Publications 2017

@article{romero_navarro_study_2017,
	title = {A study of allelic diversity underlying flowering-time adaptation in maize landraces},
	volume = {49},
	copyright = {2017 Springer Nature America, Inc.},
	issn = {1546-1718},
	url = {https://www.nature.com/articles/ng.3784},
	doi = {10.1038/ng.3784},
	abstract = {Edward Buckler, Sarah Hearne and colleagues integrate two approaches to characterize the genetic diversity of a large number of geographically distributed maize landraces. They examine flowering time and adaptation to altitude and find that the majority of the associated SNPs overlap both traits.},
	language = {en},
	number = {3},
	urldate = {2024-03-22},
	journal = {Nature Genetics},
	author = {Romero Navarro, J. Alberto and Willcox, Martha and Burgueño, Juan and Romay, Cinta and Swarts, Kelly and Trachsel, Samuel and Preciado, Ernesto and Terron, Arturo and Delgado, Humberto Vallejo and Vidal, Victor and Ortega, Alejandro and Banda, Armando Espinoza and Montiel, Noel Orlando Gómez and Ortiz-Monasterio, Ivan and Vicente, Félix San and Espinoza, Armando Guadarrama and Atlin, Gary and Wenzl, Peter and Hearne, Sarah and Buckler, Edward S.},
	month = mar,
	year = {2017},
	note = {Publisher: Nature Publishing Group},
	keywords = {Plant breeding, Plant genetics},
	pages = {476--480},
}

Edward Buckler, Sarah Hearne and colleagues integrate two approaches to characterize the genetic diversity of a large number of geographically distributed maize landraces. They examine flowering time and adaptation to altitude and find that the majority of the associated SNPs overlap both traits.

@article{swarts_genomic_2017,
	title = {Genomic estimation of complex traits reveals ancient maize adaptation to temperate {North} {America}},
	volume = {357},
	url = {https://www.science.org/doi/10.1126/science.aam9425},
	doi = {10.1126/science.aam9425},
	abstract = {By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation.},
	number = {6350},
	urldate = {2024-03-22},
	journal = {Science},
	author = {Swarts, Kelly and Gutaker, Rafal M. and Benz, Bruce and Blake, Michael and Bukowski, Robert and Holland, James and Kruse-Peeples, Melissa and Lepak, Nicholas and Prim, Lynda and Romay, M. Cinta and Ross-Ibarra, Jeffrey and Sanchez-Gonzalez, Jose de Jesus and Schmidt, Chris and Schuenemann, Verena J. and Krause, Johannes and Matson, R. G. and Weigel, Detlef and Buckler, Edward S. and Burbano, Hernán A.},
	month = aug,
	year = {2017},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {512--515},
}

By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation.

@article{lee_dimerization_2017,
	title = {Dimerization in {LBD16} and {LBD18} {Transcription} {Factors} {Is} {Critical} for {Lateral} {Root} {Formation}},
	volume = {174},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.17.00013},
	doi = {10.1104/pp.17.00013},
	abstract = {LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKEs (hereafter referred to as LBD) are plant-specific transcription factors that play important roles in a plethora of plant growth and development. The leucine (Leu) zipper-like coiled-coil motif in the lateral organ boundaries domain of the class I LBD proteins has been proposed to mediate protein dimerization, but it has not been experimentally assessed yet. LBD16 and LBD18 have been well characterized to play important roles in lateral root development in Arabidopsis (Arabidopsis thaliana). Here, we investigated the role of the coiled-coil motif in the dimerization of LBD16 and LBD18 and in transcriptional regulation and biological function. We built the molecular models of the coiled coil of LBD16 and LBD18, providing the probable Leu zipper models of the helix dimer. Using a variety of molecular techniques, such as bimolecular fluorescence complementation, luciferase complementation imaging, GST pull down, and coimmunoprecipitation assays, we showed that the conserved Leu or valine residues in the coiled-coil motif are critical for the dimerization of LBD16 or LBD18. Using transgenic Arabidopsis plants that overexpress HA:LBD16 or HA:LBD16Q in lbd16 or HA:LBD18 or HA:LBD18Q in lbd18, we demonstrated that the homodimerization of LBD18 mediated by the coiled-coil motif is crucial for transcriptional regulation via promoter binding and for lateral root formation. In addition, we found that the carboxyl-terminal region beyond the coiled-coil motif in LBD18 acts as an additional dimerization domain. These results provide a molecular basis for homodimerization and heterodimerization among the 42 Arabidopsis LBD family members for displaying their biological functions.},
	number = {1},
	urldate = {2023-11-14},
	journal = {Plant Physiology},
	author = {Lee, Han Woo and Kang, Na Young and Pandey, Shashank K. and Cho, Chuloh and Lee, Sung Haeng and Kim, Jungmook},
	month = may,
	year = {2017},
	pages = {301--311},
}

LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKEs (hereafter referred to as LBD) are plant-specific transcription factors that play important roles in a plethora of plant growth and development. The leucine (Leu) zipper-like coiled-coil motif in the lateral organ boundaries domain of the class I LBD proteins has been proposed to mediate protein dimerization, but it has not been experimentally assessed yet. LBD16 and LBD18 have been well characterized to play important roles in lateral root development in Arabidopsis (Arabidopsis thaliana). Here, we investigated the role of the coiled-coil motif in the dimerization of LBD16 and LBD18 and in transcriptional regulation and biological function. We built the molecular models of the coiled coil of LBD16 and LBD18, providing the probable Leu zipper models of the helix dimer. Using a variety of molecular techniques, such as bimolecular fluorescence complementation, luciferase complementation imaging, GST pull down, and coimmunoprecipitation assays, we showed that the conserved Leu or valine residues in the coiled-coil motif are critical for the dimerization of LBD16 or LBD18. Using transgenic Arabidopsis plants that overexpress HA:LBD16 or HA:LBD16Q in lbd16 or HA:LBD18 or HA:LBD18Q in lbd18, we demonstrated that the homodimerization of LBD18 mediated by the coiled-coil motif is crucial for transcriptional regulation via promoter binding and for lateral root formation. In addition, we found that the carboxyl-terminal region beyond the coiled-coil motif in LBD18 acts as an additional dimerization domain. These results provide a molecular basis for homodimerization and heterodimerization among the 42 Arabidopsis LBD family members for displaying their biological functions.

@article{peng_genetic_2017,
	title = {Genetic analyses reveal independent domestication origins of the emerging oil crop {Paeonia} ostii, a tree peony with a long-term cultivation history},
	volume = {7},
	copyright = {2017 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-017-04744-z},
	doi = {10.1038/s41598-017-04744-z},
	abstract = {Paeonia ostii, a member of tree peony, is an emerging oil crop with important medical and oil uses and widely cultivated in China. Dissolving the genetic diversity and domestication history of this species is important for further genetic improvements and deployments. We firstly selected 29 simple sequence repeats (SSRs) via transcriptome mining, segregation analyses and polymorphism characterizations; then, 901 individuals from the range-wide samples were genotyped using well-characterized SSR markers. We observed moderate genetic diversity among individuals, and Shaanxi Province was identified as the center of genetic diversity for our cultivated plants. Five well-separated gene pools were detected by STRUCTURE analyses, and the results suggested that multiple independent domestication origins occurred in Shaanxi Province and Tongling City (Anhui Province). Taken together, the genetic evidence and the historical records suggest multiple long-distance introductions after the plant was domesticated in Shandong, Henan and Hunan provinces. The present study provides the first genetic evaluation of the domestication history of P. ostii, and our results provide an important reference for further genetic improvements and deployments of this important crop.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Reports},
	author = {Peng, Li-Ping and Cai, Chang-Fu and Zhong, Yuan and Xu, Xing-Xing and Xian, Hong-Li and Cheng, Fang-Yun and Mao, Jian-Feng},
	month = jul,
	year = {2017},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Structural variation},
	pages = {5340},
}

Paeonia ostii, a member of tree peony, is an emerging oil crop with important medical and oil uses and widely cultivated in China. Dissolving the genetic diversity and domestication history of this species is important for further genetic improvements and deployments. We firstly selected 29 simple sequence repeats (SSRs) via transcriptome mining, segregation analyses and polymorphism characterizations; then, 901 individuals from the range-wide samples were genotyped using well-characterized SSR markers. We observed moderate genetic diversity among individuals, and Shaanxi Province was identified as the center of genetic diversity for our cultivated plants. Five well-separated gene pools were detected by STRUCTURE analyses, and the results suggested that multiple independent domestication origins occurred in Shaanxi Province and Tongling City (Anhui Province). Taken together, the genetic evidence and the historical records suggest multiple long-distance introductions after the plant was domesticated in Shandong, Henan and Hunan provinces. The present study provides the first genetic evaluation of the domestication history of P. ostii, and our results provide an important reference for further genetic improvements and deployments of this important crop.

@article{mao_approaches_2017,
	title = {Approaches used to detect and test hybridization: combining phylogenetic and population genetic analyses},
	volume = {25},
	issn = {1005-0094},
	shorttitle = {Approaches used to detect and test hybridization},
	url = {https://www.biodiversity-science.net/EN/10.17520/biods.2017097},
	doi = {10.17520/biods.2017097},
	abstract = {Hybridization among diverging (interspecific or intraspecific) groups ...},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {Biodiversity Science},
	author = {Mao, Jian-Feng and Ma, Yongpeng and Zhou, Renchao},
	month = jun,
	year = {2017},
	pages = {577},
}

Hybridization among diverging (interspecific or intraspecific) groups ...

@article{hu_predicting_2017,
	title = {Predicting {Future} {Seed} {Sourcing} of {Platycladus} orientalis ({L}.) for {Future} {Climates} {Using} {Climate} {Niche} {Models}},
	volume = {8},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/8/12/471},
	doi = {10.3390/f8120471},
	abstract = {Climate niche modeling has been widely used to assess the impact of climate change on forest trees at the species level. However, geographically divergent tree populations are expected to respond differently to climate change. Considering intraspecific local adaptation in modeling species responses to climate change will thus improve the credibility and usefulness of climate niche models, particularly for genetic resources management. In this study, we used five Platycladus orientalis (L.) seed zones (Northwestern; Northern; Central; Southern; and Subtropical) covering the entire species range in China. A climate niche model was developed and used to project the suitable climatic conditions for each of the five seed zones for current and various future climate scenarios (Representative Concentration Pathways: RCP2.6, RCP4.5, RCP6.0, and RCP8.5). Our results indicated that the Subtropical seed zone would show consistent reduction for all climate change scenarios. The remaining seed zones, however, would experience various degrees of expansion in suitable habitat relative to their current geographic distributions. Most of the seed zones would gain suitable habitats at their northern distribution margins and higher latitudes. Thus, we recommend adjusting the current forest management strategies to mitigate the negative impacts of climate change.},
	language = {en},
	number = {12},
	urldate = {2023-04-27},
	journal = {Forests},
	author = {Hu, Xian-Ge and Wang, Tongli and Liu, Si-Si and Jiao, Si-Qian and Jia, Kai-Hua and Zhou, Shan-Shan and Jin, Yuqing and Li, Yue and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	month = dec,
	year = {2017},
	note = {Number: 12
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {climate change, conifer, local adaptation, seed zone, spatial shifts},
	pages = {471},
}

Climate niche modeling has been widely used to assess the impact of climate change on forest trees at the species level. However, geographically divergent tree populations are expected to respond differently to climate change. Considering intraspecific local adaptation in modeling species responses to climate change will thus improve the credibility and usefulness of climate niche models, particularly for genetic resources management. In this study, we used five Platycladus orientalis (L.) seed zones (Northwestern; Northern; Central; Southern; and Subtropical) covering the entire species range in China. A climate niche model was developed and used to project the suitable climatic conditions for each of the five seed zones for current and various future climate scenarios (Representative Concentration Pathways: RCP2.6, RCP4.5, RCP6.0, and RCP8.5). Our results indicated that the Subtropical seed zone would show consistent reduction for all climate change scenarios. The remaining seed zones, however, would experience various degrees of expansion in suitable habitat relative to their current geographic distributions. Most of the seed zones would gain suitable habitats at their northern distribution margins and higher latitudes. Thus, we recommend adjusting the current forest management strategies to mitigate the negative impacts of climate change.

@incollection{bacete_characterization_2017,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Characterization of {Plant} {Cell} {Wall} {Damage}-{Associated} {Molecular} {Patterns} {Regulating} {Immune} {Responses}},
	isbn = {978-1-4939-6859-6},
	url = {https://doi.org/10.1007/978-1-4939-6859-6_2},
	abstract = {The plant cell wall is one of the first defensive barriers that pathogens need to overcome to successfully colonize plant tissues. Plant cell wall is considered a dynamic structure that regulates both constitutive and inducible defense mechanisms. The wall is a potential source of a diverse set of Damage-Associated Molecular Patterns (DAMPs), which are signalling molecules that trigger immune responses. However, just a few active wall ligands, such as oligogalacturonic acids (OGs), have been characterized so far. To identify additional wall-derived DAMPs, we obtained different plant wall fractions and tested their capacity to trigger immune responses using a calcium read-out system. To characterize the active DAMPs structures present in these fractions, we applied Glycome Profiling, a technology that uses a large and diverse set of specific monoclonal antibodies against wall carbohydrate ligands. The methods describe here can be used in combination with other biochemical approaches to identify and purify new plant cell wall DAMPs.},
	language = {en},
	urldate = {2023-03-10},
	booktitle = {Plant {Pattern} {Recognition} {Receptors}: {Methods} and {Protocols}},
	publisher = {Springer},
	author = {Bacete, Laura and Mélida, Hugo and Pattathil, Sivakumar and Hahn, Michael G. and Molina, Antonio and Miedes, Eva},
	editor = {Shan, Libo and He, Ping},
	year = {2017},
	doi = {10.1007/978-1-4939-6859-6_2},
	keywords = {Arabidopsis, Cell wall, Hemicellulose, Immunity, Pectin},
	pages = {13--23},
}

The plant cell wall is one of the first defensive barriers that pathogens need to overcome to successfully colonize plant tissues. Plant cell wall is considered a dynamic structure that regulates both constitutive and inducible defense mechanisms. The wall is a potential source of a diverse set of Damage-Associated Molecular Patterns (DAMPs), which are signalling molecules that trigger immune responses. However, just a few active wall ligands, such as oligogalacturonic acids (OGs), have been characterized so far. To identify additional wall-derived DAMPs, we obtained different plant wall fractions and tested their capacity to trigger immune responses using a calcium read-out system. To characterize the active DAMPs structures present in these fractions, we applied Glycome Profiling, a technology that uses a large and diverse set of specific monoclonal antibodies against wall carbohydrate ligands. The methods describe here can be used in combination with other biochemical approaches to identify and purify new plant cell wall DAMPs.

@article{barghetti_heat-shock_2017,
	title = {Heat-shock protein 40 is the key farnesylation target in meristem size control, abscisic acid signaling, and drought resistance},
	volume = {31},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/content/31/22/2282},
	doi = {10.1101/gad.301242.117},
	abstract = {Protein farnesylation is central to molecular cell biology. In plants, protein farnesyl transferase mutants are pleiotropic and exhibit defective meristem organization, hypersensitivity to the hormone abscisic acid, and increased drought resistance. The precise functions of protein farnesylation in plants remain incompletely understood because few relevant farnesylated targets have been identified. Here, we show that defective farnesylation of a single factor—heat-shock protein 40 (HSP40), encoded by the J2 and J3 genes—is sufficient to confer ABA hypersensitivity, drought resistance, late flowering, and enlarged meristems, indicating that altered function of chaperone client proteins underlies most farnesyl transferase mutant phenotypes. We also show that expression of an abiotic stress-related microRNA (miRNA) regulon controlled by the transcription factor SPL7 requires HSP40 farnesylation. Expression of a truncated SPL7 form mimicking its activated proteolysis fragment of the membrane-bound SPL7 precursor partially restores accumulation of SPL7-dependent miRNAs in farnesyl transferase mutants. These results implicate the pathway directing SPL7 activation from its membrane-bound precursor as an important target of farnesylated HSP40, consistent with our demonstration that HSP40 farnesylation facilitates its membrane association. The results also suggest that altered gene regulation via select miRNAs contributes to abiotic stress-related phenotypes of farnesyl transferase mutants.},
	language = {en},
	number = {22},
	urldate = {2022-11-30},
	journal = {Genes \& Development},
	author = {Barghetti, Andrea and Sjögren, Lars and Floris, Maïna and Paredes, Esther Botterweg and Wenkel, Stephan and Brodersen, Peter},
	month = nov,
	year = {2017},
	keywords = {Arabidopsis, abscisic acid, drought resistance, farnesylation, heat-shock proteins, meristem, microRNAs},
	pages = {2282--2295},
}

Protein farnesylation is central to molecular cell biology. In plants, protein farnesyl transferase mutants are pleiotropic and exhibit defective meristem organization, hypersensitivity to the hormone abscisic acid, and increased drought resistance. The precise functions of protein farnesylation in plants remain incompletely understood because few relevant farnesylated targets have been identified. Here, we show that defective farnesylation of a single factor—heat-shock protein 40 (HSP40), encoded by the J2 and J3 genes—is sufficient to confer ABA hypersensitivity, drought resistance, late flowering, and enlarged meristems, indicating that altered function of chaperone client proteins underlies most farnesyl transferase mutant phenotypes. We also show that expression of an abiotic stress-related microRNA (miRNA) regulon controlled by the transcription factor SPL7 requires HSP40 farnesylation. Expression of a truncated SPL7 form mimicking its activated proteolysis fragment of the membrane-bound SPL7 precursor partially restores accumulation of SPL7-dependent miRNAs in farnesyl transferase mutants. These results implicate the pathway directing SPL7 activation from its membrane-bound precursor as an important target of farnesylated HSP40, consistent with our demonstration that HSP40 farnesylation facilitates its membrane association. The results also suggest that altered gene regulation via select miRNAs contributes to abiotic stress-related phenotypes of farnesyl transferase mutants.

@article{merelo_shady_2017,
	series = {35 {Growth} and development 2017},
	title = {The shady side of leaf development: the role of the {REVOLUTA}/{KANADI1} module in leaf patterning and auxin-mediated growth promotion},
	volume = {35},
	issn = {1369-5266},
	shorttitle = {The shady side of leaf development},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526616302114},
	doi = {10.1016/j.pbi.2016.11.016},
	abstract = {Leaves are present in all land plants and are specialized organs for light harvesting. They arise at the flanks of the shoot apical meristem (SAM), and develop into lamina structures that exhibit adaxial/abaxial (upper/lower side of the leaf) polarity. At the molecular level, an intricate regulatory network determines ad-/abaxial polarity in Arabidopsis thaliana leaves, where the Class III Homeodomain Leucine Zipper (HD-ZIPIII) and KANADI (KAN) proteins are key mediators. The HD-ZIPIII REVOLUTA (REV) is expressed in the adaxial domain of lateral organs, whereas KAN1 is involved in abaxial differentiation. The REV/KAN1 module directly and antagonistically regulates the expression of several genes involved in shade-induced growth and auxin biosynthetic enzymes.},
	language = {en},
	urldate = {2022-11-30},
	journal = {Current Opinion in Plant Biology},
	author = {Merelo, Paz and Paredes, Esther Botterweg and Heisler, Marcus G and Wenkel, Stephan},
	month = feb,
	year = {2017},
	pages = {111--116},
}

Leaves are present in all land plants and are specialized organs for light harvesting. They arise at the flanks of the shoot apical meristem (SAM), and develop into lamina structures that exhibit adaxial/abaxial (upper/lower side of the leaf) polarity. At the molecular level, an intricate regulatory network determines ad-/abaxial polarity in Arabidopsis thaliana leaves, where the Class III Homeodomain Leucine Zipper (HD-ZIPIII) and KANADI (KAN) proteins are key mediators. The HD-ZIPIII REVOLUTA (REV) is expressed in the adaxial domain of lateral organs, whereas KAN1 is involved in abaxial differentiation. The REV/KAN1 module directly and antagonistically regulates the expression of several genes involved in shade-induced growth and auxin biosynthetic enzymes.

@article{straub_cross-species_2017,
	title = {Cross-{Species} {Genome}-{Wide} {Identification} of {Evolutionary} {Conserved} {MicroProteins}},
	volume = {9},
	issn = {1759-6653},
	url = {https://doi.org/10.1093/gbe/evx041},
	doi = {10.1093/gbe/evx041},
	abstract = {MicroProteins are small single-domain proteins that act by engaging their targets into different, sometimes nonproductive protein complexes. In order to identify novel microProteins in any sequenced genome of interest, we have developed miPFinder, a program that identifies and classifies potential microProteins. In the past years, several microProteins have been discovered in plants where they are mainly involved in the regulation of development by fine-tuning transcription factor activities. The miPFinder algorithm identifies all up to date known plant microProteins and extends the microProtein concept beyond transcription factors to other protein families. Here, we reveal potential microProtein candidates in several plant and animal reference genomes. A large number of these microProteins are species-specific while others evolved early and are evolutionary highly conserved. Most known microProtein genes originated from large ancestral genes by gene duplication, mutation and subsequent degradation. Gene ontology analysis shows that putative microProtein ancestors are often located in the nucleus, and involved in DNA binding and formation of protein complexes. Additionally, microProtein candidates act in plant transcriptional regulation, signal transduction and anatomical structure development. MiPFinder is freely available to find microProteins in any genome and will aid in the identification of novel microProteins in plants and animals.},
	number = {3},
	urldate = {2022-11-30},
	journal = {Genome Biology and Evolution},
	author = {Straub, Daniel and Wenkel, Stephan},
	month = mar,
	year = {2017},
	pages = {777--789},
}

MicroProteins are small single-domain proteins that act by engaging their targets into different, sometimes nonproductive protein complexes. In order to identify novel microProteins in any sequenced genome of interest, we have developed miPFinder, a program that identifies and classifies potential microProteins. In the past years, several microProteins have been discovered in plants where they are mainly involved in the regulation of development by fine-tuning transcription factor activities. The miPFinder algorithm identifies all up to date known plant microProteins and extends the microProtein concept beyond transcription factors to other protein families. Here, we reveal potential microProtein candidates in several plant and animal reference genomes. A large number of these microProteins are species-specific while others evolved early and are evolutionary highly conserved. Most known microProtein genes originated from large ancestral genes by gene duplication, mutation and subsequent degradation. Gene ontology analysis shows that putative microProtein ancestors are often located in the nucleus, and involved in DNA binding and formation of protein complexes. Additionally, microProtein candidates act in plant transcriptional regulation, signal transduction and anatomical structure development. MiPFinder is freely available to find microProteins in any genome and will aid in the identification of novel microProteins in plants and animals.

@article{wang_high_2017,
	title = {The {High} {Light} {Response} and {Redox} {Control} of {Thylakoid} {FtsH} {Protease} in {Chlamydomonas} reinhardtii},
	volume = {10},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205216302210},
	doi = {10.1016/j.molp.2016.09.012},
	abstract = {In Chlamydomonas reinhardtii, the major protease involved in the maintenance of photosynthetic machinery in thylakoid membranes, the FtsH protease, mostly forms large hetero-oligomers (∼1 MDa) comprising FtsH1 and FtsH2 subunits, whatever the light intensity for growth. Upon high light exposure, the FtsH subunits display a shorter half-life, which is counterbalanced by an increase in FTSH1/2 mRNA levels, resulting in the modest upregulation of FtsH1/2 proteins. Furthermore, we found that high light increases the protease activity through a hitherto unnoticed redox-controlled reduction of intermolecular disulfide bridges. We isolated a Chlamydomonas FTSH1 promoter-deficient mutant, ftsh1-3, resulting from the insertion of a TOC1 transposon, in which the high light-induced upregulation of FTSH1 gene expression is largely lost. In ftsh1-3, the abundance of FtsH1 and FtsH2 proteins are loosely coupled (decreased by 70\% and 30\%, respectively) with no formation of large and stable homo-oligomers. Using strains exhibiting different accumulation levels of the FtsH1 subunit after complementation of ftsh1-3, we demonstrate that high light tolerance is tightly correlated with the abundance of the FtsH protease. Thus, the response of Chlamydomonas to light stress involves higher levels of FtsH1/2 subunits associated into large complexes with increased proteolytic activity.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Wang, Fei and Qi, Yafei and Malnoë, Alizée and Choquet, Yves and Wollman, Francis-André and de Vitry, Catherine},
	month = jan,
	year = {2017},
	pages = {99--114},
}

In Chlamydomonas reinhardtii, the major protease involved in the maintenance of photosynthetic machinery in thylakoid membranes, the FtsH protease, mostly forms large hetero-oligomers (∼1 MDa) comprising FtsH1 and FtsH2 subunits, whatever the light intensity for growth. Upon high light exposure, the FtsH subunits display a shorter half-life, which is counterbalanced by an increase in FTSH1/2 mRNA levels, resulting in the modest upregulation of FtsH1/2 proteins. Furthermore, we found that high light increases the protease activity through a hitherto unnoticed redox-controlled reduction of intermolecular disulfide bridges. We isolated a Chlamydomonas FTSH1 promoter-deficient mutant, ftsh1-3, resulting from the insertion of a TOC1 transposon, in which the high light-induced upregulation of FTSH1 gene expression is largely lost. In ftsh1-3, the abundance of FtsH1 and FtsH2 proteins are loosely coupled (decreased by 70% and 30%, respectively) with no formation of large and stable homo-oligomers. Using strains exhibiting different accumulation levels of the FtsH1 subunit after complementation of ftsh1-3, we demonstrate that high light tolerance is tightly correlated with the abundance of the FtsH protease. Thus, the response of Chlamydomonas to light stress involves higher levels of FtsH1/2 subunits associated into large complexes with increased proteolytic activity.

@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{laitinen_key_2017,
	title = {A {Key} {Role} for {Apoplastic} {H2O2} in {Norway} {Spruce} {Phenolic} {Metabolism}},
	volume = {174},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/174/3/1449-1475/6117375},
	doi = {10/gbkxvh},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Laitinen, Teresa and Morreel, Kris and Delhomme, Nicolas and Gauthier, Adrien and Schiffthaler, Bastian and Nickolov, Kaloian and Brader, Günter and Lim, Kean-Jin and Teeri, Teemu H. and Street, Nathaniel R. and Boerjan, Wout and Kärkönen, Anna},
	month = jul,
	year = {2017},
	pages = {1449--1475},
}

@article{engelhorn_dynamics_2017,
	title = {Dynamics of {H3K4me3} {Chromatin} {Marks} {Prevails} over {H3K27me3} for {Gene} {Regulation} during {Flower} {Morphogenesis} in {Arabidopsis} thaliana},
	volume = {1},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2075-4655/1/2/8},
	doi = {10.3390/epigenomes1020008},
	abstract = {Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.},
	language = {en},
	number = {2},
	urldate = {2021-10-22},
	journal = {Epigenomes},
	author = {Engelhorn, Julia and Blanvillain, Robert and Kröner, Christian and Parrinello, Hugues and Rohmer, Marine and Posé, David and Ott, Felix and Schmid, Markus and Carles, Cristel C.},
	month = sep,
	year = {2017},
	note = {Number: 2
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {ChIP-seq, RNA-seq, chromatin and expression dynamics, differentiation, reproductive development},
	pages = {8},
}

Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.

@article{schneider_two_2017,
	title = {Two {Complementary} {Mechanisms} {Underpin} {Cell} {Wall} {Patterning} during {Xylem} {Vessel} {Development}},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/29/10/2433-2449/6100385},
	doi = {10/cf9j},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Schneider, Rene and Tang, Lu and Lampugnani, Edwin R. and Barkwill, Sarah and Lathe, Rahul and Zhang, Yi and McFarlane, Heather E. and Pesquet, Edouard and Niittylä, Totte and Mansfield, Shawn D. and Zhou, Yihua and Persson, Staffan},
	month = oct,
	year = {2017},
	pages = {2433--2449},
}

@article{zhao_xylem_2017,
	title = {{XYLEM} {NAC} {DOMAIN1}, an angiosperm {NAC} transcription factor, inhibits xylem differentiation through conserved motifs that interact with {RETINOBLASTOMA}‐{RELATED}},
	volume = {216},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14704},
	doi = {10/gbt5ht},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Zhao, Chengsong and Lasses, Theres and Bakó, Laszlo and Kong, Danyu and Zhao, Bingyu and Chanda, Bidisha and Bombarely, Aureliano and Cruz‐Ramírez, Alfredo and Scheres, Ben and Brunner, Amy M. and Beers, Eric P.},
	month = oct,
	year = {2017},
	pages = {76--89},
}

@article{mullin_fertility_2017,
	title = {Fertility {Variation}, {Genetic} {Relatedness}, and {Their} {Impacts} on {Gene} {Diversity} of {Seeds} {From} a {Seed} {Orchard} of {Pinus} thunbergii},
	volume = {53},
	url = {https://sciendo.com/article/10.1515/sg-2004-0037},
	doi = {10/gkzpmr},
	abstract = {Abstract Clonal differences in the number of male and female strobili were determined for five consecutive years in a clonal seed orchard of Pinus thunbergii in Korea. The effects of relatedness and clonal differences in reproductive development on gene diversity of seed (in terms of accumulated relatedness by status number) were estimated. While clonal differences were found, fertility variation was not large through all studied years. The orchard clones were divided into different regions and locations based on the geographical distribution and distance of natural stands that plus trees were selected from. Assuming that there was no relatedness among regions, locations and clones, the status number (Ns) was varied from 47.6 to 55.5 for five successive years. On average (pooling), Ns was 92\% of census number (N). Assumed relatedness among regions, locations and/or clones decreased the status number. Effect of parental selection on relatedness and orchard management was also discussed.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-30},
	journal = {Silvae Genetica},
	author = {Mullin, Undefined},
	month = oct,
	year = {2017},
	pages = {202--206},
}

Abstract Clonal differences in the number of male and female strobili were determined for five consecutive years in a clonal seed orchard of Pinus thunbergii in Korea. The effects of relatedness and clonal differences in reproductive development on gene diversity of seed (in terms of accumulated relatedness by status number) were estimated. While clonal differences were found, fertility variation was not large through all studied years. The orchard clones were divided into different regions and locations based on the geographical distribution and distance of natural stands that plus trees were selected from. Assuming that there was no relatedness among regions, locations and clones, the status number (Ns) was varied from 47.6 to 55.5 for five successive years. On average (pooling), Ns was 92% of census number (N). Assumed relatedness among regions, locations and/or clones decreased the status number. Effect of parental selection on relatedness and orchard management was also discussed.

@article{lindgren_fertility_2017,
	title = {Fertility {Variation} and {Status} {Number} {Between} a {Base} {Population} and a {Seed} {Orchard} of {Pinus} brutia},
	volume = {53},
	url = {https://www.sciendo.com/article/10.1515/sg-2004-0029},
	doi = {10/gjmhgw},
	abstract = {Abstract Female, male and total fertility variations were estimated in a base population and a seed orchard derived from the base population in Pinus brutia. Relative status number for gametes (female and male contribution) and zygotes (average of female and male contribution) were estimated based on the fertility variation. Average female and male strobilus production were 229.1 and 1003.3 in the base population, and 98.9 and 244.9 in the seed orchard for combined years, respectively. Positive and significant correlations were found between female and male strobilus production in both base population and seed orchard. The male fertility variation was higher than female fertility variation in the seed orchard, while female fertility variation was higher than male fertility variation in the base population. Coefficients of variations in female and male strobilus production were 0.721 and 0.696 in the base population, and 0.403 and 1.110 in the seed orchard for combined years, respectively. Total fertility variation was 1.41 in the base population and 1.40 in the seed orchard for combined years. The relative status numbers estimated based on the total fertility were 70\% of census number in the base population, and 71\% in the seed orchard for combined years.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-30},
	journal = {Silvae Genetica},
	author = {Lindgren, Undefined},
	month = oct,
	year = {2017},
	pages = {161--163},
}

Abstract Female, male and total fertility variations were estimated in a base population and a seed orchard derived from the base population in Pinus brutia. Relative status number for gametes (female and male contribution) and zygotes (average of female and male contribution) were estimated based on the fertility variation. Average female and male strobilus production were 229.1 and 1003.3 in the base population, and 98.9 and 244.9 in the seed orchard for combined years, respectively. Positive and significant correlations were found between female and male strobilus production in both base population and seed orchard. The male fertility variation was higher than female fertility variation in the seed orchard, while female fertility variation was higher than male fertility variation in the base population. Coefficients of variations in female and male strobilus production were 0.721 and 0.696 in the base population, and 0.403 and 1.110 in the seed orchard for combined years, respectively. Total fertility variation was 1.41 in the base population and 1.40 in the seed orchard for combined years. The relative status numbers estimated based on the total fertility were 70% of census number in the base population, and 71% in the seed orchard for combined years.

@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{matheson_inbreeding_2017,
	title = {Inbreeding in {Pinus} {Radiata} – {V}. {The} {Effects} of {Inbreeding} on {Fecundity}},
	volume = {53},
	url = {https://www.sciendo.com/article/10.1515/sg-2004-0015},
	doi = {10/gkm3fw},
	abstract = {Abstract A successful inbreeding and hybrid breeding strategy in tree improvement requires that 1) inbreeding (selfing) can produce superior inbred lines (effective purging of deleterious alleles), 2) there is heterosis among crosses of inbred lines, 3) early selection between lines is effective, and 4) inbreeding will not substantially reduce reproductive ability. We have previously reported that inbreeding depression on growth was lower in radiata pine relative to other conifers and segregation in the first two-generations of selfs generated superior inbred trees. In addition, we have observed that early selection among inbred trees (lines) was more effective than in out-crossed populations and there was an apparent heterosis in radiata pine. In this study, the effect of inbreeding on the reproductive ability in young and adult trees of radiata pine has been quantified from five populations of varied inbreeding levels (F =0, 0.125, 0.25, 0.5, and 0.75). It was observed that the effects of inbreeding depression on fecundity was higher at a young age than at older age and inbreeding depression at a young age is due to two factors: 1) a delay of reproductive age (about 8.3, and 8.5\% of trees delayed for F =0.5 and F =0.75 populations, respectively) and},
	language = {en},
	number = {1-6},
	urldate = {2021-06-15},
	journal = {Silvae Genetica},
	author = {Matheson, Undefined},
	month = oct,
	year = {2017},
	pages = {80--88},
}

Abstract A successful inbreeding and hybrid breeding strategy in tree improvement requires that 1) inbreeding (selfing) can produce superior inbred lines (effective purging of deleterious alleles), 2) there is heterosis among crosses of inbred lines, 3) early selection between lines is effective, and 4) inbreeding will not substantially reduce reproductive ability. We have previously reported that inbreeding depression on growth was lower in radiata pine relative to other conifers and segregation in the first two-generations of selfs generated superior inbred trees. In addition, we have observed that early selection among inbred trees (lines) was more effective than in out-crossed populations and there was an apparent heterosis in radiata pine. In this study, the effect of inbreeding on the reproductive ability in young and adult trees of radiata pine has been quantified from five populations of varied inbreeding levels (F =0, 0.125, 0.25, 0.5, and 0.75). It was observed that the effects of inbreeding depression on fecundity was higher at a young age than at older age and inbreeding depression at a young age is due to two factors: 1) a delay of reproductive age (about 8.3, and 8.5% of trees delayed for F =0.5 and F =0.75 populations, respectively) and

@article{lindgren_fertility_2017,
	title = {Fertility {Variation} and its {Implications} on {Relatedness} in {Seed} {Crops} in {Seedling} {Seed} {Orchards} of {Eucalyptus} camaldulensis and {E}. tereticornis},
	volume = {56},
	url = {https://www.sciendo.com/article/10.1515/sg-2007-0036},
	doi = {10/gjmhg2},
	abstract = {Seedling seed orchards of Eucalyptus tereticornis (N =192 \& 505) and E. camaldulensis (N =182 \& 525) were established at two sites (one moist and one dry) in southern India. The fertility (based on the number of flowers and fruits) was registered for each tree at age eight and nine years. E. camaldulensis on the moist location had 73\% fertile trees and low fertility difference (sibling coefficient, Ψ, was 2.27) at eight years. whereas Only 23\% trees were fertile in the E. tereticornis orchard at the same site and the fertility variation was high (Ψ =11.71). In the dry location, fertility was almost the same in both species at nine years, with 45 \& 51\% fertile trees in E. camaldulensis (Ψ =5.4) and E. tereticornis (Ψ = 5.2) respectively. Though the fertility trends were the same in both years, the number of fertile trees was comparatively higher at nine years (except in the low flowering E. tereticornis orchard at the moist site) in both the sites. Gene diversity values of the seed crop estimated for two consecutive years are fairly high except for the E. tereticornis (GD = 0.9650 and 0.9690) orchard located in the moist site. The implications},
	language = {en},
	number = {1-6},
	urldate = {2021-06-10},
	journal = {Silvae Genetica},
	author = {Lindgren, D.},
	month = oct,
	year = {2017},
	pages = {253--259},
}

Seedling seed orchards of Eucalyptus tereticornis (N =192 & 505) and E. camaldulensis (N =182 & 525) were established at two sites (one moist and one dry) in southern India. The fertility (based on the number of flowers and fruits) was registered for each tree at age eight and nine years. E. camaldulensis on the moist location had 73% fertile trees and low fertility difference (sibling coefficient, Ψ, was 2.27) at eight years. whereas Only 23% trees were fertile in the E. tereticornis orchard at the same site and the fertility variation was high (Ψ =11.71). In the dry location, fertility was almost the same in both species at nine years, with 45 & 51% fertile trees in E. camaldulensis (Ψ =5.4) and E. tereticornis (Ψ = 5.2) respectively. Though the fertility trends were the same in both years, the number of fertile trees was comparatively higher at nine years (except in the low flowering E. tereticornis orchard at the moist site) in both the sites. Gene diversity values of the seed crop estimated for two consecutive years are fairly high except for the E. tereticornis (GD = 0.9650 and 0.9690) orchard located in the moist site. The implications

@article{lindgren_strategies_2017,
	title = {Strategies for {Optimal} {Deployment} of {Related} {Clones} into {Seed} {Orchards}},
	volume = {57},
	url = {https://www.sciendo.com/article/10.1515/sg-2008-0018},
	doi = {10/gkhnqv},
	abstract = {This study deals with how the deployed proportion of each candidate clone can be decided at the establishment of a seed orchard when the breeding values are available for each candidate in a population of unrelated half-sib families. The following deployment strategies were compared: (a) truncation selection by selecting the clones with the breeding values exceeding certain threshold and deploying equal number of ramets (Truncation strategy); (b) truncation selection by selecting only one best individual within each family (Truncation unrelated); (c) maximizing gain at a given effective clone number (Linear deployment); (d) linear deployment by selecting one best individual within each family (Linear deployment unrelated) and (e) maximizing net gain at a given gene diversity (Optimal proportions). The study focused on the latest alternative and described its superiority and characteristics for a number of possible typical cases. The genetic gain adjusted for predicted inbreeding depression (Net gain), gene diversity and effective clone number were considered as the main ranking criteria. The strategies optimizing the number of related individuals and the linear deployment strategy with restriction on relatedness returned the highest Net gain. If there is a large diversity to select from (the status number of the candidates is more},
	language = {en},
	number = {1-6},
	urldate = {2021-06-10},
	journal = {Silvae Genetica},
	author = {Lindgren, D.},
	month = oct,
	year = {2017},
	pages = {119--127},
}

This study deals with how the deployed proportion of each candidate clone can be decided at the establishment of a seed orchard when the breeding values are available for each candidate in a population of unrelated half-sib families. The following deployment strategies were compared: (a) truncation selection by selecting the clones with the breeding values exceeding certain threshold and deploying equal number of ramets (Truncation strategy); (b) truncation selection by selecting only one best individual within each family (Truncation unrelated); (c) maximizing gain at a given effective clone number (Linear deployment); (d) linear deployment by selecting one best individual within each family (Linear deployment unrelated) and (e) maximizing net gain at a given gene diversity (Optimal proportions). The study focused on the latest alternative and described its superiority and characteristics for a number of possible typical cases. The genetic gain adjusted for predicted inbreeding depression (Net gain), gene diversity and effective clone number were considered as the main ranking criteria. The strategies optimizing the number of related individuals and the linear deployment strategy with restriction on relatedness returned the highest Net gain. If there is a large diversity to select from (the status number of the candidates is more

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

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

@article{lindgren_evaluation_2017,
	title = {Evaluation of {Pollen} {Contamination} in an {Advanced} {Scots} {Pine} {Seed} {Orchard}},
	volume = {58},
	url = {https://www.sciendo.com/article/10.1515/sg-2009-0033},
	doi = {10/gjcmqd},
	abstract = {The pollination pattern in a Scots pine (Pinus sylvestris L.) seed orchard consisting of 28 clones was studied using nine microsatellite (SSR) loci. The nine SSR loci produced unique multilocus genotypes for each of the orchard’s 28 clones and allowed paternal assignment of the studied 305 seed using paternity exclusion probability of 99.9\%. Fifty two percent of the studied seeds were sired by outside the orchard pollen sources (i.e., pollen contamination) and as expected, low selfing (2.3\%) was detected. These results are valuable for the evaluation of the seed orchard function and the impact of contamination on the expected genetic gain.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Lindgren, D.},
	month = oct,
	year = {2017},
	pages = {262--269},
}

The pollination pattern in a Scots pine (Pinus sylvestris L.) seed orchard consisting of 28 clones was studied using nine microsatellite (SSR) loci. The nine SSR loci produced unique multilocus genotypes for each of the orchard’s 28 clones and allowed paternal assignment of the studied 305 seed using paternity exclusion probability of 99.9%. Fifty two percent of the studied seeds were sired by outside the orchard pollen sources (i.e., pollen contamination) and as expected, low selfing (2.3%) was detected. These results are valuable for the evaluation of the seed orchard function and the impact of contamination on the expected genetic gain.

@article{lindgren_annual_2017,
	title = {Annual {Fertility} {Variation} in {Clonal} {Seed} {Orchards} of {Teak} ({Tectona} grandis {L}.f.) and its {Impact} on {Seed} {Crop}},
	volume = {58},
	url = {https://www.sciendo.com/article/10.1515/sg-2009-0011},
	doi = {10/gjcmjw},
	abstract = {Fertility variation was studied in two clonal seed orchards (CSO) of teak in four consecutive years (2003-2006). Both orchards were raised in 1976 with grafts of phenotypes selected for growth and form. The seed orchards of CSO I (Topslip, Tamil Nadu State) and CSO II (Walayar, Kerala State) have 15 and 20 clones, respectively, with 13 common clones. The proportion of flowering ramets was generally low ranging from 16 to 53\% across years. The best fruit yield during the study period was around 18 kg ha-1 in CSO I and 17 kg ha-1 in CSO II. Highly significant clonal variation and clone by year and clone by site interactions were observed for fertility traits. The clonal contribution was more skewed in poor flowering years than in abundant flowering years and in CSO II than in CSO I. Broad sense heritability for flower and fruit production per tree was low to moderate (0.16 to 0.55). Flower and fruit production by individual ramets in successive years were positively correlated. Correlations between reproductive and growth traits were generally low, but correlation was strong between flowering and fruiting. Fertility variation and group coancestry were higher in poor flowering years than in abundant years},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Lindgren, D.},
	month = oct,
	year = {2017},
	pages = {85--93},
}

Fertility variation was studied in two clonal seed orchards (CSO) of teak in four consecutive years (2003-2006). Both orchards were raised in 1976 with grafts of phenotypes selected for growth and form. The seed orchards of CSO I (Topslip, Tamil Nadu State) and CSO II (Walayar, Kerala State) have 15 and 20 clones, respectively, with 13 common clones. The proportion of flowering ramets was generally low ranging from 16 to 53% across years. The best fruit yield during the study period was around 18 kg ha-1 in CSO I and 17 kg ha-1 in CSO II. Highly significant clonal variation and clone by year and clone by site interactions were observed for fertility traits. The clonal contribution was more skewed in poor flowering years than in abundant flowering years and in CSO II than in CSO I. Broad sense heritability for flower and fruit production per tree was low to moderate (0.16 to 0.55). Flower and fruit production by individual ramets in successive years were positively correlated. Correlations between reproductive and growth traits were generally low, but correlation was strong between flowering and fruiting. Fertility variation and group coancestry were higher in poor flowering years than in abundant years

@article{mullin_estimation_2017,
	title = {Estimation of {Clonal} {Variation} in {Seed} {Cone} {Production} {Over} {Time} in a {Scots} pine ({Pinus} sylvestris {L}.) {Seed} {Orchard}},
	volume = {58},
	url = {https://www.sciendo.com/article/10.1515/sg-2009-0007},
	doi = {10/gjcm9v},
	abstract = {Possibilities for early selection of clones for future seed cone production were studied in a clonal seed orchard of Scots pine (Pinus sylvestris L.) in northern Sweden over the first 30 years following establishment. The annual data were modelled as series of bivariate analyses. The correlations between cone production of clones in any individual year and that of a previous year, and cumulative cone production over all years were studied. The corresponding multivariate analysis for a full data fit simultaneously was best estimated with a genetic distance-based power model (AR). The genetic (variation among clones) and environmental variation were of the same magnitude. The genetic correlations were larger than the phenotypic correlations and both increased with orchard age. Basing selection of clones on a single observation at an early age to improve future cone production was not effective, but efficiency increased if cumulative cone count over many years was used. Year-to-year genetic correlations indicated that early forecasts by clone of cone production at mature ages are highly uncertain. Reliable predictions (moderate correlations) could be achieved only if based on rather mature grafts, 14 or more years after establishment.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Mullin, Tim J.},
	month = oct,
	year = {2017},
	pages = {53--62},
}

Possibilities for early selection of clones for future seed cone production were studied in a clonal seed orchard of Scots pine (Pinus sylvestris L.) in northern Sweden over the first 30 years following establishment. The annual data were modelled as series of bivariate analyses. The correlations between cone production of clones in any individual year and that of a previous year, and cumulative cone production over all years were studied. The corresponding multivariate analysis for a full data fit simultaneously was best estimated with a genetic distance-based power model (AR). The genetic (variation among clones) and environmental variation were of the same magnitude. The genetic correlations were larger than the phenotypic correlations and both increased with orchard age. Basing selection of clones on a single observation at an early age to improve future cone production was not effective, but efficiency increased if cumulative cone count over many years was used. Year-to-year genetic correlations indicated that early forecasts by clone of cone production at mature ages are highly uncertain. Reliable predictions (moderate correlations) could be achieved only if based on rather mature grafts, 14 or more years after establishment.

@article{salojarvi_genome_2017,
	title = {Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch},
	volume = {49},
	issn = {1061-4036, 1546-1718},
	url = {http://www.nature.com/articles/ng.3862},
	doi = {10/f96grj},
	abstract = {Abstract
            
              Silver birch (
              Betula pendula
              ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred
              B. pendula
              individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes
              PHYC
              and
              FRS10
              correlated with latitude and longitude and temperature, and with precipitation for
              PHYC
              . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes
              KAK
              and
              MED5A
              .},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Genetics},
	author = {Salojärvi, Jarkko and Smolander, Olli-Pekka and Nieminen, Kaisa and Rajaraman, Sitaram and Safronov, Omid and Safdari, Pezhman and Lamminmäki, Airi and Immanen, Juha and Lan, Tianying and Tanskanen, Jaakko and Rastas, Pasi and Amiryousefi, Ali and Jayaprakash, Balamuralikrishna and Kammonen, Juhana I and Hagqvist, Risto and Eswaran, Gugan and Ahonen, Viivi Helena and Serra, Juan Alonso and Asiegbu, Fred O and de Dios Barajas-Lopez, Juan and Blande, Daniel and Blokhina, Olga and Blomster, Tiina and Broholm, Suvi and Brosché, Mikael and Cui, Fuqiang and Dardick, Chris and Ehonen, Sanna E and Elomaa, Paula and Escamez, Sacha and Fagerstedt, Kurt V and Fujii, Hiroaki and Gauthier, Adrien and Gollan, Peter J and Halimaa, Pauliina and Heino, Pekka I and Himanen, Kristiina and Hollender, Courtney and Kangasjärvi, Saijaliisa and Kauppinen, Leila and Kelleher, Colin T and Kontunen-Soppela, Sari and Koskinen, J Patrik and Kovalchuk, Andriy and Kärenlampi, Sirpa O and Kärkönen, Anna K and Lim, Kean-Jin and Leppälä, Johanna and Macpherson, Lee and Mikola, Juha and Mouhu, Katriina and Mähönen, Ari Pekka and Niinemets, Ülo and Oksanen, Elina and Overmyer, Kirk and Palva, E Tapio and Pazouki, Leila and Pennanen, Ville and Puhakainen, Tuula and Poczai, Péter and Possen, Boy J H M and Punkkinen, Matleena and Rahikainen, Moona M and Rousi, Matti and Ruonala, Raili and van der Schoot, Christiaan and Shapiguzov, Alexey and Sierla, Maija and Sipilä, Timo P and Sutela, Suvi and Teeri, Teemu H and Tervahauta, Arja I and Vaattovaara, Aleksia and Vahala, Jorma and Vetchinnikova, Lidia and Welling, Annikki and Wrzaczek, Michael and Xu, Enjun and Paulin, Lars G and Schulman, Alan H and Lascoux, Martin and Albert, Victor A and Auvinen, Petri and Helariutta, Ykä and Kangasjärvi, Jaakko},
	month = jun,
	year = {2017},
	pages = {904--912},
}

Abstract Silver birch ( Betula pendula ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A .

@article{maurya_photoperiod-_2017,
	title = {Photoperiod- and temperature-mediated control of growth cessation and dormancy in trees: a molecular perspective},
	volume = {120},
	issn = {1095-8290},
	shorttitle = {Photoperiod- and temperature-mediated control of growth cessation and dormancy in trees},
	doi = {10/gbx6rk},
	abstract = {Background: How plants adapt their developmental patterns to regular seasonal changes is an important question in biology. The annual growth cycle in perennial long-lived trees is yet another example of how plants can adapt to seasonal changes. The two main signals that plants rely on to respond to seasonal changes are photoperiod and temperature, and these signals have critical roles in the temporal regulation of the annual growth cycle of trees.
Scope: This review presents the latest findings to provide insight into the molecular mechanisms that underlie how photoperiodic and temperature signals regulate seasonal growth in trees.
Conclusion: The results point to a high level of conservation in the signalling pathways that mediate photoperiodic control of seasonal growth in trees and flowering in annual plants such as arabidopsis. Furthermore, the data indicate that symplastic communication may mediate certain aspects of seasonal growth. Although considerable insight into the control of phenology in model plants such as poplar and spruce has been obtained, the future challenge is extending these studies to other, non-model trees.},
	language = {eng},
	number = {3},
	journal = {Annals of Botany},
	author = {Maurya, Jay P. and Bhalerao, Rishikesh P.},
	month = sep,
	year = {2017},
	pmid = {28605491},
	pmcid = {PMC5591416},
	keywords = {Hybrid aspen (Populus tremula × P. tremuloides), Photoperiod, Picea, Plant Dormancy, Populus, Seasons, Temperature, Trees, dormancy, ecodormant, endodormant, growth cessation, phenology, seasonal growth},
	pages = {351--360},
}

Background: How plants adapt their developmental patterns to regular seasonal changes is an important question in biology. The annual growth cycle in perennial long-lived trees is yet another example of how plants can adapt to seasonal changes. The two main signals that plants rely on to respond to seasonal changes are photoperiod and temperature, and these signals have critical roles in the temporal regulation of the annual growth cycle of trees. Scope: This review presents the latest findings to provide insight into the molecular mechanisms that underlie how photoperiodic and temperature signals regulate seasonal growth in trees. Conclusion: The results point to a high level of conservation in the signalling pathways that mediate photoperiodic control of seasonal growth in trees and flowering in annual plants such as arabidopsis. Furthermore, the data indicate that symplastic communication may mediate certain aspects of seasonal growth. Although considerable insight into the control of phenology in model plants such as poplar and spruce has been obtained, the future challenge is extending these studies to other, non-model trees.

@article{roach_spatially_2017,
	title = {Spatially resolved metabolic analysis reveals a central role for transcriptional control in carbon allocation to wood},
	volume = {68},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/68/13/3529/3883921},
	doi = {10/gbs95x},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Roach, Melissa and Arrivault, Stéphanie and Mahboubi, Amir and Krohn, Nicole and Sulpice, Ronan and Stitt, Mark and Niittylä, Totte},
	month = jun,
	year = {2017},
	pages = {3529--3539},
}

@article{tan_evaluating_2017,
	title = {Evaluating the accuracy of genomic prediction of growth and wood traits in two {Eucalyptus} species and their {F1} hybrids},
	volume = {17},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-1059-6},
	doi = {10/gbvt7q},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Plant Biology},
	author = {Tan, Biyue and Grattapaglia, Dario and Martins, Gustavo Salgado and Ferreira, Karina Zamprogno and Sundberg, Björn and Ingvarsson, Pär K.},
	month = dec,
	year = {2017},
	pages = {110},
}

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

@article{kacprzyk_retraction_2017,
	title = {The retraction of the protoplast during {PCD} is an active, and interruptible, calcium-flux driven process},
	volume = {260},
	issn = {01689452},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168945217300717},
	doi = {10/gbjxkx},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Science},
	author = {Kacprzyk, Joanna and Brogan, Niall P. and Daly, Cara T. and Doyle, Siamsa M. and Diamond, Mark and Molony, Elizabeth M. and McCabe, Paul F.},
	month = jul,
	year = {2017},
	pages = {50--59},
}

@article{maaroufi_nitrogen_2017,
	title = {Nitrogen enrichment impacts on boreal litter decomposition are driven by changes in soil microbiota rather than litter quality},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-04523-w},
	doi = {10/gbnjm6},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Maaroufi, Nadia I. and Nordin, Annika and Palmqvist, Kristin and Gundale, Michael J.},
	month = dec,
	year = {2017},
	pages = {4083},
}

@article{fries_damage_2017,
	title = {Damage by pathogens and insects to {Scots} pine and lodgepole pine 25 years after reciprocal plantings in {Canada} and {Sweden}},
	volume = {32},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2016.1247463},
	doi = {10/f94bmc},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Fries, Anders},
	month = aug,
	year = {2017},
	pages = {459--472},
}

@article{minina_metacaspases_2017,
	title = {Metacaspases versus caspases in development and cell fate regulation},
	volume = {24},
	issn = {1350-9047, 1476-5403},
	url = {http://www.nature.com/articles/cdd201718},
	doi = {10/f9rg58},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Cell Death \& Differentiation},
	author = {Minina, E A and Coll, N S and Tuominen, H and Bozhkov, P V},
	month = aug,
	year = {2017},
	pages = {1314--1325},
}

@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{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{di_mambro_auxin_2017,
	title = {Auxin minimum triggers the developmental switch from cell division to cell differentiation in the \textit{{Arabidopsis}} root},
	volume = {114},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1705833114},
	doi = {10/gbwhtt},
	abstract = {In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the
              Arabidopsis
              root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin’s control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.},
	language = {en},
	number = {36},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Di Mambro, Riccardo and De Ruvo, Micol and Pacifici, Elena and Salvi, Elena and Sozzani, Rosangela and Benfey, Philip N. and Busch, Wolfgang and Novak, Ondrej and Ljung, Karin and Di Paola, Luisa and Marée, Athanasius F. M. and Costantino, Paolo and Grieneisen, Verônica A. and Sabatini, Sabrina},
	month = sep,
	year = {2017},
	pages = {E7641--E7649},
}

In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin’s control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.

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

@article{decker_substrate_2017,
	title = {Substrate {Specificity} and {Inhibitor} {Sensitivity} of {Plant} {UDP}-{Sugar} {Producing} {Pyrophosphorylases}},
	volume = {8},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2017.01610/full},
	doi = {10/gcjkns},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Decker, Daniel and Kleczkowski, Leszek A.},
	month = sep,
	year = {2017},
	pages = {1610},
}

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

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

@article{yazdanpanah_differentially_2017,
	title = {Differentially expressed genes during the imbibition of dormant and after-ripened seeds – a reverse genetics approach},
	volume = {17},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-1098-z},
	doi = {10/gbx65c},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Plant Biology},
	author = {Yazdanpanah, Farzaneh and Hanson, Johannes and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = dec,
	year = {2017},
	pages = {151},
}

@article{adolfsson_enhanced_2017,
	title = {Enhanced {Secondary}- and {Hormone} {Metabolism} in {Leaves} of {Arbuscular} {Mycorrhizal} \textit{{Medicago} truncatula}},
	volume = {175},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/175/1/392-411/6117013},
	doi = {10/gbvxq8},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Adolfsson, Lisa and Nziengui, Hugues and Abreu, Ilka N and Šimura, Jan and Beebo, Azeez and Herdean, Andrei and Aboalizadeh, Jila and Široká, Jitka and Moritz, Thomas and Novák, Ondřej and Ljung, Karin and Schoefs, Benoît and Spetea, Cornelia},
	month = sep,
	year = {2017},
	pages = {392--411},
}

@article{martins_brassinosteroid_2017,
	title = {Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature},
	volume = {8},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-017-00355-4},
	doi = {10/gbttbb},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Martins, Sara and Montiel-Jorda, Alvaro and Cayrel, Anne and Huguet, Stéphanie and Roux, Christine Paysant-Le and Ljung, Karin and Vert, Grégory},
	month = dec,
	year = {2017},
	pages = {309},
}

@article{kloth_sieve_2017,
	title = {{SIEVE} {ELEMENT}-{LINING} {CHAPERONE1} {Restricts} {Aphid} {Feeding} on {Arabidopsis} during {Heat} {Stress}},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/29/10/2450-2464/6100440},
	doi = {10/gckrdb},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Kloth, Karen J. and Busscher-Lange, Jacqueline and Wiegers, Gerrie L. and Kruijer, Willem and Buijs, Gonda and Meyer, Rhonda C. and Albrectsen, Benedicte R. and Bouwmeester, Harro J. and Dicke, Marcel and Jongsma, Maarten A.},
	month = oct,
	year = {2017},
	pages = {2450--2464},
}

@article{mao_arabidopsis_2017,
	title = {Arabidopsis {BTB}/{POZ} protein-dependent {PENETRATION3} trafficking and disease susceptibility},
	volume = {3},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-017-0039-z},
	doi = {10/gcpsmb},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Mao, Hailiang and Aryal, Bibek and Langenecker, Tobias and Hagmann, Jörg and Geisler, Markus and Grebe, Markus},
	month = nov,
	year = {2017},
	pages = {854--858},
}

@article{capovilla_contribution_2017,
	title = {Contribution of major {FLM} isoforms to temperature-dependent flowering in {Arabidopsis} thaliana},
	volume = {68},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/68/18/5117/4210925},
	doi = {10/gcjrww},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Capovilla, Giovanna and Symeonidi, Efthymia and Wu, Rui and Schmid, Markus},
	month = nov,
	year = {2017},
	pages = {5117--5127},
}

@article{oyewole_incorporating_2017,
	title = {Incorporating mass flow strongly promotes {N} flux rates in boreal forest soils},
	volume = {114},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071716307684},
	doi = {10/gbzwvh},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Oyewole, Olusegun Ayodeji and Inselsbacher, Erich and Näsholm, Torgny and Jämtgård, Sandra},
	month = nov,
	year = {2017},
	pages = {263--269},
}

@article{majda_mechanochemical_2017,
	title = {Mechanochemical {Polarization} of {Contiguous} {Cell} {Walls} {Shapes} {Plant} {Pavement} {Cells}},
	volume = {43},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580717308304},
	doi = {10/gcjnxj},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Developmental Cell},
	author = {Majda, Mateusz and Grones, Peter and Sintorn, Ida-Maria and Vain, Thomas and Milani, Pascale and Krupinski, Pawel and Zagórska-Marek, Beata and Viotti, Corrado and Jönsson, Henrik and Mellerowicz, Ewa J. and Hamant, Olivier and Robert, Stéphanie},
	month = nov,
	year = {2017},
	pages = {290--304.e4},
}

@article{zas_genetic_2017,
	title = {Genetic variation in resistance of {Norway} spruce seedlings to damage by the pine weevil {Hylobius} abietis},
	volume = {13},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-017-1193-1},
	doi = {10/gcps32},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Zas, Rafael and Björklund, Niklas and Sampedro, Luis and Hellqvist, Claes and Karlsson, Bo and Jansson, Stefan and Nordlander, Göran},
	month = oct,
	year = {2017},
	pages = {111},
}

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

@article{buckley_improving_2017,
	title = {Improving in situ recovery of soil nitrogen using the microdialysis technique},
	volume = {114},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071717305357},
	doi = {10/gbzt4z},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Buckley, Scott and Brackin, Richard and Näsholm, Torgny and Schmidt, Susanne and Jämtgård, Sandra},
	month = nov,
	year = {2017},
	pages = {93--103},
}

@article{nummelin_forest_2017,
	title = {Forest future s by {Swedish} students – developing a mind mapping method for data collection},
	volume = {32},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2017.1287303},
	doi = {10/gbv2r6},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Nummelin, Tuomas and Widmark, Camilla and Riala, Maria and Sténs, Anna and Nordström, Eva-Maria and Nordin, Annika},
	month = nov,
	year = {2017},
	pages = {807--817},
}

@article{dubreuil_quantitative_2017,
	title = {A quantitative model of the phytochrome-{PIF} light signalling initiating chloroplast development},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-13473-2},
	doi = {10/gchdr4},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Dubreuil, Carole and Ji, Yan and Strand, Åsa and Grönlund, Andreas},
	month = dec,
	year = {2017},
	pages = {13884},
}

@article{mishra_active-site_2017,
	title = {Active-site plasticity revealed in the asymmetric dimer of {AnPrx6} the 1-{Cys} peroxiredoxin and molecular chaperone from {Anabaena} sp. {PCC} 7120},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-17044-3},
	doi = {10/gc2fwt},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Mishra, Yogesh and Hall, Michael and Locmelis, Roland and Nam, Kwangho and Söderberg, Christopher A. G. and Storm, Patrik and Chaurasia, Neha and Rai, Lal Chand and Jansson, Stefan and Schröder, Wolfgang P. and Sauer, Uwe H.},
	month = dec,
	year = {2017},
	pages = {17151},
}

@article{escamez_collection_2017,
	title = {A collection of genetically engineered {Populus} trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-16013-0},
	doi = {10/gcmn8b},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Escamez, Sacha and Latha Gandla, Madhavi and Derba-Maceluch, Marta and Lundqvist, Sven-Olof and Mellerowicz, Ewa J. and Jönsson, Leif J. and Tuominen, Hannele},
	month = dec,
	year = {2017},
	pages = {15798},
}

@article{yan_type_2017,
	title = {Type {B} {Response} {Regulators} {Act} {As} {Central} {Integrators} in {Transcriptional} {Control} of the {Auxin} {Biosynthesis} {Enzyme} {TAA1}},
	volume = {175},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/175/3/1438-1454/6117004},
	doi = {10/gckj69},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Yan, Zhenwei and Liu, Xin and Ljung, Karin and Li, Shuning and Zhao, Wanying and Yang, Fan and Wang, Meiling and Tao, Yi},
	month = nov,
	year = {2017},
	pages = {1438--1454},
}

@article{franklin_carbon_2017,
	title = {The carbon bonus of organic nitrogen enhances nitrogen use efficiency of plants: {The} carbon bonus of organic nitrogen},
	volume = {40},
	issn = {01407791},
	shorttitle = {The carbon bonus of organic nitrogen enhances nitrogen use efficiency of plants},
	url = {http://doi.wiley.com/10.1111/pce.12772},
	doi = {10/f9grn5},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Franklin, Oskar and Cambui, Camila Aguetoni and Gruffman, Linda and Palmroth, Sari and Oren, Ram and Näsholm, Torgny},
	month = jan,
	year = {2017},
	pages = {25--35},
}

@article{metcalfe_informing_2017,
	title = {Informing climate models with rapid chamber measurements of forest carbon uptake},
	volume = {23},
	issn = {13541013},
	url = {http://doi.wiley.com/10.1111/gcb.13451},
	doi = {10/f3vbr8},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {Metcalfe, Daniel B. and Ricciuto, Daniel and Palmroth, Sari and Campbell, Catherine and Hurry, Vaughan and Mao, Jiafu and Keel, Sonja G. and Linder, Sune and Shi, Xiaoying and Näsholm, Torgny and Ohlsson, Klas E. A. and Blackburn, M. and Thornton, Peter E. and Oren, Ram},
	month = may,
	year = {2017},
	pages = {2130--2139},
}

@article{soler_eucalyptus_2017,
	title = {The \textit{{Eucalyptus}} linker histone variant {EgH1}.3 cooperates with the transcription factor {EgMYB1} to control lignin biosynthesis during wood formation},
	volume = {213},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14129},
	doi = {10/f3t5cj},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Soler, Marçal and Plasencia, Anna and Larbat, Romain and Pouzet, Cécile and Jauneau, Alain and Rivas, Susana and Pesquet, Edouard and Lapierre, Catherine and Truchet, Isabelle and Grima‐Pettenati, Jacqueline},
	month = jan,
	year = {2017},
	pages = {287--299},
}

@article{osullivan_thermal_2017,
	title = {Thermal limits of leaf metabolism across biomes},
	volume = {23},
	issn = {13541013},
	url = {http://doi.wiley.com/10.1111/gcb.13477},
	doi = {10/f9hd2s},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {O'sullivan, Odhran S. and Heskel, Mary A. and Reich, Peter B. and Tjoelker, Mark G. and Weerasinghe, Lasantha K. and Penillard, Aurore and Zhu, Lingling and Egerton, John J. G. and Bloomfield, Keith J. and Creek, Danielle and Bahar, Nur H. A. and Griffin, Kevin L. and Hurry, Vaughan and Meir, Patrick and Turnbull, Matthew H. and Atkin, Owen K.},
	month = jan,
	year = {2017},
	pages = {209--223},
}

@article{bandau_genotypic_2017,
	title = {Genotypic variability in {Populus} tremula {L}. affects how anthropogenic nitrogen enrichment influences litter decomposition},
	volume = {410},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-016-3033-8},
	doi = {10/f9n2mz},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Plant and Soil},
	author = {Bandau, Franziska and Albrectsen, Benedicte Riber and Julkunen-Tiitto, Riitta and Gundale, Michael J.},
	month = jan,
	year = {2017},
	pages = {467--481},
}

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

@article{rende_cytosolic_2017,
	title = {Cytosolic invertase contributes to the supply of substrate for cellulose biosynthesis in developing wood},
	volume = {214},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14392},
	doi = {10.1111/nph.14392},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Rende, Umut and Wang, Wei and Gandla, Madhavi Latha and Jönsson, Leif J. and Niittylä, Totte},
	month = apr,
	year = {2017},
	pages = {796--807},
}

@article{baena-gonzalez_shaping_2017,
	title = {Shaping plant development through the {SnRK1}–{TOR} metabolic regulators},
	volume = {35},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526616302242},
	doi = {10.1016/j.pbi.2016.12.004},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Baena-González, Elena and Hanson, Johannes},
	month = feb,
	year = {2017},
	pages = {152--157},
}

@article{bai_extensive_2017,
	title = {Extensive translational regulation during seed germination revealed by polysomal profiling},
	volume = {214},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14355},
	doi = {10.1111/nph.14355},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Bing and Peviani, Alessia and Horst, Sjors and Gamm, Magdalena and Snel, Berend and Bentsink, Leónie and Hanson, Johannes},
	month = apr,
	year = {2017},
	pages = {233--244},
}

@article{escamez_contribution_2017,
	title = {Contribution of cellular autolysis to tissular functions during plant development},
	volume = {35},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526616302126},
	doi = {10.1016/j.pbi.2016.11.017},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Escamez, Sacha and Tuominen, Hannele},
	month = feb,
	year = {2017},
	pages = {124--130},
}

@article{ganeteg_amino_2017,
	title = {Amino acid transporter mutants of \textit{{Arabidopsis}} provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil: {Organic} nitrogen uptake by {Arabidopsis} mutants},
	volume = {40},
	issn = {01407791},
	shorttitle = {Amino acid transporter mutants of \textit{{Arabidopsis}} provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil},
	url = {http://doi.wiley.com/10.1111/pce.12881},
	doi = {10.1111/pce.12881},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Ganeteg, Ulrika and Ahmad, Iftikhar and Jämtgård, Sandra and Aguetoni-Cambui, Camila and Inselsbacher, Erich and Svennerstam, Henrik and Schmidt, Susanne and Näsholm, Torgny},
	month = mar,
	year = {2017},
	pages = {413--423},
}

@article{bhalerao_environmental_2017,
	title = {Environmental and hormonal control of cambial stem cell dynamics},
	volume = {68},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw466},
	doi = {10.1093/jxb/erw466},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Bhalerao, Rishikesh P. and Fischer, Urs},
	month = jan,
	year = {2017},
	pages = {79--87},
}

@article{lesniewska_defense_2017,
	title = {Defense {Responses} in {Aspen} with {Altered} {Pectin} {Methylesterase} {Activity} {Reveal} the {Hormonal} {Inducers} of {Tyloses}},
	volume = {173},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/173/2/1409-1419/6116100},
	doi = {10.1104/pp.16.01443},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Leśniewska, Joanna and Öhman, David and Krzesłowska, Magdalena and Kushwah, Sunita and Barciszewska-Pacak, Maria and Kleczkowski, Leszek A. and Sundberg, Björn and Moritz, Thomas and Mellerowicz, Ewa J.},
	month = feb,
	year = {2017},
	pages = {1409--1419},
}

@incollection{kleine-vehn_high-resolution_2017,
	address = {New York, NY},
	title = {High-{Resolution} {Cell}-{Type} {Specific} {Analysis} of {Cytokinins} in {Sorted} {Root} {Cell} {Populations} of {Arabidopsis} thaliana},
	volume = {1497},
	isbn = {978-1-4939-6467-3 978-1-4939-6469-7},
	url = {http://link.springer.com/10.1007/978-1-4939-6469-7_19},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Plant {Hormones}},
	publisher = {Springer New York},
	author = {Novák, Ondřej and Antoniadi, Ioanna and Ljung, Karin},
	editor = {Kleine-Vehn, Jürgen and Sauer, Michael},
	year = {2017},
	doi = {10.1007/978-1-4939-6469-7_19},
	note = {Series Title: Methods in Molecular Biology},
	pages = {231--248},
}

@article{keech_redox_2017,
	title = {The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations},
	volume = {40},
	issn = {0140-7791, 1365-3040},
	shorttitle = {The redox control of photorespiration},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12713},
	doi = {10.1111/pce.12713},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Keech, Olivier and Gardeström, Per and Kleczkowski, Leszek A. and Rouhier, Nicolas},
	month = apr,
	year = {2017},
	pages = {553--569},
}

@article{robertson_lineage-specific_2017,
	title = {Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification},
	volume = {18},
	issn = {1474-760X},
	url = {http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1241-z},
	doi = {10.1186/s13059-017-1241-z},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Genome Biology},
	author = {Robertson, Fiona M. and Gundappa, Manu Kumar and Grammes, Fabian and Hvidsten, Torgeir R. and Redmond, Anthony K. and Lien, Sigbjørn and Martin, Samuel A. M. and Holland, Peter W. H. and Sandve, Simen R. and Macqueen, Daniel J.},
	month = dec,
	year = {2017},
	pages = {111},
}

@incollection{fernie_vitro_2017,
	address = {New York, NY},
	title = {In {Vitro} {Alkylation} {Methods} for {Assessing} the {Protein} {Redox} {State}},
	volume = {1653},
	isbn = {978-1-4939-7224-1 978-1-4939-7225-8},
	url = {http://link.springer.com/10.1007/978-1-4939-7225-8_4},
	urldate = {2021-06-07},
	booktitle = {Photorespiration},
	publisher = {Springer New York},
	author = {Zannini, Flavien and Couturier, Jérémy and Keech, Olivier and Rouhier, Nicolas},
	editor = {Fernie, Alisdair R. and Bauwe, Hermann and Weber, Andreas P.M.},
	year = {2017},
	doi = {10.1007/978-1-4939-7225-8_4},
	note = {Series Title: Methods in Molecular Biology},
	pages = {51--64},
}

@article{bygdell_protein_2017,
	title = {Protein expression in tension wood formation monitored at high tissue resolution in {Populus}},
	volume = {68},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/68/13/3405/3867560},
	doi = {10.1093/jxb/erx186},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Bygdell, Joakim and Srivastava, Vaibhav and Obudulu, Ogonna and Srivastava, Manoj K and Nilsson, Robert and Sundberg, Björn and Trygg, Johan and Mellerowicz, Ewa J and Wingsle, Gunnar},
	month = jun,
	year = {2017},
	pages = {3405--3417},
}

@article{jonsson_ethylene_2017,
	title = {Ethylene {Regulates} {Differential} {Growth} via {BIG} {ARF}-{GEF}-{Dependent} {Post}-{Golgi} {Secretory} {Trafficking} in {Arabidopsis}},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/29/5/1039-1052/6099211},
	doi = {10.1105/tpc.16.00743},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Jonsson, Kristoffer and Boutté, Yohann and Singh, Rajesh Kumar and Gendre, Delphine and Bhalerao, Rishikesh P.},
	month = may,
	year = {2017},
	pages = {1039--1052},
}

@article{ingvarsson_small-_2017,
	title = {Small- and large-scale heterogeneity in genetic variation across the collard flycatcher genome: implications for estimating genetic diversity in nonmodel organisms},
	volume = {17},
	issn = {1755098X},
	shorttitle = {Small- and large-scale heterogeneity in genetic variation across the collard flycatcher genome},
	url = {http://doi.wiley.com/10.1111/1755-0998.12632},
	doi = {10.1111/1755-0998.12632},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Molecular Ecology Resources},
	author = {Ingvarsson, Pär K. and Wang, Jing},
	month = jul,
	year = {2017},
	pages = {583--585},
}

@article{giacomello_spatially_2017,
	title = {Spatially resolved transcriptome profiling in model plant species},
	volume = {3},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/nplants201761},
	doi = {10.1038/nplants.2017.61},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Giacomello, Stefania and Salmén, Fredrik and Terebieniec, Barbara K. and Vickovic, Sanja and Navarro, José Fernandez and Alexeyenko, Andrey and Reimegård, Johan and McKee, Lauren S. and Mannapperuma, Chanaka and Bulone, Vincent and Ståhl, Patrik L. and Sundström, Jens F. and Street, Nathaniel R. and Lundeberg, Joakim},
	month = jun,
	year = {2017},
	pages = {17061},
}

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

@article{conn_circrna_2017,
	title = {A {circRNA} from {SEPALLATA3} regulates splicing of its cognate {mRNA} through {R}-loop formation},
	volume = {3},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/nplants201753},
	doi = {10.1038/nplants.2017.53},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Conn, Vanessa M. and Hugouvieux, Véronique and Nayak, Aditya and Conos, Stephanie A. and Capovilla, Giovanna and Cildir, Gökhan and Jourdain, Agnès and Tergaonkar, Vinay and Schmid, Markus and Zubieta, Chloe and Conn, Simon J.},
	month = may,
	year = {2017},
	pages = {17053},
}

@article{you_temporal_2017,
	title = {Temporal dynamics of gene expression and histone marks at the {Arabidopsis} shoot meristem during flowering},
	volume = {8},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms15120},
	doi = {10.1038/ncomms15120},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {You, Yuan and Sawikowska, Aneta and Neumann, Manuela and Posé, David and Capovilla, Giovanna and Langenecker, Tobias and Neher, Richard A. and Krajewski, Paweł and Schmid, Markus},
	month = aug,
	year = {2017},
	pages = {15120},
}

@article{pawar_muro_2017,
	title = {In muro deacetylation of xylan affects lignin properties and improves saccharification of aspen wood},
	volume = {10},
	issn = {1754-6834},
	url = {http://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-017-0782-4},
	doi = {10.1186/s13068-017-0782-4},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Biotechnology for Biofuels},
	author = {Pawar, Prashant Mohan-Anupama and Derba-Maceluch, Marta and Chong, Sun-Li and Gandla, Madhavi Latha and Bashar, Shamrat Shafiul and Sparrman, Tobias and Ahvenainen, Patrik and Hedenström, Mattias and Özparpucu, Merve and Rüggeberg, Markus and Serimaa, Ritva and Lawoko, Martin and Tenkanen, Maija and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	month = dec,
	year = {2017},
	pages = {98},
}

@article{miranda_sll1783_2017,
	title = {Sll1783, a monooxygenase associated with polysaccharide processing in the unicellular cyanobacterium \textit{{Synechocystis}} {PCC} 6803},
	volume = {161},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12582},
	doi = {10.1111/ppl.12582},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Miranda, Hélder and Immerzeel, Peter and Gerber, Lorenz and Hörnaeus, Katarina and Lind, Sara Bergström and Pattanaik, Bagmi and Lindberg, Pia and Mamedov, Fikret and Lindblad, Peter},
	month = oct,
	year = {2017},
	pages = {182--195},
}

@article{fallath_mediator18_2017,
	title = {{MEDIATOR18} and {MEDIATOR20} confer susceptibility to {Fusarium} oxysporum in {Arabidopsis} thaliana},
	volume = {12},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0176022},
	doi = {10.1371/journal.pone.0176022},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Fallath, Thorya and Kidd, Brendan N. and Stiller, Jiri and Davoine, Celine and Björklund, Stefan and Manners, John M. and Kazan, Kemal and Schenk, Peer M.},
	editor = {Wu, Keqiang},
	month = apr,
	year = {2017},
	pages = {e0176022},
}

@article{tolu_spatial_2017,
	title = {Spatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal {Swedish} lake},
	volume = {14},
	issn = {1726-4189},
	url = {https://bg.copernicus.org/articles/14/1773/2017/},
	doi = {10.5194/bg-14-1773-2017},
	abstract = {Abstract. The composition of sediment organic matter (OM) exerts a strong control on biogeochemical processes in lakes, such as those involved in the fate of carbon, nutrients and trace metals. While between-lake spatial variability of OM quality is increasingly investigated, we explored in this study how the molecular composition of sediment OM varies spatially within a single lake and related this variability to physical parameters and elemental geochemistry. Surface sediment samples (0–10 cm) from 42 locations in Härsvatten – a small boreal forest lake with a complex basin morphometry – were analyzed for OM molecular composition using pyrolysis gas chromatography mass spectrometry for the contents of 23 major and trace elements and biogenic silica. We identified 162 organic compounds belonging to different biochemical classes of OM (e.g., carbohydrates, lignin and lipids). Close relationships were found between the spatial patterns of sediment OM molecular composition and elemental geochemistry. Differences in the source types of OM (i.e., terrestrial, aquatic plant and algal) were linked to the individual basin morphometries and chemical status of the lake. The variability in OM molecular composition was further driven by the degradation status of these different source pools, which appeared to be related to sedimentary physicochemical parameters (e.g., redox conditions) and to the molecular structure of the organic compounds. Given the high spatial variation in OM molecular composition within Härsvatten and its close relationship with elemental geochemistry, the potential for large spatial variability across lakes should be considered when studying biogeochemical processes involved in the cycling of carbon, nutrients and trace elements or when assessing lake budgets.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Biogeosciences},
	author = {Tolu, Julie and Rydberg, Johan and Meyer-Jacob, Carsten and Gerber, Lorenz and Bindler, Richard},
	month = apr,
	year = {2017},
	pages = {1773--1792},
}

Abstract. The composition of sediment organic matter (OM) exerts a strong control on biogeochemical processes in lakes, such as those involved in the fate of carbon, nutrients and trace metals. While between-lake spatial variability of OM quality is increasingly investigated, we explored in this study how the molecular composition of sediment OM varies spatially within a single lake and related this variability to physical parameters and elemental geochemistry. Surface sediment samples (0–10 cm) from 42 locations in Härsvatten – a small boreal forest lake with a complex basin morphometry – were analyzed for OM molecular composition using pyrolysis gas chromatography mass spectrometry for the contents of 23 major and trace elements and biogenic silica. We identified 162 organic compounds belonging to different biochemical classes of OM (e.g., carbohydrates, lignin and lipids). Close relationships were found between the spatial patterns of sediment OM molecular composition and elemental geochemistry. Differences in the source types of OM (i.e., terrestrial, aquatic plant and algal) were linked to the individual basin morphometries and chemical status of the lake. The variability in OM molecular composition was further driven by the degradation status of these different source pools, which appeared to be related to sedimentary physicochemical parameters (e.g., redox conditions) and to the molecular structure of the organic compounds. Given the high spatial variation in OM molecular composition within Härsvatten and its close relationship with elemental geochemistry, the potential for large spatial variability across lakes should be considered when studying biogeochemical processes involved in the cycling of carbon, nutrients and trace elements or when assessing lake budgets.

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

@article{steenackers_cis-cinnamic_2017,
	title = {cis-{Cinnamic} {Acid} {Is} a {Novel}, {Natural} {Auxin} {Efflux} {Inhibitor} {That} {Promotes} {Lateral} {Root} {Formation}},
	volume = {173},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/173/1/552-565/6116022},
	doi = {10.1104/pp.16.00943},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Steenackers, Ward and Klíma, Petr and Quareshy, Mussa and Cesarino, Igor and Kumpf, Robert P. and Corneillie, Sander and Araújo, Pedro and Viaene, Tom and Goeminne, Geert and Nowack, Moritz K. and Ljung, Karin and Friml, Jiří and Blakeslee, Joshua J. and Novák, Ondřej and Zažímalová, Eva and Napier, Richard and Boerjan, Wout and Vanholme, Bartel},
	month = jan,
	year = {2017},
	pages = {552--565},
}

@article{sun_altered_2017,
	title = {Altered expression of maize {PLASTOCHRON1} enhances biomass and seed yield by extending cell division duration},
	volume = {8},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms14752},
	doi = {10.1038/ncomms14752},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Sun, Xiaohuan and Cahill, James and Van Hautegem, Tom and Feys, Kim and Whipple, Clinton and Novák, Ondrej and Delbare, Sofie and Versteele, Charlot and Demuynck, Kirin and De Block, Jolien and Storme, Veronique and Claeys, Hannes and Van Lijsebettens, Mieke and Coussens, Griet and Ljung, Karin and De Vliegher, Alex and Muszynski, Michael and Inzé, Dirk and Nelissen, Hilde},
	month = apr,
	year = {2017},
	pages = {14752},
}

@article{poxson_regulating_2017,
	title = {Regulating plant physiology with organic electronics},
	volume = {114},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1617758114},
	doi = {10.1073/pnas.1617758114},
	abstract = {The organic electronic ion pump (OEIP) provides flow-free and accurate delivery of small signaling compounds at high spatiotemporal resolution. To date, the application of OEIPs has been limited to delivery of nonaromatic molecules to mammalian systems, particularly for neuroscience applications. However, many long-standing questions in plant biology remain unanswered due to a lack of technology that precisely delivers plant hormones, based on cyclic alkanes or aromatic structures, to regulate plant physiology. Here, we report the employment of OEIPs for the delivery of the plant hormone auxin to induce differential concentration gradients and modulate plant physiology. We fabricated OEIP devices based on a synthesized dendritic polyelectrolyte that enables electrophoretic transport of aromatic substances. Delivery of auxin to transgenic
              Arabidopsis thaliana
              seedlings in vivo was monitored in real time via dynamic fluorescent auxin-response reporters and induced physiological responses in roots. Our results provide a starting point for technologies enabling direct, rapid, and dynamic electronic interaction with the biochemical regulation systems of plants.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Poxson, David J. and Karady, Michal and Gabrielsson, Roger and Alkattan, Aziz Y. and Gustavsson, Anna and Doyle, Siamsa M. and Robert, Stéphanie and Ljung, Karin and Grebe, Markus and Simon, Daniel T. and Berggren, Magnus},
	month = may,
	year = {2017},
	pages = {4597--4602},
}

The organic electronic ion pump (OEIP) provides flow-free and accurate delivery of small signaling compounds at high spatiotemporal resolution. To date, the application of OEIPs has been limited to delivery of nonaromatic molecules to mammalian systems, particularly for neuroscience applications. However, many long-standing questions in plant biology remain unanswered due to a lack of technology that precisely delivers plant hormones, based on cyclic alkanes or aromatic structures, to regulate plant physiology. Here, we report the employment of OEIPs for the delivery of the plant hormone auxin to induce differential concentration gradients and modulate plant physiology. We fabricated OEIP devices based on a synthesized dendritic polyelectrolyte that enables electrophoretic transport of aromatic substances. Delivery of auxin to transgenic Arabidopsis thaliana seedlings in vivo was monitored in real time via dynamic fluorescent auxin-response reporters and induced physiological responses in roots. Our results provide a starting point for technologies enabling direct, rapid, and dynamic electronic interaction with the biochemical regulation systems of plants.

@article{mahler_gene_2017,
	title = {Gene co-expression network connectivity is an important determinant of selective constraint},
	volume = {13},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1006402},
	doi = {10.1371/journal.pgen.1006402},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Mähler, Niklas and Wang, Jing and Terebieniec, Barbara K. and Ingvarsson, Pär K. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	editor = {Springer, Nathan M.},
	month = apr,
	year = {2017},
	pages = {e1006402},
}

@article{le_hir_at_2017,
	title = {At \textit{{bHLH68}} transcription factor contributes to the regulation of {ABA} homeostasis and drought stress tolerance in \textit{{Arabidopsis} thaliana}},
	volume = {160},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12549},
	doi = {10.1111/ppl.12549},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Le Hir, Rozenn and Castelain, Mathieu and Chakraborti, Dipankar and Moritz, Thomas and Dinant, Sylvie and Bellini, Catherine},
	month = jul,
	year = {2017},
	pages = {312--327},
}

@article{pacurar_arabidopsis_2017,
	title = {The {Arabidopsis} {Cop9} signalosome subunit 4 ({CSN4}) is involved in adventitious root formation},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-00744-1},
	doi = {10.1038/s41598-017-00744-1},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Pacurar, Daniel Ioan and Pacurar, Monica Lacramioara and Lakehal, Abdellah and Pacurar, Andrea Mariana and Ranjan, Alok and Bellini, Catherine},
	month = dec,
	year = {2017},
	pages = {628},
}

@article{sullivan_interspecific_2017,
	title = {Interspecific {Plastome} {Recombination} {Reflects} {Ancient} {Reticulate} {Evolution} in {Picea} ({Pinaceae})},
	volume = {34},
	issn = {0737-4038, 1537-1719},
	url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msx111},
	doi = {10.1093/molbev/msx111},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Molecular Biology and Evolution},
	author = {Sullivan, Alexis R. and Schiffthaler, Bastian and Thompson, Stacey Lee and Street, Nathaniel R. and Wang, Xiao-Ru},
	month = jul,
	year = {2017},
	pages = {1689--1701},
}

@article{ge_shade_2017,
	title = {{SHADE} {AVOIDANCE} 4 {Is} {Required} for {Proper} {Auxin} {Distribution} in the {Hypocotyl}},
	volume = {173},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/173/1/788-800/6116141},
	doi = {10.1104/pp.16.01491},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Ge, Yanhua and Yan, Fenglian and Zourelidou, Melina and Wang, Meiling and Ljung, Karin and Fastner, Astrid and Hammes, Ulrich Z. and Di Donato, Martin and Geisler, Markus and Schwechheimer, Claus and Tao, Yi},
	month = jan,
	year = {2017},
	pages = {788--800},
}

@article{pawar_downregulation_2017,
	title = {Downregulation of {RWA} genes in hybrid aspen affects xylan acetylation and wood saccharification},
	volume = {214},
	copyright = {© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.14489},
	doi = {https://doi.org/10.1111/nph.14489},
	abstract = {High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter::GUS lines in hybrid aspen (Populus tremula × tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25\% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Pawar, Prashant Mohan-Anupama and Ratke, Christine and Balasubramanian, Vimal K. and Chong, Sun-Li and Gandla, Madhavi Latha and Adriasola, Mathilda and Sparrman, Tobias and Hedenström, Mattias and Szwaj, Klaudia and Derba-Maceluch, Marta and Gaertner, Cyril and Mouille, Gregory and Ezcurra, Ines and Tenkanen, Maija and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	year = {2017},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14489},
	keywords = {Cas1p, Populus, REDUCED CELL WALL ACETYLATION, saccharification, wood acetylation, xylan, xylan acetylation, xylem},
	pages = {1491--1505},
}

High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter::GUS lines in hybrid aspen (Populus tremula × tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.

@article{pawar_downregulation_2017,
	title = {Downregulation of {\textless}span style="font-variant:small-caps;"{\textgreater}{RWA}{\textless}/span{\textgreater} genes in hybrid aspen affects xylan acetylation and wood saccharification},
	volume = {214},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Downregulation of {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14489},
	doi = {10.1111/nph.14489},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Pawar, Prashant Mohan‐Anupama and Ratke, Christine and Balasubramanian, Vimal K. and Chong, Sun‐Li and Gandla, Madhavi Latha and Adriasola, Mathilda and Sparrman, Tobias and Hedenström, Mattias and Szwaj, Klaudia and Derba‐Maceluch, Marta and Gaertner, Cyril and Mouille, Gregory and Ezcurra, Ines and Tenkanen, Maija and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	month = jun,
	year = {2017},
	pages = {1491--1505},
}

@article{novak_zooming_2017,
	title = {Zooming {In} on {Plant} {Hormone} {Analysis}: {Tissue}- and {Cell}-{Specific} {Approaches}},
	volume = {68},
	issn = {1543-5008, 1545-2123},
	shorttitle = {Zooming {In} on {Plant} {Hormone} {Analysis}},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-042916-040812},
	doi = {10.1146/annurev-arplant-042916-040812},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annual Review of Plant Biology},
	author = {Novák, Ondřej and Napier, Richard and Ljung, Karin},
	month = apr,
	year = {2017},
	pages = {323--348},
}

@article{norman_landscape_2017,
	title = {Landscape relatedness: detecting contemporary fine-scale spatial structure in wild populations},
	volume = {32},
	issn = {0921-2973, 1572-9761},
	shorttitle = {Landscape relatedness},
	url = {http://link.springer.com/10.1007/s10980-016-0434-2},
	doi = {10.1007/s10980-016-0434-2},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Landscape Ecology},
	author = {Norman, Anita J. and Stronen, Astrid V. and Fuglstad, Geir-Arne and Ruiz-Gonzalez, Aritz and Kindberg, Jonas and Street, Nathaniel R. and Spong, Göran},
	month = jan,
	year = {2017},
	pages = {181--194},
}

@article{vernoux_auxin_2017,
	title = {Auxin 2016: a burst of auxin in the warm south of {China}},
	volume = {144},
	issn = {1477-9129, 0950-1991},
	shorttitle = {Auxin 2016},
	url = {https://journals.biologists.com/dev/article/144/4/533/48302/Auxin-2016-a-burst-of-auxin-in-the-warm-south-of},
	doi = {10.1242/dev.144790},
	abstract = {The luxurious vegetation at Sanya, the most southern location in China on the island of Hainan, provided a perfect environment for the ‘Auxin 2016’ meeting in October. As we review here, participants from all around the world discussed the latest advances in auxin transport, metabolism and signaling pathways, highlighting how auxin acts during plant development and in response to the environment in combination with other hormones. The meeting also provided a rich perspective on the evolution of the role of auxin, from algae to higher plants.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Vernoux, Teva and Robert, Stéphanie},
	month = feb,
	year = {2017},
	pages = {533--540},
}

The luxurious vegetation at Sanya, the most southern location in China on the island of Hainan, provided a perfect environment for the ‘Auxin 2016’ meeting in October. As we review here, participants from all around the world discussed the latest advances in auxin transport, metabolism and signaling pathways, highlighting how auxin acts during plant development and in response to the environment in combination with other hormones. The meeting also provided a rich perspective on the evolution of the role of auxin, from algae to higher plants.

@article{fischer_erecta_2017,
	title = {The \textit{{ERECTA}} and \textit{{ERECTA}} ‐like genes control a developmental shift during xylem formation in \textit{{Arabidopsis}}},
	volume = {213},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14440},
	doi = {10.1111/nph.14440},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Fischer, Urs and Teichmann, Thomas},
	month = mar,
	year = {2017},
	pages = {1562--1563},
}

@article{decker_identification_2017,
	title = {Identification and characterization of inhibitors of {UDP}-glucose and {UDP}-sugar pyrophosphorylases for \textit{in vivo} studies},
	volume = {90},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13531},
	doi = {10.1111/tpj.13531},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Decker, Daniel and Öberg, Christopher and Kleczkowski, Leszek A.},
	month = jun,
	year = {2017},
	pages = {1093--1107},
}

@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{weiste_arabidopsis_2017,
	title = {The {Arabidopsis} {bZIP11} transcription factor links low-energy signalling to auxin-mediated control of primary root growth},
	volume = {13},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1006607},
	doi = {10.1371/journal.pgen.1006607},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Weiste, Christoph and Pedrotti, Lorenzo and Selvanayagam, Jebasingh and Muralidhara, Prathibha and Fröschel, Christian and Novák, Ondřej and Ljung, Karin and Hanson, Johannes and Dröge-Laser, Wolfgang},
	editor = {Reed, Jason},
	month = feb,
	year = {2017},
	pages = {e1006607},
}

@article{ponzio_dual_2017,
	title = {Dual herbivore attack and herbivore density affect metabolic profiles of \textit{{Brassica} nigra} leaves: {Plant} metabolome during dual insect attack},
	volume = {40},
	issn = {01407791},
	shorttitle = {Dual herbivore attack and herbivore density affect metabolic profiles of \textit{{Brassica} nigra} leaves},
	url = {http://doi.wiley.com/10.1111/pce.12926},
	doi = {10.1111/pce.12926},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Ponzio, Camille and Papazian, Stefano and Albrectsen, Benedicte R. and Dicke, Marcel and Gols, Rieta},
	month = aug,
	year = {2017},
	pages = {1356--1367},
}

@article{hurry_metabolic_2017,
	title = {Metabolic reprogramming in response to cold stress is like real estate, it's all about location},
	volume = {40},
	copyright = {© 2017 John Wiley \& Sons Ltd},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12923},
	doi = {https://doi.org/10.1111/pce.12923},
	abstract = {This article comments on: Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Hurry, Vaughan},
	year = {2017},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.12923},
	pages = {599--601},
}

This article comments on: Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana

@article{razzak_differential_2017,
	title = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light: {Scots} pine response to light intensity and shade},
	volume = {40},
	issn = {01407791},
	shorttitle = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light},
	url = {http://doi.wiley.com/10.1111/pce.12921},
	doi = {10.1111/pce.12921},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Razzak, Abdur and Ranade, Sonali Sachin and Strand, Åsa and García-Gil, M. R.},
	month = aug,
	year = {2017},
	pages = {1332--1340},
}

@article{edlund_contrasting_2017,
	title = {Contrasting patterns of cytokinins between years in senescing aspen leaves},
	volume = {40},
	issn = {0140-7791, 1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12899},
	doi = {10.1111/pce.12899},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Edlund, Erik and Novak, Ondrej and Karady, Michal and Ljung, Karin and Jansson, Stefan},
	month = may,
	year = {2017},
	pages = {622--634},
}

@incollection{de_lucas_quick_2017,
	address = {New York, NY},
	title = {Quick {Histochemical} {Staining} {Methods} to {Detect} {Cell} {Death} in {Xylem} {Elements} of {Plant} {Tissues}},
	volume = {1544},
	isbn = {978-1-4939-6720-9 978-1-4939-6722-3},
	url = {http://link.springer.com/10.1007/978-1-4939-6722-3_3},
	urldate = {2021-06-07},
	booktitle = {Xylem},
	publisher = {Springer New York},
	author = {Escamez, Sacha and Bollhöner, Benjamin and Tuominen, Hannele},
	editor = {de Lucas, Miguel and Etchhells, J. Peter},
	year = {2017},
	doi = {10.1007/978-1-4939-6722-3_3},
	note = {Series Title: Methods in Molecular Biology},
	pages = {27--36},
}

@incollection{de_lucas_analysis_2017,
	address = {New York, NY},
	title = {Analysis of {Lignin} {Composition} and {Distribution} {Using} {Fluorescence} {Laser} {Confocal} {Microspectroscopy}},
	volume = {1544},
	isbn = {978-1-4939-6720-9 978-1-4939-6722-3},
	url = {http://link.springer.com/10.1007/978-1-4939-6722-3_17},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Xylem},
	publisher = {Springer New York},
	author = {Decou, Raphaël and Serk, Henrik and Ménard, Delphine and Pesquet, Edouard},
	editor = {de Lucas, Miguel and Etchhells, J. Peter},
	year = {2017},
	doi = {10.1007/978-1-4939-6722-3_17},
	note = {Series Title: Methods in Molecular Biology},
	pages = {233--247},
}

@article{hall_hhoa_2017,
	title = {The {HhoA} protease from {Synechocystis} sp. {PCC} 6803 – {Novel} insights into structure and activity regulation},
	volume = {198},
	issn = {10478477},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1047847716302507},
	doi = {10.1016/j.jsb.2016.12.004},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Journal of Structural Biology},
	author = {Hall, Michael and Wagner, Raik and Lam, Xuan Tam and Funk, Christiane and Persson, Karina},
	month = jun,
	year = {2017},
	pages = {147--153},
}

@incollection{de_lucas_establishment_2017,
	address = {New York, NY},
	title = {Establishment and {Utilization} of {Habituated} {Cell} {Suspension} {Cultures} for {Hormone}-{Inducible} {Xylogenesis}},
	volume = {1544},
	isbn = {978-1-4939-6720-9 978-1-4939-6722-3},
	url = {http://link.springer.com/10.1007/978-1-4939-6722-3_4},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Xylem},
	publisher = {Springer New York},
	author = {Ménard, Delphine and Serk, Henrik and Decou, Raphaël and Pesquet, Edouard},
	editor = {de Lucas, Miguel and Etchhells, J. Peter},
	year = {2017},
	doi = {10.1007/978-1-4939-6722-3_4},
	note = {Series Title: Methods in Molecular Biology},
	pages = {37--57},
}

@article{blokhina_laser_2017,
	title = {Laser {Capture} {Microdissection} {Protocol} for {Xylem} {Tissues} of {Woody} {Plants}},
	volume = {07},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01965/full},
	doi = {10.3389/fpls.2016.01965},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Blokhina, Olga and Valerio, Concetta and Sokołowska, Katarzyna and Zhao, Lei and Kärkönen, Anna and Niittylä, Totte and Fagerstedt, Kurt},
	month = jan,
	year = {2017},
}

@article{goretti_transcriptional_2017,
	title = {Transcriptional and {Post}-transcriptional {Mechanisms} {Limit} {Heading} {Date} 1 ({Hd1}) {Function} to {Adapt} {Rice} to {High} {Latitudes}},
	volume = {13},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1006530},
	doi = {10.1371/journal.pgen.1006530},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Goretti, Daniela and Martignago, Damiano and Landini, Martina and Brambilla, Vittoria and Gómez-Ariza, Jorge and Gnesutta, Nerina and Galbiati, Francesca and Collani, Silvio and Takagi, Hiroki and Terauchi, Ryohei and Mantovani, Roberto and Fornara, Fabio},
	editor = {Lu, Tiegang},
	month = jan,
	year = {2017},
	pages = {e1006530},
}

@article{cintas_potential_2017,
	title = {The potential role of forest management in {Swedish} scenarios towards climate neutrality by mid century},
	volume = {383},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112716303619},
	doi = {10.1016/j.foreco.2016.07.015},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Cintas, Olivia and Berndes, Göran and Hansson, Julia and Poudel, Bishnu Chandra and Bergh, Johan and Börjesson, Pål and Egnell, Gustaf and Lundmark, Tomas and Nordin, Annika},
	month = jan,
	year = {2017},
	pages = {73--84},
}

@article{schiffthaler_batchmap_2017,
	title = {{BatchMap}: {A} parallel implementation of the {OneMap} {R} package for fast computation of {F1} linkage maps in outcrossing species},
	volume = {12},
	issn = {1932-6203},
	shorttitle = {{BatchMap}},
	url = {https://dx.plos.org/10.1371/journal.pone.0189256},
	doi = {10.1371/journal.pone.0189256},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Schiffthaler, Bastian and Bernhardsson, Carolina and Ingvarsson, Pär K. and Street, Nathaniel R.},
	editor = {Candela, Hector},
	month = dec,
	year = {2017},
	pages = {e0189256},
}