsle, Gunnar and Nilsson, Ove and Björklund, Stefan},
	month = may,
	year = {2011},
	pmid = {21536906},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {RNA polymerase II, phytochrome flowering time 1, transcriptional regulation},
	pages = {8245--8250},
}

Development in plants is controlled by abiotic environmental cues such as day length, light quality, temperature, drought, and salinity. These signals are sensed by a variety of systems and transmitted by different signal transduction pathways. Ultimately, these pathways are integrated to control expression of specific target genes, which encode proteins that regulate development and differentiation. The molecular mechanisms for such integration have remained elusive. We here show that a linear 130-amino-acids-long sequence in the Med25 subunit of the Arabidopsis thaliana Mediator is a common target for the drought response element binding protein 2A, zinc finger homeodomain 1, and Myb-like transcription factors which are involved in different stress response pathways. In addition, our results show that Med25 together with drought response element binding protein 2A also function in repression of PhyB-mediated light signaling and thus integrate signals from different regulatory pathways.

@article{pin_antagonistic_2010,
	title = {An {Antagonistic} {Pair} of {FT} {Homologs} {Mediates} the {Control} of {Flowering} {Time} in {Sugar} {Beet}},
	volume = {330},
	copyright = {Copyright © 2010, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/330/6009/1397},
	doi = {10/brjf2w},
	abstract = {Just Beet It
Flowering time regulation is important for plants to maximize their reproductive output. By investigating copies of genes that are strong and central activators of flowering in many different species (homologs of the FT gene in Arabidopsis), Pin et al. (p. 1397) found that during evolution, the regulation of flowering time in sugar beet (Beta vulgaris) has come under the control of two FT-like genes. Functional differences in these genes owing to small mutations in a critical domain have caused a duplicated copy of the flowering promoter FT to turn into a flowering repressor in sugar beet. These changes may explain why cultivated beets are unable to flower until their second year after passing through the winter, a behavior important for increasing crop yield.
Cultivated beets (Beta vulgaris ssp. vulgaris) are unable to form reproductive shoots during the first year of their life cycle. Flowering only occurs if plants get vernalized, that is, pass through the winter, and are subsequently exposed to an increasing day length (photoperiod) in spring. Here, we show that the regulation of flowering time in beets is controlled by the interplay of two paralogs of the FLOWERING LOCUS T (FT) gene in Arabidopsis that have evolved antagonistic functions. BvFT2 is functionally conserved with FT and essential for flowering. In contrast, BvFT1 represses flowering and its down-regulation is crucial for the vernalization response in beets. These data suggest that the beet has evolved a different strategy relative to Arabidopsis and cereals to regulate vernalization.
A homolog of a flowering time gene has evolved a flowering repression function, affecting the seasonal cold response in beet.
A homolog of a flowering time gene has evolved a flowering repression function, affecting the seasonal cold response in beet.},
	language = {en},
	number = {6009},
	urldate = {2021-06-08},
	journal = {Science},
	author = {Pin, Pierre A. and Benlloch, Reyes and Bonnet, Dominique and Wremerth-Weich, Elisabeth and Kraft, Thomas and Gielen, Jan J. L. and Nilsson, Ove},
	month = dec,
	year = {2010},
	pages = {1397--1400},
}

Just Beet It Flowering time regulation is important for plants to maximize their reproductive output. By investigating copies of genes that are strong and central activators of flowering in many different species (homologs of the FT gene in Arabidopsis), Pin et al. (p. 1397) found that during evolution, the regulation of flowering time in sugar beet (Beta vulgaris) has come under the control of two FT-like genes. Functional differences in these genes owing to small mutations in a critical domain have caused a duplicated copy of the flowering promoter FT to turn into a flowering repressor in sugar beet. These changes may explain why cultivated beets are unable to flower until their second year after passing through the winter, a behavior important for increasing crop yield. Cultivated beets (Beta vulgaris ssp. vulgaris) are unable to form reproductive shoots during the first year of their life cycle. Flowering only occurs if plants get vernalized, that is, pass through the winter, and are subsequently exposed to an increasing day length (photoperiod) in spring. Here, we show that the regulation of flowering time in beets is controlled by the interplay of two paralogs of the FLOWERING LOCUS T (FT) gene in Arabidopsis that have evolved antagonistic functions. BvFT2 is functionally conserved with FT and essential for flowering. In contrast, BvFT1 represses flowering and its down-regulation is crucial for the vernalization response in beets. These data suggest that the beet has evolved a different strategy relative to Arabidopsis and cereals to regulate vernalization. A homolog of a flowering time gene has evolved a flowering repression function, affecting the seasonal cold response in beet. A homolog of a flowering time gene has evolved a flowering repression function, affecting the seasonal cold response in beet.

@article{nilsson_plant_2009,
	title = {Plant {Evolution}: {Measuring} the {Length} of the {Day}},
	volume = {19},
	issn = {09609822},
	shorttitle = {Plant {Evolution}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982209006782},
	doi = {10/bd48qv},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Nilsson, Ove},
	month = apr,
	year = {2009},
	pages = {R302--R303},
}

@article{rieu_genetic_2008,
	title = {Genetic {Analysis} {Reveals} {That} {C19}-{GA} 2-{Oxidation} {Is} a {Major} {Gibberellin} {Inactivation} {Pathway} in \textit{{Arabidopsis}}},
	volume = {20},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/20/9/2420/6092501},
	doi = {10/bb7kzv},
	abstract = {Abstract
            Bioactive hormone concentrations are regulated both at the level of hormone synthesis and through controlled inactivation. Based on the ubiquitous presence of 2β-hydroxylated gibberellins (GAs), a major inactivating pathway for the plant hormone GA seems to be via GA 2-oxidation. In this study, we used various approaches to determine the role of C19-GA 2-oxidation in regulating GA concentration and GA-responsive plant growth and development. We show that Arabidopsis thaliana has five C19-GA 2-oxidases, transcripts for one or more of which are present in all organs and at all stages of development examined. Expression of four of the five genes is subject to feed-forward regulation. By knocking out all five Arabidopsis C19-GA 2-oxidases, we show that C19-GA 2-oxidation limits bioactive GA content and regulates plant development at various stages during the plant life cycle: C19-GA 2-oxidases prevent seed germination in the absence of light and cold stimuli, delay the vegetative and floral phase transitions, limit the number of flowers produced per inflorescence, and suppress elongation of the pistil prior to fertilization. Under GA-limited conditions, further roles are revealed, such as limiting elongation of the main stem and side shoots. We conclude that C19-GA 2-oxidation is a major GA inactivation pathway regulating development in Arabidopsis.},
	language = {en},
	number = {9},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Rieu, Ivo and Eriksson, Sven and Powers, Stephen J. and Gong, Fan and Griffiths, Jayne and Woolley, Lindsey and Benlloch, Reyes and Nilsson, Ove and Thomas, Stephen G. and Hedden, Peter and Phillips, Andrew L.},
	month = oct,
	year = {2008},
	pages = {2420--2436},
}

Abstract Bioactive hormone concentrations are regulated both at the level of hormone synthesis and through controlled inactivation. Based on the ubiquitous presence of 2β-hydroxylated gibberellins (GAs), a major inactivating pathway for the plant hormone GA seems to be via GA 2-oxidation. In this study, we used various approaches to determine the role of C19-GA 2-oxidation in regulating GA concentration and GA-responsive plant growth and development. We show that Arabidopsis thaliana has five C19-GA 2-oxidases, transcripts for one or more of which are present in all organs and at all stages of development examined. Expression of four of the five genes is subject to feed-forward regulation. By knocking out all five Arabidopsis C19-GA 2-oxidases, we show that C19-GA 2-oxidation limits bioactive GA content and regulates plant development at various stages during the plant life cycle: C19-GA 2-oxidases prevent seed germination in the absence of light and cold stimuli, delay the vegetative and floral phase transitions, limit the number of flowers produced per inflorescence, and suppress elongation of the pistil prior to fertilization. Under GA-limited conditions, further roles are revealed, such as limiting elongation of the main stem and side shoots. We conclude that C19-GA 2-oxidation is a major GA inactivation pathway regulating development in Arabidopsis.

@article{rieu_gibberellin_2007,
	title = {The gibberellin biosynthetic genes {AtGA20ox1} and {AtGA20ox2} act, partially redundantly, to promote growth and development throughout the {Arabidopsis} life cycle: {GA20ox} function in {Arabidopsis}},
	volume = {53},
	issn = {09607412},
	shorttitle = {The gibberellin biosynthetic genes {AtGA20ox1} and {AtGA20ox2} act, partially redundantly, to promote growth and development throughout the {Arabidopsis} life cycle},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03356.x},
	doi = {10/cqvbmx},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Rieu, Ivo and Ruiz-Rivero, Omar and Fernandez-Garcia, Nieves and Griffiths, Jayne and Powers, Stephen J. and Gong, Fan and Linhartova, Terezie and Eriksson, Sven and Nilsson, Ove and Thomas, Stephen G. and Phillips, Andrew L. and Hedden, Peter},
	month = oct,
	year = {2007},
	pages = {488--504},
}

@article{bohlenius_coft_2006,
	title = {{CO}/{FT} regulatory module controls timing of flowering and seasonal growth cessation in trees},
	volume = {312},
	issn = {0036-8075},
	doi = {10/csznqf},
	abstract = {Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.},
	language = {English},
	number = {5776},
	journal = {Science},
	author = {Bohlenius, H. and Huang, T. and Charbonnel-Campaa, L. and Brunner, A. M. and Jansson, S. and Strauss, S. H. and Nilsson, O.},
	month = may,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000237628800042},
	keywords = {arabidopsis, aspen populus-tremula, black cottonwood, bud set, candidate gene, ft, induction, phytochrome, protein, shoot   apex},
	pages = {1040--1043},
}

Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

@article{tuskan_genome_2006,
	title = {The genome of black cottonwood, {Populus} trichocarpa ({Torr}. \& {Gray})},
	volume = {313},
	issn = {0036-8075},
	doi = {10/c7hs34},
	abstract = {We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.},
	language = {English},
	number = {5793},
	journal = {Science},
	author = {Tuskan, G. A. and DiFazio, S. and Jansson, S. and Bohlmann, J. and Grigoriev, I. and Hellsten, U. and Putnam, N. and Ralph, S. and Rombauts, S. and Salamov, A. and Schein, J. and Sterck, L. and Aerts, A. and Bhalerao, Rishikesh P. and Bhalerao, R. P. and Blaudez, D. and Boerjan, W. and Brun, A. and Brunner, A. and Busov, V. and Campbell, M. and Carlson, J. and Chalot, M. and Chapman, J. and Chen, G.-L. and Cooper, D. and Coutinho, P. M. and Couturier, J. and Covert, S. and Cronk, Q. and Cunningham, R. and Davis, J. and Degroeve, S. and Dejardin, A. and dePamphilis, C. and Detter, J. and Dirks, B. and Dubchak, I. and Duplessis, S. and Ehlting, J. and Ellis, B. and Gendler, K. and Goodstein, D. and Gribskov, M. and Grimwood, J. and Groover, A. and Gunter, L. and Hamberger, B. and Heinze, B. and Helariutta, Y. and Henrissat, B. and Holligan, D. and Holt, R. and Huang, W. and Islam-Faridi, N. and Jones, S. and Jones-Rhoades, M. and Jorgensen, R. and Joshi, C. and Kangasjarvi, J. and Karlsson, J. and Kelleher, C. and Kirkpatrick, R. and Kirst, M. and Kohler, A. and Kalluri, U. and Larimer, F. and Leebens-Mack, J. and Leple, J.-C. and Locascio, P. and Lou, Y. and Lucas, S. and Martin, F. and Montanini, B. and Napoli, C. and Nelson, D. R. and Nelson, C. and Nieminen, K. and Nilsson, O. and Pereda, V. and Peter, G. and Philippe, R. and Pilate, G. and Poliakov, A. and Razumovskaya, J. and Richardson, P. and Rinaldi, C. and Ritland, K. and Rouze, P. and Ryaboy, D. and Schmutz, J. and Schrader, J. and Segerman, B. and Shin, H. and Siddiqui, A. and Sterky, F. and Terry, A. and Tsai, C.-J. and Uberbacher, E. and Unneberg, P. and Vahala, J. and Wall, K. and Wessler, S. and Yang, G. and Yin, T. and Douglas, C. and Marra, M. and Sandberg, G. and Van de Peer, Y. and Rokhsar, D.},
	month = sep,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000240498900035},
	keywords = {arabidopsis-thaliana, cinnamyl alcohol-dehydrogenase, gene-expression, gravitational induction, hybrid poplar, lignin biosynthesis, phenylpropanoid metabolism, quaking   aspen, resistance genes, transcriptional regulators},
	pages = {1596--1604},
}

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

@article{norberg_blade_2005,
	title = {The {BLADE} {ON} {PETIOLE} genes act redundantly to control the growth and development of lateral organs},
	volume = {132},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.01815},
	doi = {10.1242/dev.01815},
	abstract = {Developmental processes in multicellular organisms involve an intricate balance between mechanisms that promote cell division activity and growth, and others that promote cell differentiation. Leaf development in Arabidopsis thaliana is controlled by genes like BLADE ON PETIOLE1(BOP1), which prevent the development of ectopic meristematic activity that leads to the formation of new organs, and JAGGED(JAG), which control the proximodistal development of the leaf by regulating cell-division activity. We have isolated and characterized the BOP1 gene together with a functionally redundant close homolog that we name BOP2. The BOP genes are members of a gene family containing ankyrin repeats and a BTB/POZ domain, suggesting a role in protein-protein interaction. We show that the BOP genes are expressed in the proximal parts of plant lateral organs where they repress the transcription not only of class 1 knox genes but also of JAG. We also show that the BOP genes are acting together with the flower meristem identity gene LEAFY in the suppression of bract formation. These findings show that the BOP genes are important regulators of the growth and development of lateral organs.},
	number = {9},
	urldate = {2021-06-11},
	journal = {Development},
	author = {Norberg, Mikael and Holmlund, Mattias and Nilsson, Ove},
	month = may,
	year = {2005},
	pages = {2203--2213},
}

Developmental processes in multicellular organisms involve an intricate balance between mechanisms that promote cell division activity and growth, and others that promote cell differentiation. Leaf development in Arabidopsis thaliana is controlled by genes like BLADE ON PETIOLE1(BOP1), which prevent the development of ectopic meristematic activity that leads to the formation of new organs, and JAGGED(JAG), which control the proximodistal development of the leaf by regulating cell-division activity. We have isolated and characterized the BOP1 gene together with a functionally redundant close homolog that we name BOP2. The BOP genes are members of a gene family containing ankyrin repeats and a BTB/POZ domain, suggesting a role in protein-protein interaction. We show that the BOP genes are expressed in the proximal parts of plant lateral organs where they repress the transcription not only of class 1 knox genes but also of JAG. We also show that the BOP genes are acting together with the flower meristem identity gene LEAFY in the suppression of bract formation. These findings show that the BOP genes are important regulators of the growth and development of lateral organs.

@article{huang_mrna_2005,
	title = {The {mRNA} of the {Arabidopsis} {Gene} {FT} {Moves} from {Leaf} to {Shoot} {Apex} and {Induces} {Flowering}},
	volume = {309},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/309/5741/1694},
	doi = {10.1126/science.1117768},
	abstract = {Day length controls flowering time in many plants. The day-length signal is perceived in the leaf, but how this signal is transduced to the shoot apex, where floral initiation occurs, is not known. In Arabidopsis, the day-length response depends on the induction of the FLOWERING LOCUS T (FT) gene. We show here that local induction of FT in a single Arabidopsis leaf is sufficient to trigger flowering. The FT messenger RNA is transported to the shoot apex, where downstream genes are activated. These data suggest that the FT mRNA is an important component of the elusive “florigen” signal that moves from leaf to shoot apex.
The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT.
The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT.},
	language = {en},
	number = {5741},
	urldate = {2021-06-11},
	journal = {Science},
	author = {Huang, Tao and Böhlenius, Henrik and Eriksson, Sven and Parcy, François and Nilsson, Ove},
	month = sep,
	year = {2005},
	pmid = {16099949},
	note = {Publisher: American Association for the Advancement of Science
Section: Research Article},
	pages = {1694--1696},
}

Day length controls flowering time in many plants. The day-length signal is perceived in the leaf, but how this signal is transduced to the shoot apex, where floral initiation occurs, is not known. In Arabidopsis, the day-length response depends on the induction of the FLOWERING LOCUS T (FT) gene. We show here that local induction of FT in a single Arabidopsis leaf is sufficient to trigger flowering. The FT messenger RNA is transported to the shoot apex, where downstream genes are activated. These data suggest that the FT mRNA is an important component of the elusive “florigen” signal that moves from leaf to shoot apex. The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT. The long-sought "florigen" that moves from leaf to shoot and induces flowering as days lengthen is the messenger RNA for the Flowering Locus T gene FT.

@article{sterky_populus_2004,
	title = {A {Populus} {EST} resource for plant functional genomics},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/101/38/13951},
	doi = {10/brt6bx},
	abstract = {Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide {\textgreater}4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.},
	language = {en},
	number = {38},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Sterky, Fredrik and Bhalerao, Rupali R. and Unneberg, Per and Segerman, Bo and Nilsson, Peter and Brunner, Amy M. and Charbonnel-Campaa, Laurence and Lindvall, Jenny Jonsson and Tandre, Karolina and Strauss, Steven H. and Sundberg, Björn and Gustafsson, Petter and Uhlén, Mathias and Bhalerao, Rishikesh P. and Nilsson, Ove and Sandberg, Göran and Karlsson, Jan and Lundeberg, Joakim and Jansson, Stefan},
	month = sep,
	year = {2004},
	pmid = {15353603},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {13951--13956},
}

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide \textgreater4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

@article{andersson_transcriptional_2004,
	title = {A transcriptional timetable of autumn senescence},
	volume = {5},
	issn = {1474-760X},
	doi = {10/dw5fcc},
	abstract = {Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92\%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.},
	language = {English},
	number = {4},
	journal = {Genome Biology},
	author = {Andersson, A. and Keskitalo, J. and Sjodin, A. and Bhalerao, Rishikesh P. and Sterky, F. and Wissel, K. and Tandre, K. and Aspeborg, H. and Moyle, R. and Ohmiya, Y. and Bhalerao, R. and Brunner, A. and Gustafsson, P. and Karlsson, J. and Lundeberg, J. and Nilsson, O. and Sandberg, G. and Strauss, S. and Sundberg, B. and Uhlen, M. and Jansson, S. and Nilsson, P.},
	year = {2004},
	note = {Place: London
Publisher: Bmc
WOS:000220584700010},
	keywords = {aspen, biology, cytosolic glutamine-synthetase, gene-expression, genomics, leaf senescence, leaves, plants, programmed cell-death, proteins},
	pages = {R24},
}

Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

@article{brunner_revisiting_2004,
	title = {Revisiting tree maturation and floral initiation in the poplar functional genomics era},
	volume = {164},
	issn = {0028-646X},
	doi = {10/bhcb7q},
	abstract = {The recent release of the Populus trichocarpa genome sequence will dramatically enhance the efficiency of functional and comparative genomics research in trees. This provides researchers studying various developmental processes related to the perennial and tree life strategies with a completely new set of tools. Intimately associated with the life strategy of trees are their abilities to maintain juvenile or nonflowering phases for years to decades, and once reproductively competent, to alternate between the production of vegetative and reproductive shoots. Most of what we know about the regulation of the floral transition comes from research on Arabidopsis thaliana, a small, herbaceous, rapid-cycling, annual plant. In this review, we discuss the similarities and differences between Arabidopsis and tree flowering, and how recent findings in Arabidopsis, coupled to comparative and functional genomics in poplars, will help answer the question of how tree maturation and floral initiation is regulated.},
	language = {English},
	number = {1},
	journal = {New Phytologist},
	author = {Brunner, A. M. and Nilsson, O.},
	month = oct,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000223662000006},
	keywords = {Populus, activation, arabidopsis, expression, floral initiation, flowering time, gene, genomics, gibberellin, induction, juvenile phase, pathways, phase-change, populus, tree maturation},
	pages = {43--51},
}

The recent release of the Populus trichocarpa genome sequence will dramatically enhance the efficiency of functional and comparative genomics research in trees. This provides researchers studying various developmental processes related to the perennial and tree life strategies with a completely new set of tools. Intimately associated with the life strategy of trees are their abilities to maintain juvenile or nonflowering phases for years to decades, and once reproductively competent, to alternate between the production of vegetative and reproductive shoots. Most of what we know about the regulation of the floral transition comes from research on Arabidopsis thaliana, a small, herbaceous, rapid-cycling, annual plant. In this review, we discuss the similarities and differences between Arabidopsis and tree flowering, and how recent findings in Arabidopsis, coupled to comparative and functional genomics in poplars, will help answer the question of how tree maturation and floral initiation is regulated.

@article{bhalerao_out_2003,
	title = {Out of the woods: forest biotechnology enters the genomic era},
	volume = {14},
	issn = {0958-1669},
	shorttitle = {Out of the woods},
	url = {https://www.sciencedirect.com/science/article/pii/S0958166903000296},
	doi = {10/fp8hj9},
	abstract = {Trees represent a unique life form of upmost importance for mankind, as these organisms have developed a perennial lifestyle that produces the majority of terrestrial biomass. The difference between trees and annual plants is one of the main arguments behind the effort to sequence the entire genome of the poplar tree. This initiative is being backed up with a full-scale functional genomics effort on trees that will set a completely new agenda for forest research.},
	language = {en},
	number = {2},
	urldate = {2021-07-05},
	journal = {Current Opinion in Biotechnology},
	author = {Bhalerao, Rishikesh and Nilsson, Ove and Sandberg, Goran},
	month = apr,
	year = {2003},
	pages = {206--213},
}

Trees represent a unique life form of upmost importance for mankind, as these organisms have developed a perennial lifestyle that produces the majority of terrestrial biomass. The difference between trees and annual plants is one of the main arguments behind the effort to sequence the entire genome of the poplar tree. This initiative is being backed up with a full-scale functional genomics effort on trees that will set a completely new agenda for forest research.

@article{estravis_barcala_whole-genome_nodate,
	title = {Whole-genome resequencing facilitates the development of a {50K} single nucleotide polymorphism genotyping array for {Scots} pine ({Pinus} sylvestris {L}.) and its transferability to other pine species},
	volume = {n/a},
	copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535},
	doi = {10.1111/tpj.16535},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84\%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.},
	language = {en},
	number = {n/a},
	urldate = {2023-11-24},
	journal = {The Plant Journal},
	author = {Estravis Barcala, Maximiliano and van der Valk, Tom and Chen, Zhiqiang and Funda, Tomas and Chaudhary, Rajiv and Klingberg, Adam and Fundova, Irena and Suontama, Mari and Hallingbäck, Henrik and Bernhardsson, Carolina and Nystedt, Björn and Ingvarsson, Pär K. and Sherwood, Ellen and Street, Nathaniel and Gyllensten, Ulf and Nilsson, Ove and Wu, Harry X.},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535},
	keywords = {Pinus sylvestris, SNP array, genome resequencing, genome-wide association studies, genomic selection, pines},
}

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