Publications 2019

@article{yoshida_soseki-based_2019,
	title = {A {SOSEKI}-based coordinate system interprets global polarity cues in {Arabidopsis}},
	volume = {5},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-019-0363-6},
	doi = {10/gfvgd3},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Yoshida, Saiko and van der Schuren, Alja and van Dop, Maritza and van Galen, Luc and Saiga, Shunsuke and Adibi, Milad and Möller, Barbara and ten Hove, Colette A. and Marhavý, Peter and Smith, Richard and Friml, Jiri and Weijers, Dolf},
	month = feb,
	year = {2019},
	pages = {160--166},
}

@article{lee_lbd16_2019,
	title = {{LBD16} and {LBD18} acting downstream of {ARF7} and {ARF19} are involved in adventitious root formation in {Arabidopsis}},
	volume = {19},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-019-1659-4},
	doi = {10.1186/s12870-019-1659-4},
	abstract = {Adventitious root (AR) formation is a complex genetic trait, which is controlled by various endogenous and environmental cues. Auxin is known to play a central role in AR formation; however, the mechanisms underlying this role are not well understood.},
	number = {1},
	urldate = {2023-11-14},
	journal = {BMC Plant Biology},
	author = {Lee, Han Woo and Cho, Chuloh and Pandey, Shashank K. and Park, Yoona and Kim, Min-Jung and Kim, Jungmook},
	month = jan,
	year = {2019},
	keywords = {Adventitious root formation, Arabidopsis thaliana, Auxin response factor, LBD16, LBD18, Lateral organ boundaries domain},
	pages = {46},
}

Adventitious root (AR) formation is a complex genetic trait, which is controlled by various endogenous and environmental cues. Auxin is known to play a central role in AR formation; however, the mechanisms underlying this role are not well understood.

@article{cho_lbd13_2019,
	title = {{LBD13} positively regulates lateral root formation in {Arabidopsis}},
	volume = {249},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-018-03087-x},
	doi = {10.1007/s00425-018-03087-x},
	abstract = {Lateral Organ Boundaries Domain 13 (LBD13), which is expressed in emerged lateral roots and encodes a transcriptional activator, plays an important role in lateral root formation in Arabidopsis.},
	language = {en},
	number = {4},
	urldate = {2023-11-14},
	journal = {Planta},
	author = {Cho, Chuloh and Jeon, Eunkyeong and Pandey, Shashank K. and Ha, Se Hoon and Kim, Jungmook},
	month = apr,
	year = {2019},
	keywords = {Arabidopsis thaliana, LBD14, Lateral organ boundaries domain, Lateral root, Protoplasts, RNAi, Transcription factor},
	pages = {1251--1258},
}

Lateral Organ Boundaries Domain 13 (LBD13), which is expressed in emerged lateral roots and encodes a transcriptional activator, plays an important role in lateral root formation in Arabidopsis.

@article{jin_genome-wide_2019,
	title = {Genome-{Wide} {Variant} {Identification} and {High}-{Density} {Genetic} {Map} {Construction} {Using} {RADseq} for {Platycladus} orientalis ({Cupressaceae})},
	volume = {9},
	issn = {2160-1836},
	url = {https://doi.org/10.1534/g3.119.400684},
	doi = {10.1534/g3.119.400684},
	abstract = {Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4\%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of \<20\%, the remaining 23,926 loci (22\% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.},
	number = {11},
	urldate = {2023-04-27},
	journal = {G3 Genes/Genomes/Genetics},
	author = {Jin, Yuqing and Zhao, Wei and Nie, Shuai and Liu, Si-Si and El-Kassaby, Yousry A and Wang, Xiao-Ru and Mao, Jian-Feng},
	month = nov,
	year = {2019},
	pages = {3663--3672},
}

Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.

@article{liu_complete_2019,
	title = {The complete chloroplast genome sequence annotation for {Malania} oleifera, a critically endangered and important bioresource tree},
	volume = {11},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-018-1005-4},
	doi = {10.1007/s12686-018-1005-4},
	abstract = {In this study, we characterize the chloroplast genome of Malania oleifera Chun et S. Lee, the only species of this genus and member of the Olacaceae family. M. oleifera is an interesting seed oil plant for medicinal purposes. It is also a critically endangered species, which is currently recorded on the International Union for Conservation of Nature (IUCN) Red List and in the “Red Data Book of Chinese Plants: the Rare and Endangered Plants”. Its total chloroplast genome length is 125,050 bp, including a large single copy region of 76,387 bp, a short single copy gene region of 15 bp, and a pair of inverted repeats (IRs) of 24,324 bp. We annotated 80 genes in this chloroplast genome, including 51 protein-coding genes, 4 ribosomal RNAs, 4 pseudogenes and 21 tRNA genes. We found 15 genes duplicated in the IR regions, and the overall GC content was found to be 38.17\%. Phylogenetic analysis showed that M. oleifera is closely related to Erythropalum scandens comparing nine chloroplast genomes from Santalales.},
	language = {en},
	number = {3},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Liu, Si-Si and Hu, Yi-Heng and Maghuly, Fatemeh and Porth, Ilga Mercedes and Mao, Jian-Feng},
	month = sep,
	year = {2019},
	keywords = {Chloroplast genome, Malania oleifera, Phylogenetic analysis},
	pages = {271--274},
}

In this study, we characterize the chloroplast genome of Malania oleifera Chun et S. Lee, the only species of this genus and member of the Olacaceae family. M. oleifera is an interesting seed oil plant for medicinal purposes. It is also a critically endangered species, which is currently recorded on the International Union for Conservation of Nature (IUCN) Red List and in the “Red Data Book of Chinese Plants: the Rare and Endangered Plants”. Its total chloroplast genome length is 125,050 bp, including a large single copy region of 76,387 bp, a short single copy gene region of 15 bp, and a pair of inverted repeats (IRs) of 24,324 bp. We annotated 80 genes in this chloroplast genome, including 51 protein-coding genes, 4 ribosomal RNAs, 4 pseudogenes and 21 tRNA genes. We found 15 genes duplicated in the IR regions, and the overall GC content was found to be 38.17%. Phylogenetic analysis showed that M. oleifera is closely related to Erythropalum scandens comparing nine chloroplast genomes from Santalales.

@article{zhou_-depth_2019,
	title = {In-depth transcriptome characterization uncovers distinct gene family expansions for {Cupressus} gigantea important to this long-lived species’ adaptability to environmental cues},
	volume = {20},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-019-5584-6},
	doi = {10.1186/s12864-019-5584-6},
	abstract = {Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization.},
	number = {1},
	urldate = {2023-04-27},
	journal = {BMC Genomics},
	author = {Zhou, Shan-Shan and Xing, Zhen and Liu, Hui and Hu, Xian-Ge and Gao, Qiong and Xu, Jie and Jiao, Si-Qian and Jia, Kai-Hua and Jin, Yu Qing and Zhao, Wei and Porth, Ilga and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	month = mar,
	year = {2019},
	keywords = {Cupressus gigantea, De novo transcriptome assembly, Ecology, Gene family evolution, Gene functional annotation},
	pages = {213},
}

Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization.

@article{zhou_floral_2019,
	title = {Floral development and the formation of functionally unisexual flowers in {Xanthoceras} sorbifolium ({Sapindaceae}), a morphologically andromonoecious tree endemic to northern {China}},
	volume = {33},
	issn = {1432-2285},
	url = {https://doi.org/10.1007/s00468-019-01879-6},
	doi = {10.1007/s00468-019-01879-6},
	abstract = {Xanthoceras sorbifolium is apparently andromonoecious but exhibits a cryptically monoecious breeding system. Sexual differentiation in male and functional female flowers occurs 2 weeks before flowering.},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {Trees},
	author = {Zhou, Qingyuan and Cai, Qing and Zheng, Yuanrun and Wu, Zhiyan and Mao, Jianfeng},
	month = dec,
	year = {2019},
	keywords = {Andromonoecy, Floral development, Monoecy, Systematic relationship, Xanthoceras sorbifolium},
	pages = {1571--1582},
}

Xanthoceras sorbifolium is apparently andromonoecious but exhibits a cryptically monoecious breeding system. Sexual differentiation in male and functional female flowers occurs 2 weeks before flowering.

@article{xu_late_2019,
	title = {Late {Pleistocene} speciation of three closely related tree peonies endemic to the {Qinling}–{Daba} {Mountains}, a major glacial refugium in {Central} {China}},
	volume = {9},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.5284},
	doi = {10.1002/ece3.5284},
	abstract = {Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China.},
	language = {en},
	number = {13},
	urldate = {2023-04-27},
	journal = {Ecology and Evolution},
	author = {Xu, Xing-Xing and Cheng, Fang-Yun and Peng, Li-Ping and Sun, Yan-Qiang and Hu, Xian-Ge and Li, San-Yuan and Xian, Hong-Li and Jia, Kai-Hua and Abbott, Richard J. and Mao, Jian-Feng},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.5284},
	keywords = {ecological niche modeling, genetic divergence, multiple refugia, niche divergence, phylogeography, speciation, tree peony},
	pages = {7528--7548},
}

Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China.

@article{xu_genome_2019,
	title = {Genome sequence of {Malania} oleifera, a tree with great value for nervonic acid production},
	volume = {8},
	issn = {2047-217X},
	url = {https://doi.org/10.1093/gigascience/giy164},
	doi = {10.1093/gigascience/giy164},
	abstract = {Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82\% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail.Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.},
	number = {2},
	urldate = {2023-04-27},
	journal = {GigaScience},
	author = {Xu, Chao-Qun and Liu, Hui and Zhou, Shan-Shan and Zhang, Dong-Xu and Zhao, Wei and Wang, Sihai and Chen, Fu and Sun, Yan-Qiang and Nie, Shuai and Jia, Kai-Hua and Jiao, Si-Qian and Zhang, Ren-Gang and Yun, Quan-Zheng and Guan, Wenbin and Wang, Xuewen and Gao, Qiong and Bennetzen, Jeffrey L and Maghuly, Fatemeh and Porth, Ilga and Van de Peer, Yves and Wang, Xiao-Ru and Ma, Yongpeng and Mao, Jian-Feng},
	month = feb,
	year = {2019},
	pages = {giy164},
}

Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail.Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.

@article{peng_modelling_2019,
	title = {Modelling environmentally suitable areas for the potential introduction and cultivation of the emerging oil crop {Paeonia} ostii in {China}},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-39449-y},
	doi = {10.1038/s41598-019-39449-y},
	abstract = {Paeonia ostii is a traditional ornamental and medicinal species that has attracted considerable interest for its high oil value. To facilitate the effective and rational cultivation and application of P. ostii in China, it is necessary to determine its potential spatial habitat distribution and environmental requirements. Using high-resolution environmental data for current and future climate scenarios, the potential suitable area and climatic requirements of P. ostii were modelled. Among the 11 environmental variables investigated, growing degree days, precipitation of the wettest month, mean temperature of the coldest quarter, global UV-B radiation, annual precipitation, and soil pH played major roles in determining the suitability of a habitat for the cultivation of P. ostii. Under the current environmental conditions in China, a total area of 20.31 × 105 km2 is suitable for growing P. ostii, accounting for 21.16\% of the country’s total land area. Under the two future climate scenario/year combinations (i.e., representative concentration pathways [RCPs], RCP2.6 and RCP8.5 in 2050), this species would increase its suitable area at high latitudes while decrease at low latitudes. These results present valuable information and a theoretical reference point for identifying the suitable cultivation areas of P. ostii.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Reports},
	author = {Peng, Li-Ping and Cheng, Fang-Yun and Hu, Xian-Ge and Mao, Jian-Feng and Xu, Xing-Xing and Zhong, Yuan and Li, San-Yuan and Xian, Hong-Li},
	month = mar,
	year = {2019},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Biogeography, Ecological modelling},
	pages = {3213},
}

Paeonia ostii is a traditional ornamental and medicinal species that has attracted considerable interest for its high oil value. To facilitate the effective and rational cultivation and application of P. ostii in China, it is necessary to determine its potential spatial habitat distribution and environmental requirements. Using high-resolution environmental data for current and future climate scenarios, the potential suitable area and climatic requirements of P. ostii were modelled. Among the 11 environmental variables investigated, growing degree days, precipitation of the wettest month, mean temperature of the coldest quarter, global UV-B radiation, annual precipitation, and soil pH played major roles in determining the suitability of a habitat for the cultivation of P. ostii. Under the current environmental conditions in China, a total area of 20.31 × 105 km2 is suitable for growing P. ostii, accounting for 21.16% of the country’s total land area. Under the two future climate scenario/year combinations (i.e., representative concentration pathways [RCPs], RCP2.6 and RCP8.5 in 2050), this species would increase its suitable area at high latitudes while decrease at low latitudes. These results present valuable information and a theoretical reference point for identifying the suitable cultivation areas of P. ostii.

@article{ouyang_complete_2019,
	title = {Complete plastome sequences of {Picea} asperata and {P}. crassifolia and comparative analyses with {P}. abies and {P}. morrisonicola},
	volume = {62},
	issn = {0831-2796},
	url = {https://cdnsciencepub.com/doi/10.1139/gen-2018-0195},
	doi = {10.1139/gen-2018-0195},
	abstract = {Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (psbJ-petA, trnT-psaM, trnS-trnD, trnL-rps4, psaC-ccsA, and rps7-trnL) and one gene (ycf1). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of Picea as well as Pinaceae in general.},
	number = {5},
	urldate = {2023-04-27},
	journal = {Genome},
	author = {Ouyang, Fangqun and Hu, Jiwen and Wang, Junchen and Ling, Juanjuan and Wang, Zhi and Wang, Nan and Ma, Jianwei and Zhang, Hanguo and Mao, Jian-Feng and Wang, Junhui},
	month = may,
	year = {2019},
	note = {Publisher: NRC Research Press},
	pages = {317--328},
}

Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (psbJ-petA, trnT-psaM, trnS-trnD, trnL-rps4, psaC-ccsA, and rps7-trnL) and one gene (ycf1). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of Picea as well as Pinaceae in general.

@article{jiao_development_2019,
	title = {Development of novel {EST}-{SSR} markers for {Ephedra} sinica ({Ephedraceae}) by transcriptome database mining},
	volume = {7},
	issn = {2168-0450},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.1212},
	doi = {10.1002/aps3.1212},
	abstract = {Premise of the Study Ephedra sinica (Ephedraceae) is a gymnosperm shrub with a wide distribution across Central and Eastern Asia. It is widely cultivated as a medicinal plant, but its wild populations are monitored to determine whether protection is needed. Methods and Results Thirty-six microsatellite markers, including 11 polymorphic markers, were developed from E. distachya RNA-Seq data deposited in the National Center for Biotechology Information dbEST database. Among 100 genotyped E. sinica individuals originating from five different population groups, the allele number ranged from three to 22 per locus. Levels of observed and expected heterozygosity ranged from 0 to 0.866 (average 0.176) and 0 to 0.876 (average 0.491), respectively. Allelic polymorphism information content ranged from 0.000 to 0.847 (average 0.333). Cross-species amplifications were successfully conducted with two related Ephedra species for all 11 di- or trinucleotide simple sequence repeats. Conclusions This study provides the first set of microsatellite markers for genetic monitoring and surveying of this medicinal plant.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Applications in Plant Sciences},
	author = {Jiao, Si-Qian and Sun, Yan-Qiang and Zhang, Dong-Xu and Gao, Qiong and Jin, Yuqing and Liu, Hui and Ma, Yongpeng and Yang, Yong and Porth, Ilga and Mao, Jian-Feng},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.1212},
	keywords = {Ephedra sinica, Ephedraceae, expressed sequence tag–simple sequence repeat (EST-SSR) marker, genetic diversity, gymnosperm, medicinal plant},
	pages = {e01212},
}

Premise of the Study Ephedra sinica (Ephedraceae) is a gymnosperm shrub with a wide distribution across Central and Eastern Asia. It is widely cultivated as a medicinal plant, but its wild populations are monitored to determine whether protection is needed. Methods and Results Thirty-six microsatellite markers, including 11 polymorphic markers, were developed from E. distachya RNA-Seq data deposited in the National Center for Biotechology Information dbEST database. Among 100 genotyped E. sinica individuals originating from five different population groups, the allele number ranged from three to 22 per locus. Levels of observed and expected heterozygosity ranged from 0 to 0.866 (average 0.176) and 0 to 0.876 (average 0.491), respectively. Allelic polymorphism information content ranged from 0.000 to 0.847 (average 0.333). Cross-species amplifications were successfully conducted with two related Ephedra species for all 11 di- or trinucleotide simple sequence repeats. Conclusions This study provides the first set of microsatellite markers for genetic monitoring and surveying of this medicinal plant.

@article{hu_local_2019,
	title = {Local {Adaptation} and {Response} of {Platycladus} orientalis ({L}.) {Franco} {Populations} to {Climate} {Change}},
	volume = {10},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/10/8/622},
	doi = {10.3390/f10080622},
	abstract = {Knowledge about the local adaptation and response of forest tree populations to the climate is important for assessing the impact of climate change and developing adaptive genetic resource management strategies. However, such information is not available for most plant species. Here, based on 69 provenances tested at 19 common garden experimental sites, we developed a universal response function (URF) for tree height at seven years of age for the important and wide-spread native Chinese tree species Platycladus orientalis (L.) Franco. URF was recently used to predict the potential growth response of a population originating from any climate and growing in any climate conditions. The developed model integrated both genetic and environmental effects, and explained 55\% of the total variation in tree height observed among provenances and test sites in China. We found that local provenances performed better than non-local counterparts in habitats located in central, eastern, and southwestern China, showing the evidence of local adaptation as compared to other regions. In contrast, non-local provenances outperformed local ones in peripheral areas in northern and northwestern China, suggesting an adaptational lag in these areas. Future projections suggest that the suitable habitat areas of P. orientalis would expand by 15\%–39\% and shift northward by 0.8–3 degrees in latitude; however, the projected tree height of this species would decline by 4\%–8\% if local provenances were used. If optimal provenances were used, tree height growth could be improved by 13\%–15\%, along with 59\%–71\% suitable habitat expansion. Thus, assisted migration with properly selected seed sources would be effective in avoiding maladaptation in new plantations under a changing climate for P. orientalis.},
	language = {en},
	number = {8},
	urldate = {2023-04-27},
	journal = {Forests},
	author = {Hu, Xian-Ge and Mao, Jian-Feng and El-Kassaby, Yousry A. and Jia, Kai-Hua and Jiao, Si-Qian and Zhou, Shan-Shan and Li, Yue and Coops, Nicholas C. and Wang, Tongli},
	month = aug,
	year = {2019},
	note = {Number: 8
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Platycladus orientalis}, adaptation, assisted migration, climate change, provenance test, universal response function},
	pages = {622},
}

Knowledge about the local adaptation and response of forest tree populations to the climate is important for assessing the impact of climate change and developing adaptive genetic resource management strategies. However, such information is not available for most plant species. Here, based on 69 provenances tested at 19 common garden experimental sites, we developed a universal response function (URF) for tree height at seven years of age for the important and wide-spread native Chinese tree species Platycladus orientalis (L.) Franco. URF was recently used to predict the potential growth response of a population originating from any climate and growing in any climate conditions. The developed model integrated both genetic and environmental effects, and explained 55% of the total variation in tree height observed among provenances and test sites in China. We found that local provenances performed better than non-local counterparts in habitats located in central, eastern, and southwestern China, showing the evidence of local adaptation as compared to other regions. In contrast, non-local provenances outperformed local ones in peripheral areas in northern and northwestern China, suggesting an adaptational lag in these areas. Future projections suggest that the suitable habitat areas of P. orientalis would expand by 15%–39% and shift northward by 0.8–3 degrees in latitude; however, the projected tree height of this species would decline by 4%–8% if local provenances were used. If optimal provenances were used, tree height growth could be improved by 13%–15%, along with 59%–71% suitable habitat expansion. Thus, assisted migration with properly selected seed sources would be effective in avoiding maladaptation in new plantations under a changing climate for P. orientalis.

@article{el-kassaby_concept_2019,
	title = {Concept for gene conservation strategy for the endangered {Chinese} yellowhorn, {Xanthoceras} sorbifolium, based on simulation of pairwise kinship coefficients},
	volume = {432},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112718314543},
	doi = {10.1016/j.foreco.2018.10.045},
	abstract = {A molecular markers-based conservation strategy framework for the endemic endangered Chinese yellowhorn, Xanthoceras sorbifolium, is developed. The method utilizes pairwise kinship coefficients, a measure of genetic similarity/dissimilarity, between individuals and contrasts two simulated mating schemes that either promote “no co-ancestry” or “co-ancestry” through multiple matings of particular individuals as well as a “hybrid” scenario involving both “no co-ancestry” and “co-ancestry” mating schemes. Selection of mating individuals is focused on maximizing genetic dissimilarity, hence capturing maximum genetic diversity. These approaches were compared on a population of 79 ancient yellowhorn trees scattered across 13 populations. Simulated matings were evaluated based on their average pairwise kinship, effective population size, and average number of alleles/locus. In this regard, no co-ancestry has been proven to be superior to co-ancestry mating scheme; however, co-ancestry offered opportunities for increasing effective population size, a desirable attribute for combating the detrimental effect of genetic drift. The hybrid approach, with reduced number of crosses, produced acceptable condition with maximum genetic diversity and high effective population size and genetic dissimilarity among the produced offspring. The advantages and disadvantages of marker-based gene conservation are highlighted and discussed. Subject area: Conservation genetics and biodiversity.},
	language = {en},
	urldate = {2023-04-27},
	journal = {Forest Ecology and Management},
	author = {El-Kassaby, Yousry A. and Wang, Qing and Wang, Tongli and Ratcliffe, Blaise and Bi, Quan-Xin and Wang, Zhou and Mao, Jian-Feng and Guan, Wenbin},
	month = jan,
	year = {2019},
	keywords = {Conservation, Genetic diversity, Microsatellites, Pairwise kinship relationship, Yellowhorn},
	pages = {976--982},
}

A molecular markers-based conservation strategy framework for the endemic endangered Chinese yellowhorn, Xanthoceras sorbifolium, is developed. The method utilizes pairwise kinship coefficients, a measure of genetic similarity/dissimilarity, between individuals and contrasts two simulated mating schemes that either promote “no co-ancestry” or “co-ancestry” through multiple matings of particular individuals as well as a “hybrid” scenario involving both “no co-ancestry” and “co-ancestry” mating schemes. Selection of mating individuals is focused on maximizing genetic dissimilarity, hence capturing maximum genetic diversity. These approaches were compared on a population of 79 ancient yellowhorn trees scattered across 13 populations. Simulated matings were evaluated based on their average pairwise kinship, effective population size, and average number of alleles/locus. In this regard, no co-ancestry has been proven to be superior to co-ancestry mating scheme; however, co-ancestry offered opportunities for increasing effective population size, a desirable attribute for combating the detrimental effect of genetic drift. The hybrid approach, with reduced number of crosses, produced acceptable condition with maximum genetic diversity and high effective population size and genetic dissimilarity among the produced offspring. The advantages and disadvantages of marker-based gene conservation are highlighted and discussed. Subject area: Conservation genetics and biodiversity.

@article{yadav_b-box-containing_2019,
	title = {The {B}-{Box}-{Containing} {MicroProtein} {miP1a}/{BBX31} {Regulates} {Photomorphogenesis} and {UV}-{B} {Protection}},
	volume = {179},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.18.01258},
	doi = {10.1104/pp.18.01258},
	abstract = {The bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) represents a major hub in the light-signaling cascade both under visible and UV-B light. The mode of transcriptional regulation of HY5, especially under UV-B light, is not well characterized. B-BOX (BBX) transcription factors regulate HY5 transcription and also posttranscriptionally modulate HY5 to control photomorphogenesis under white light. Here, we identify BBX31 as a key signaling intermediate in visible and UV-B light signal transduction in Arabidopsis (Arabidopsis thaliana). BBX31 expression is induced by UV-B radiation in a fluence-dependent manner. HY5 directly binds to the promoter of BBX31 and regulates its transcript levels. Loss- and gain-of-function mutants of BBX31 indicate that it acts as a negative regulator of photomorphogenesis under white light but is a positive regulator of UV-B signaling. Genetic interaction studies suggest that BBX31 regulates photomorphogenesis independent of HY5. We found no evidence for a direct BBX31-HY5 interaction, and they primarily regulate different sets of genes in white light. Under high doses of UV-B radiation, BBX31 promotes the accumulation of UV-protective flavonoids and phenolic compounds. It enhances tolerance to UV-B radiation by regulating genes involved in photoprotection and DNA repair in a HY5-dependent manner. Under UV-B radiation, overexpression of BBX31 enhances HY5 transcriptional levels in a UV RESISTANCE LOCUS8-dependent manner, suggesting that BBX31 might regulate HY5 transcription.},
	number = {4},
	urldate = {2022-11-30},
	journal = {Plant Physiology},
	author = {Yadav, Arpita and Bakshi, Souvika and Yadukrishnan, Premachandran and Lingwan, Maneesh and Dolde, Ulla and Wenkel, Stephan and Masakapalli, Shyam Kumar and Datta, Sourav},
	month = apr,
	year = {2019},
	pages = {1876--1892},
}

The bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) represents a major hub in the light-signaling cascade both under visible and UV-B light. The mode of transcriptional regulation of HY5, especially under UV-B light, is not well characterized. B-BOX (BBX) transcription factors regulate HY5 transcription and also posttranscriptionally modulate HY5 to control photomorphogenesis under white light. Here, we identify BBX31 as a key signaling intermediate in visible and UV-B light signal transduction in Arabidopsis (Arabidopsis thaliana). BBX31 expression is induced by UV-B radiation in a fluence-dependent manner. HY5 directly binds to the promoter of BBX31 and regulates its transcript levels. Loss- and gain-of-function mutants of BBX31 indicate that it acts as a negative regulator of photomorphogenesis under white light but is a positive regulator of UV-B signaling. Genetic interaction studies suggest that BBX31 regulates photomorphogenesis independent of HY5. We found no evidence for a direct BBX31-HY5 interaction, and they primarily regulate different sets of genes in white light. Under high doses of UV-B radiation, BBX31 promotes the accumulation of UV-protective flavonoids and phenolic compounds. It enhances tolerance to UV-B radiation by regulating genes involved in photoprotection and DNA repair in a HY5-dependent manner. Under UV-B radiation, overexpression of BBX31 enhances HY5 transcriptional levels in a UV RESISTANCE LOCUS8-dependent manner, suggesting that BBX31 might regulate HY5 transcription.

@article{marhava_re-activation_2019,
	title = {Re-activation of {Stem} {Cell} {Pathways} for {Pattern} {Restoration} in {Plant} {Wound} {Healing}},
	volume = {177},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867419304015},
	doi = {10/gfz9tc},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Cell},
	author = {Marhava, Petra and Hoermayer, Lukas and Yoshida, Saiko and Marhavý, Peter and Benková, Eva and Friml, Jiří},
	month = may,
	year = {2019},
	pages = {957--969.e13},
}

@article{cattaneo_conditional_2019,
	title = {Conditional effects of the epigenetic regulator {JUMONJI} 14 in {Arabidopsis} root growth},
	volume = {146},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.183905},
	doi = {10.1242/dev.183905},
	abstract = {Methylation of lysine 4 in histone 3 (H3K4) is a post-translational modification that promotes gene expression. H3K4 methylation can be reversed by specific demethylases with an enzymatic Jumonji C domain. In Arabidopsis thaliana, H3K4-specific JUMONJI (JMJ) proteins distinguish themselves by the association with an F/Y-rich (FYR) domain. Here, we report that jmj14 mutations partially suppress reduced root meristem size and growth vigor of brevis radix (brx) mutants. Similar to its close homologs, JMJ15, JMJ16 and JMJ18, the JMJ14 promoter confers expression in mature root vasculature. Yet, unlike jmj14, neither jmj16 nor jmj18 mutation markedly suppresses brx phenotypes. Domain-swapping experiments suggest that the specificity of JMJ14 function resides in the FYR domain. Despite JMJ14 promoter activity in the mature vasculature, jmj14 mutation affects root meristem size. However, JMJ14 protein is observed throughout the meristem, suggesting that the JMJ14 transcript region contributes substantially to the spatial aspect of JMJ14 expression. In summary, our data reveal a role for JMJ14 in root growth in sensitized genetic backgrounds that depends on its FYR domain and regulatory input from the JMJ14 cistron.},
	number = {23},
	urldate = {2022-05-02},
	journal = {Development},
	author = {Cattaneo, Pietro and Graeff, Moritz and Marhava, Petra and Hardtke, Christian S.},
	month = dec,
	year = {2019},
	pages = {dev183905},
}

Methylation of lysine 4 in histone 3 (H3K4) is a post-translational modification that promotes gene expression. H3K4 methylation can be reversed by specific demethylases with an enzymatic Jumonji C domain. In Arabidopsis thaliana, H3K4-specific JUMONJI (JMJ) proteins distinguish themselves by the association with an F/Y-rich (FYR) domain. Here, we report that jmj14 mutations partially suppress reduced root meristem size and growth vigor of brevis radix (brx) mutants. Similar to its close homologs, JMJ15, JMJ16 and JMJ18, the JMJ14 promoter confers expression in mature root vasculature. Yet, unlike jmj14, neither jmj16 nor jmj18 mutation markedly suppresses brx phenotypes. Domain-swapping experiments suggest that the specificity of JMJ14 function resides in the FYR domain. Despite JMJ14 promoter activity in the mature vasculature, jmj14 mutation affects root meristem size. However, JMJ14 protein is observed throughout the meristem, suggesting that the JMJ14 transcript region contributes substantially to the spatial aspect of JMJ14 expression. In summary, our data reveal a role for JMJ14 in root growth in sensitized genetic backgrounds that depends on its FYR domain and regulatory input from the JMJ14 cistron.

@article{kumar_poplar_2019,
	title = {Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on {RNA} expression data},
	volume = {99},
	issn = {0960-7412, 1365-313X},
	shorttitle = {Poplar carbohydrate‐active enzymes},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14417},
	doi = {10.1111/tpj.14417},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Kumar, Vikash and Hainaut, Matthieu and Delhomme, Nicolas and Mannapperuma, Chanaka and Immerzeel, Peter and Street, Nathaniel R. and Henrissat, Bernard and Mellerowicz, Ewa J.},
	month = aug,
	year = {2019},
	pages = {589--609},
}

@article{bernhardsson_ultra-dense_2019,
	title = {An {Ultra}-{Dense} {Haploid} {Genetic} {Map} for {Evaluating} the {Highly} {Fragmented} {Genome} {Assembly} of {Norway} {Spruce} ({Picea} abies )},
	volume = {9},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/9/5/1623/6026441},
	doi = {10/gjcr63},
	abstract = {Abstract
            Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60\% of the total genome size but is highly fragmented, consisting of \>10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6\% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8\% of the anchored scaffolds and 1.6\% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Bernhardsson, Carolina and Vidalis, Amaryllis and Wang, Xi and Scofield, Douglas G and Schiffthaler, Bastian and Baison, John and Street, Nathaniel R and García-Gil, M Rosario and Ingvarsson, Pär K},
	month = may,
	year = {2019},
	pages = {1623--1632},
}

Abstract Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

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

@article{doyle_role_2019,
	title = {A role for the auxin precursor anthranilic acid in root gravitropism via regulation of {PIN}-{FORMED} protein polarity and relocalisation in {Arabidopsis}},
	volume = {223},
	issn = {0028-646X, 1469-8137},
	shorttitle = {A role for the auxin precursor anthranilic acid in root gravitropism via regulation of {PIN}-{FORMED} protein polarity and relocalisation in {Arabidopsis}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15877},
	doi = {10.1111/nph.15877},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Doyle, Siamsa M. and Rigal, Adeline and Grones, Peter and Karady, Michal and Barange, Deepak K. and Majda, Mateusz and Pařízková, Barbora and Karampelias, Michael and Zwiewka, Marta and Pěnčík, Aleš and Almqvist, Fredrik and Ljung, Karin and Novák, Ondřej and Robert, Stéphanie},
	month = aug,
	year = {2019},
	pages = {1420--1432},
}

@incollection{giacomello_high_2019,
	title = {High {Spatial} {Resolution} {Profiling} in {Tree} {Species}},
	isbn = {978-1-119-31299-4},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0688},
	abstract = {Until recently, the majority of genomics assays have been performed on bulk tissue samples containing multiple cell types. Tissues such as the wood formation zone in trees contain a complex mix of cell types organised in three-dimensional space. Moreover, cells within the wood formation zone represent a continual developmental progression from meristematic cambial initials through to cell death. This spatiotemporal developmental gradient and cell type information are not assayed by bulk samples. New and improved sampling methods coupled to next-generation sequencing assays are enabling the generation of high spatial resolution and single-cell transcriptomics data, offering unprecedented insight into the biology of unique cell types and cell developmental programs. We overview the application of these approaches to the study of wood development, in particular, and highlight challenges associated with the analysis of such data.},
	language = {en},
	urldate = {2021-10-20},
	booktitle = {Annual {Plant} {Reviews} online},
	publisher = {American Cancer Society},
	author = {Giacomello, Stefania and Delhomme, Nicolas and Niittylä, Totte and Tuominen, Hannele and Street, Nathaniel R.},
	year = {2019},
	doi = {10.1002/9781119312994.apr0688},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0688},
	keywords = {RNA sequencing, cell type, single cell, spatial resolution, transcriptome, wood formation, xylem},
	pages = {329--360},
}

Until recently, the majority of genomics assays have been performed on bulk tissue samples containing multiple cell types. Tissues such as the wood formation zone in trees contain a complex mix of cell types organised in three-dimensional space. Moreover, cells within the wood formation zone represent a continual developmental progression from meristematic cambial initials through to cell death. This spatiotemporal developmental gradient and cell type information are not assayed by bulk samples. New and improved sampling methods coupled to next-generation sequencing assays are enabling the generation of high spatial resolution and single-cell transcriptomics data, offering unprecedented insight into the biology of unique cell types and cell developmental programs. We overview the application of these approaches to the study of wood development, in particular, and highlight challenges associated with the analysis of such data.

@article{wessels_ap2erf_2019,
	title = {An {AP2}/{ERF} transcription factor {ERF139} coordinates xylem cell expansion and secondary cell wall deposition},
	volume = {224},
	issn = {0028-646X, 1469-8137},
	shorttitle = {An {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15960},
	doi = {10/gjcsfs},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Wessels, Bernard and Seyfferth, Carolin and Escamez, Sacha and Vain, Thomas and Antos, Kamil and Vahala, Jorma and Delhomme, Nicolas and Kangasjärvi, Jaakko and Eder, Michaela and Felten, Judith and Tuominen, Hannele},
	month = dec,
	year = {2019},
	pages = {1585--1599},
}

@article{dinant_synchrotron_2019,
	title = {Synchrotron {FTIR} and {Raman} spectroscopy provide unique spectral fingerprints for {Arabidopsis} floral stem vascular tissues},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/3/871/5165365},
	doi = {10.1093/jxb/ery396},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Dinant, S and Wolff, N and De Marco, F and Vilaine, F and Gissot, L and Aubry, E and Sandt, C and Bellini, C. and Le Hir, R},
	month = feb,
	year = {2019},
	pages = {871--884},
}

@article{taylor_sustainable_2019,
	title = {Sustainable bioenergy for climate mitigation: developing drought-tolerant trees and grasses},
	volume = {124},
	issn = {0305-7364, 1095-8290},
	shorttitle = {Sustainable bioenergy for climate mitigation},
	url = {https://academic.oup.com/aob/article/124/4/513/5609063},
	doi = {10.1093/aob/mcz146},
	abstract = {Abstract
            
              Background and Aims
              Bioenergy crops are central to climate mitigation strategies that utilize biogenic carbon, such as BECCS (bioenergy with carbon capture and storage), alongside the use of biomass for heat, power, liquid fuels and, in the future, biorefining to chemicals. Several promising lignocellulosic crops are emerging that have no food role – fast-growing trees and grasses – but are well suited as bioenergy feedstocks, including Populus, Salix, Arundo, Miscanthus, Panicum and Sorghum.
            
            
              Scope
              These promising crops remain largely undomesticated and, until recently, have had limited germplasm resources. In order to avoid competition with food crops for land and nature conservation, it is likely that future bioenergy crops will be grown on marginal land that is not needed for food production and is of poor quality and subject to drought stress. Thus, here we define an ideotype for drought tolerance that will enable biomass production to be maintained in the face of moderate drought stress. This includes traits that can readily be measured in wide populations of several hundred unique genotypes for genome-wide association studies, alongside traits that are informative but can only easily be assessed in limited numbers or training populations that may be more suitable for genomic selection. Phenotyping, not genotyping, is now the major bottleneck for progress, since in all lignocellulosic crops studied extensive use has been made of next-generation sequencing such that several thousand markers are now available and populations are emerging that will enable rapid progress for drought-tolerance breeding. The emergence of novel technologies for targeted genotyping by sequencing are particularly welcome. Genome editing has already been demonstrated for Populus and offers significant potential for rapid deployment of drought-tolerant crops through manipulation of ABA receptors, as demonstrated in Arabidopsis, with other gene targets yet to be tested.
            
            
              Conclusions
              Bioenergy is predicted to be the fastest-developing renewable energy over the coming decade and significant investment over the past decade has been made in developing genomic resources and in collecting wild germplasm from within the natural ranges of several tree and grass crops. Harnessing these resources for climate-resilient crops for the future remains a challenge but one that is likely to be successful.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Annals of Botany},
	author = {Taylor, G and Donnison, I S and Murphy-Bokern, D and Morgante, M and Bogeat-Triboulot, M-B and Bhalerao, Rishikesh P. and Hertzberg, M and Polle, A and Harfouche, A and Alasia, F and Petoussi, V and Trebbi, D and Schwarz, K and Keurentjes, J J B and Centritto, M and Genty, B and Flexas, J and Grill, E and Salvi, S and Davies, W J},
	month = oct,
	year = {2019},
	pages = {513--520},
}

Abstract Background and Aims Bioenergy crops are central to climate mitigation strategies that utilize biogenic carbon, such as BECCS (bioenergy with carbon capture and storage), alongside the use of biomass for heat, power, liquid fuels and, in the future, biorefining to chemicals. Several promising lignocellulosic crops are emerging that have no food role – fast-growing trees and grasses – but are well suited as bioenergy feedstocks, including Populus, Salix, Arundo, Miscanthus, Panicum and Sorghum. Scope These promising crops remain largely undomesticated and, until recently, have had limited germplasm resources. In order to avoid competition with food crops for land and nature conservation, it is likely that future bioenergy crops will be grown on marginal land that is not needed for food production and is of poor quality and subject to drought stress. Thus, here we define an ideotype for drought tolerance that will enable biomass production to be maintained in the face of moderate drought stress. This includes traits that can readily be measured in wide populations of several hundred unique genotypes for genome-wide association studies, alongside traits that are informative but can only easily be assessed in limited numbers or training populations that may be more suitable for genomic selection. Phenotyping, not genotyping, is now the major bottleneck for progress, since in all lignocellulosic crops studied extensive use has been made of next-generation sequencing such that several thousand markers are now available and populations are emerging that will enable rapid progress for drought-tolerance breeding. The emergence of novel technologies for targeted genotyping by sequencing are particularly welcome. Genome editing has already been demonstrated for Populus and offers significant potential for rapid deployment of drought-tolerant crops through manipulation of ABA receptors, as demonstrated in Arabidopsis, with other gene targets yet to be tested. Conclusions Bioenergy is predicted to be the fastest-developing renewable energy over the coming decade and significant investment over the past decade has been made in developing genomic resources and in collecting wild germplasm from within the natural ranges of several tree and grass crops. Harnessing these resources for climate-resilient crops for the future remains a challenge but one that is likely to be successful.

@article{lakehal_molecular_2019,
	title = {A {Molecular} {Framework} for the {Control} of {Adventitious} {Rooting} by {TIR1}/{AFB2}-{Aux}/{IAA}-{Dependent} {Auxin} {Signaling} in {Arabidopsis}},
	volume = {12},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205219302904},
	doi = {10.1016/j.molp.2019.09.001},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Lakehal, Abdellah and Chaabouni, Salma and Cavel, Emilie and Le Hir, Rozenn and Ranjan, Alok and Raneshan, Zahra and Novák, Ondřej and Păcurar, Daniel I. and Perrone, Irene and Jobert, François and Gutierrez, Laurent and Bakó, Laszlo and Bellini, Catherine},
	month = nov,
	year = {2019},
	pages = {1499--1514},
}

@article{gendre_rho--plant-activated_2019,
	title = {Rho-of-plant-activated root hair formation requires \textit{{Arabidopsis} {YIP4a}/b} gene function},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/doi/10.1242/dev.168559/264580/Rho-of-plant-activated-root-hair-formation},
	doi = {10/ghtbhf},
	abstract = {Root hairs are protrusions from root epidermal cells with critical roles in plant soil interactions. While much is known about patterning, polarity and tip growth of root hairs, contributions of membrane trafficking to hair initiation remain poorly understood. Here we demonstrate that the trans-Golgi network-localized YPT-INTERACTING PROTEINS 4a/b contribute to activation and plasma membrane accumulation of Rho-of-plant (ROP) small GTPases during hair initiation, identifying YIP4a/b as central trafficking components in ROP-dependent root hair formation.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Gendre, Delphine and Baral, Anirban and Dang, Xie and Esnay, Nicolas and Boutté, Yohann and Stanislas, Thomas and Vain, Thomas and Claverol, Stéphane and Gustavsson, Anna and Lin, Deshu and Grebe, Markus and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2019},
	pages = {dev.168559},
}

Root hairs are protrusions from root epidermal cells with critical roles in plant soil interactions. While much is known about patterning, polarity and tip growth of root hairs, contributions of membrane trafficking to hair initiation remain poorly understood. Here we demonstrate that the trans-Golgi network-localized YPT-INTERACTING PROTEINS 4a/b contribute to activation and plasma membrane accumulation of Rho-of-plant (ROP) small GTPases during hair initiation, identifying YIP4a/b as central trafficking components in ROP-dependent root hair formation.

@article{wang_surveillance_2019,
	title = {Surveillance of cell wall diffusion barrier integrity modulates water and solute transport in plants},
	volume = {9},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-019-40588-5},
	doi = {10/gjcrr9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Wang, Peng and Calvo-Polanco, Monica and Reyt, Guilhem and Barberon, Marie and Champeyroux, Chloe and Santoni, Véronique and Maurel, Christophe and Franke, Rochus B. and Ljung, Karin and Novak, Ondrej and Geldner, Niko and Boursiac, Yann and Salt, David E.},
	month = dec,
	year = {2019},
	pages = {4227},
}

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

@article{collani_ft_2019,
	title = {{FT} {Modulates} {Genome}-{Wide} {DNA}-{Binding} of the {bZIP} {Transcription} {Factor} {FD}},
	volume = {180},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/180/1/367-380/6117581},
	doi = {10/gjdxbs},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Collani, Silvio and Neumann, Manuela and Yant, Levi and Schmid, Markus},
	month = may,
	year = {2019},
	pages = {367--380},
}

@article{klemencic_phylogenetic_2019,
	title = {Phylogenetic {Distribution} and {Diversity} of {Bacterial} {Pseudo}-{Orthocaspases} {Underline} {Their} {Putative} {Role} in {Photosynthesis}},
	volume = {10},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00293/full},
	doi = {10/gh97fw},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Klemenčič, Marina and Asplund-Samuelsson, Johannes and Dolinar, Marko and Funk, Christiane},
	month = mar,
	year = {2019},
	pages = {293},
}

@article{verger_mechanical_2019,
	title = {Mechanical {Conflicts} in {Twisting} {Growth} {Revealed} by {Cell}-{Cell} {Adhesion} {Defects}},
	volume = {10},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00173/full},
	doi = {10/gkf56m},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Verger, Stéphane and Liu, Mengying and Hamant, Olivier},
	month = feb,
	year = {2019},
	pages = {173},
}

@article{gomez_extraplastidial_2019,
	title = {Extra‐plastidial degradation of chlorophyll and photosystem {I} in tobacco leaves involving ‘senescence‐associated vacuoles’},
	volume = {99},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14337},
	doi = {10/gjdznq},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Gomez, Facundo M. and Carrión, Cristian A. and Costa, María L. and Desel, Christine and Kieselbach, Thomas and Funk, Christiane and Krupinska, Karin and Guiamet, Juan},
	month = aug,
	year = {2019},
	pages = {465--477},
}

@article{chen_functional_2019,
	title = {Functional {Expression} of {Gloeobacter} {Rhodopsin} in {PSI}-{Less} {Synechocystis} sp. {PCC6803}},
	volume = {7},
	issn = {2296-4185},
	url = {https://www.frontiersin.org/article/10.3389/fbioe.2019.00067/full},
	doi = {10/gjdw99},
	urldate = {2021-06-07},
	journal = {Frontiers in Bioengineering and Biotechnology},
	author = {Chen, Que and Arents, Jos and Schuurmans, J. Merijn and Ganapathy, Srividya and de Grip, Willem J. and Cheregi, Otilia and Funk, Christiane and Branco dos Santos, Filipe and Hellingwerf, Klaas J.},
	month = mar,
	year = {2019},
	pages = {67},
}

@article{klemencic_evolution_2019,
	title = {Evolution and structural diversity of metacaspases},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/7/2039/5421715},
	doi = {10/gjdxdf},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Klemenčič, Marina and Funk, Christiane},
	month = apr,
	year = {2019},
	pages = {2039--2047},
}

@article{dong_regulatory_2019,
	title = {Regulatory {Diversification} of {INDEHISCENT} in the {Capsella} {Genus} {Directs} {Variation} in {Fruit} {Morphology}},
	volume = {29},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219300867},
	doi = {10/gfv5z4},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Dong, Yang and Jantzen, Friederike and Stacey, Nicola and Łangowski, Łukasz and Moubayidin, Laila and Šimura, Jan and Ljung, Karin and Østergaard, Lars},
	month = mar,
	year = {2019},
	pages = {1038--1046.e4},
}

@article{wang_opener_2019,
	title = {{OPENER} {Is} a {Nuclear} {Envelope} and {Mitochondria} {Localized} {Protein} {Required} for {Cell} {Cycle} {Progression} in {Arabidopsis}},
	volume = {31},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/31/7/1446-1465/5985717},
	doi = {10/gjcsgx},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Wang, Wei and Zhang, Xueyang and Niittylä, Totte},
	month = jul,
	year = {2019},
	pages = {1446--1465},
}

@article{grebe_unique_2019,
	title = {The unique photosynthetic apparatus of {Pinaceae}: analysis of photosynthetic complexes in {Picea} abies},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	shorttitle = {The unique photosynthetic apparatus of {Pinaceae}},
	url = {https://academic.oup.com/jxb/article/70/12/3211/5425460},
	doi = {10/gjdz35},
	abstract = {Abstract
            Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Grebe, Steffen and Trotta, Andrea and Bajwa, Azfar A and Suorsa, Marjaana and Gollan, Peter J and Jansson, Stefan and Tikkanen, Mikko and Aro, Eva-Mari},
	month = jun,
	year = {2019},
	pages = {3211--3225},
}

Abstract Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.

@article{fischer_dynamics_2019,
	title = {The {Dynamics} of {Cambial} {Stem} {Cell} {Activity}},
	volume = {70},
	issn = {1543-5008, 1545-2123},
	url = {https://www.annualreviews.org/doi/10.1146/annurev-arplant-050718-100402},
	doi = {10/gjcsp3},
	abstract = {Stem cell populations in meristematic tissues at distinct locations in the plant body provide the potency of continuous plant growth. Primary meristems, at the apices of the plant body, contribute mainly to the elongation of the main plant axes, whereas secondary meristems in lateral positions are responsible for the thickening of these axes. The stem cells of the vascular cambium—a secondary lateral meristem—produce the secondary phloem (bast) and secondary xylem (wood). The sites of primary and secondary growth are spatially separated, and mobile signals are expected to coordinate growth rates between apical and lateral stem cell populations. Although the underlying mechanisms have not yet been uncovered, it seems likely that hormones, peptides, and mechanical cues orchestrate primary and secondary growth. In this review, we highlight the current knowledge and recent discoveries of how cambial stem cell activity is regulated, with a focus on mobile signals and the response of cambial activity to environmental and stress factors.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annual Review of Plant Biology},
	author = {Fischer, Urs and Kucukoglu, Melis and Helariutta, Ykä and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2019},
	pages = {293--319},
}

Stem cell populations in meristematic tissues at distinct locations in the plant body provide the potency of continuous plant growth. Primary meristems, at the apices of the plant body, contribute mainly to the elongation of the main plant axes, whereas secondary meristems in lateral positions are responsible for the thickening of these axes. The stem cells of the vascular cambium—a secondary lateral meristem—produce the secondary phloem (bast) and secondary xylem (wood). The sites of primary and secondary growth are spatially separated, and mobile signals are expected to coordinate growth rates between apical and lateral stem cell populations. Although the underlying mechanisms have not yet been uncovered, it seems likely that hormones, peptides, and mechanical cues orchestrate primary and secondary growth. In this review, we highlight the current knowledge and recent discoveries of how cambial stem cell activity is regulated, with a focus on mobile signals and the response of cambial activity to environmental and stress factors.

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

@article{ranade_transcriptome_2019,
	title = {Transcriptome analysis of shade avoidance and shade tolerance in conifers},
	volume = {250},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-019-03160-z},
	doi = {10/gjcr99},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {299--318},
}

@article{sylvestre-gonon_functional_2019,
	title = {Functional, {Structural} and {Biochemical} {Features} of {Plant} {Serinyl}-{Glutathione} {Transferases}},
	volume = {10},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00608/full},
	doi = {10/gjdxch},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Sylvestre-Gonon, Elodie and Law, Simon R. and Schwartz, Mathieu and Robe, Kevin and Keech, Olivier and Didierjean, Claude and Dubos, Christian and Rouhier, Nicolas and Hecker, Arnaud},
	month = may,
	year = {2019},
	pages = {608},
}

@article{miskolczi_long-range_2019,
	title = {Long-range mobile signals mediate seasonal control of shoot growth},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1902199116},
	doi = {10/gg4gdt},
	abstract = {In perennial plants, seasonal shifts provide cues that control adaptive growth patterns of the shoot apex. However, where these seasonal cues are sensed and communicated to the shoot apex remains unknown. We demonstrate that systemic signals from leaves play key roles in seasonal control of shoot growth in model tree hybrid aspen. Grafting experiments reveal that the tree ortholog of
              Arabidopsis
              flowering time regulator
              FLOWERING LOCUS T
              (
              FT
              ) and the plant hormone gibberellic acid (GA) systemically convey seasonal cues to the shoot apex. GA (unlike
              FT
              ) also acts locally in shoot apex, downstream of
              FT
              in seasonal growth control. At the shoot apex, antagonistic factors—
              LAP1
              , a target of
              FT
              and the
              FT
              antagonist
              TERMINAL FLOWER 1
              (
              TFL1
              )—act locally to promote and suppress seasonal growth, respectively. These data reveal seasonal changes perceived in leaves that are communicated to the shoot apex by systemic signals that, in concert with locally acting components, control adaptive growth patterns.},
	language = {en},
	number = {22},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Miskolczi, Pál and Singh, Rajesh Kumar and Tylewicz, Szymon and Azeez, Abdul and Maurya, Jay P. and Tarkowská, Danuše and Novák, Ondřej and Jonsson, Kristoffer and Bhalerao, Rishikesh P.},
	month = may,
	year = {2019},
	pages = {10852--10857},
}

In perennial plants, seasonal shifts provide cues that control adaptive growth patterns of the shoot apex. However, where these seasonal cues are sensed and communicated to the shoot apex remains unknown. We demonstrate that systemic signals from leaves play key roles in seasonal control of shoot growth in model tree hybrid aspen. Grafting experiments reveal that the tree ortholog of Arabidopsis flowering time regulator FLOWERING LOCUS T ( FT ) and the plant hormone gibberellic acid (GA) systemically convey seasonal cues to the shoot apex. GA (unlike FT ) also acts locally in shoot apex, downstream of FT in seasonal growth control. At the shoot apex, antagonistic factors— LAP1 , a target of FT and the FT antagonist TERMINAL FLOWER 1 ( TFL1 )—act locally to promote and suppress seasonal growth, respectively. These data reveal seasonal changes perceived in leaves that are communicated to the shoot apex by systemic signals that, in concert with locally acting components, control adaptive growth patterns.

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

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

@article{marhavy_singlecell_2019,
	title = {Single‐cell damage elicits regional, nematode‐restricting ethylene responses in roots},
	volume = {38},
	issn = {0261-4189, 1460-2075},
	url = {https://onlinelibrary.wiley.com/doi/10.15252/embj.2018100972},
	doi = {10/gf2hvf},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The EMBO Journal},
	author = {Marhavý, Peter and Kurenda, Andrzej and Siddique, Shahid and Dénervaud Tendon, Valerie and Zhou, Feng and Holbein, Julia and Hasan, M Shamim and Grundler, Florian MW and Farmer, Edward E and Geldner, Niko},
	month = may,
	year = {2019},
}

@article{schubert_evolution_2019,
	title = {Evolution of {Cold} {Acclimation} and {Its} {Role} in {Niche} {Transition} in the {Temperate} {Grass} {Subfamily} {Pooideae}},
	volume = {180},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/180/1/404-419/6117721},
	doi = {10/gjdxb7},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Schubert, Marian and Grønvold, Lars and Sandve, Simen R. and Hvidsten, Torgeir R. and Fjellheim, Siri},
	month = may,
	year = {2019},
	pages = {404--419},
}

@article{erguvan_imagej_2019,
	title = {{ImageJ} {SurfCut}: a user-friendly pipeline for high-throughput extraction of cell contours from {3D} image stacks},
	volume = {17},
	issn = {1741-7007},
	shorttitle = {{ImageJ} {SurfCut}},
	url = {https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0657-1},
	doi = {10/gf2hww},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Biology},
	author = {Erguvan, Özer and Louveaux, Marion and Hamant, Olivier and Verger, Stéphane},
	month = dec,
	year = {2019},
	pages = {38},
}

@article{yu_abscisic_2019,
	title = {Abscisic acid signalling mediates biomass trade‐off and allocation in poplar},
	volume = {223},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15878},
	doi = {10/ghtbhc},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Yu, Dade and Wildhagen, Henning and Tylewicz, Szymon and Miskolczi, Pal C. and Bhalerao, Rishikesh P. and Polle, Andrea},
	month = aug,
	year = {2019},
	pages = {1192--1203},
}

@article{tranbarger_pip_2019,
	title = {The {PIP} {Peptide} of {INFLORESCENCE} {DEFICIENT} {IN} {ABSCISSION} {Enhances} {Populus} {Leaf} and {Elaeis} guineensis {Fruit} {Abscission}},
	volume = {8},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/8/6/143},
	doi = {10/gjcsh4},
	abstract = {The programmed loss of a plant organ is called abscission, which is an important cell separation process that occurs with different organs throughout the life of a plant. The use of floral organ abscission in Arabidopsis thaliana as a model has allowed greater understanding of the complexities of organ abscission, but whether the regulatory pathways are conserved throughout the plant kingdom and for all organ abscission types is unknown. One important pathway that has attracted much attention involves a peptide ligand-receptor signalling system that consists of the secreted peptide IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and at least two leucine-rich repeat (LRR) receptor-like kinases (RLK), HAESA (HAE) and HAESA-LIKE2 (HSL2). In the current study we examine the bioactive potential of IDA peptides in two different abscission processes, leaf abscission in Populus and ripe fruit abscission in oil palm, and find in both cases treatment with IDA peptides enhances cell separation and abscission of both organ types. Our results provide evidence to suggest that the IDA–HAE–HSL2 pathway is conserved and functions in these phylogenetically divergent dicot and monocot species during both leaf and fruit abscission, respectively.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plants},
	author = {Tranbarger, Timothy John and Domonhédo, Hubert and Cazemajor, Michel and Dubreuil, Carole and Fischer, Urs and Morcillo, Fabienne},
	month = may,
	year = {2019},
	pages = {143},
}

The programmed loss of a plant organ is called abscission, which is an important cell separation process that occurs with different organs throughout the life of a plant. The use of floral organ abscission in Arabidopsis thaliana as a model has allowed greater understanding of the complexities of organ abscission, but whether the regulatory pathways are conserved throughout the plant kingdom and for all organ abscission types is unknown. One important pathway that has attracted much attention involves a peptide ligand-receptor signalling system that consists of the secreted peptide IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and at least two leucine-rich repeat (LRR) receptor-like kinases (RLK), HAESA (HAE) and HAESA-LIKE2 (HSL2). In the current study we examine the bioactive potential of IDA peptides in two different abscission processes, leaf abscission in Populus and ripe fruit abscission in oil palm, and find in both cases treatment with IDA peptides enhances cell separation and abscission of both organ types. Our results provide evidence to suggest that the IDA–HAE–HSL2 pathway is conserved and functions in these phylogenetically divergent dicot and monocot species during both leaf and fruit abscission, respectively.

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

@article{maaroufi_anthropogenic_2019,
	title = {Anthropogenic nitrogen enrichment enhances soil carbon accumulation by impacting saprotrophs rather than ectomycorrhizal fungal activity},
	volume = {25},
	issn = {1354-1013, 1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14722},
	doi = {10/ghmmzn},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {Maaroufi, Nadia I. and Nordin, Annika and Palmqvist, Kristin and Hasselquist, Niles J. and Forsmark, Benjamin and Rosenstock, Nicholas P. and Wallander, Håkan and Gundale, Michael J.},
	month = sep,
	year = {2019},
	pages = {2900--2914},
}

@article{ingvarsson_effects_2019,
	title = {The effects of clonal forestry on genetic diversity in wild and domesticated stands of forest trees},
	volume = {34},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2018.1469665},
	doi = {10/gjcr7m},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Ingvarsson, Pär K. and Dahlberg, Helena},
	month = jul,
	year = {2019},
	pages = {370--379},
}

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

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

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

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

@article{wegrzyn_cyberinfrastructure_2019,
	title = {Cyberinfrastructure to {Improve} {Forest} {Health} and {Productivity}: {The} {Role} of {Tree} {Databases} in {Connecting} {Genomes}, {Phenomes}, and the {Environment}},
	volume = {10},
	issn = {1664-462X},
	shorttitle = {Cyberinfrastructure to {Improve} {Forest} {Health} and {Productivity}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00813/full},
	doi = {10/ghpwhz},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Wegrzyn, Jill L. and Staton, Margaret A. and Street, Nathaniel R. and Main, Dorrie and Grau, Emily and Herndon, Nic and Buehler, Sean and Falk, Taylor and Zaman, Sumaira and Ramnath, Risharde and Richter, Peter and Sun, Lang and Condon, Bradford and Almsaeed, Abdullah and Chen, Ming and Mannapperuma, Chanaka and Jung, Sook and Ficklin, Stephen},
	month = jun,
	year = {2019},
	pages = {813},
}

@article{martinez_use_2019,
	title = {Use of pulsed electric field permeabilization to extract astaxanthin from the {Nordic} microalga {Haematococcus} pluvialis},
	volume = {289},
	issn = {09608524},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960852419309241},
	doi = {10/gjdzmd},
	language = {en},
	urldate = {2021-06-07},
	journal = {Bioresource Technology},
	author = {Martínez, Juan Manuel and Gojkovic, Zivan and Ferro, Lorenza and Maza, Marcos and Álvarez, Ignacio and Raso, Javier and Funk, Christiane},
	month = oct,
	year = {2019},
	pages = {121694},
}

@article{huber_deg10_2019,
	title = {{DEG10} contributes to mitochondrial proteostasis, root growth, and seed yield in {Arabidopsis}},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/19/5423/5521462},
	doi = {10/gjdz5r},
	abstract = {Abstract
            Maintaining mitochondrial proteome integrity is especially important under stress conditions to ensure a continued ATP supply for protection and adaptation responses in plants. Deg/HtrA proteases are important factors in the cellular protein quality control system, but little is known about their function in mitochondria. Here we analyzed the expression pattern and physiological function of Arabidopsis thaliana DEG10, which has homologs in all photosynthetic eukaryotes. Both expression of DEG10:GFP fusion proteins and immunoblotting after cell fractionation showed an unambiguous subcellular localization exclusively in mitochondria. DEG10 promoter:GUS fusion constructs showed that DEG10 is expressed in trichomes but also in the vascular tissue of roots and aboveground organs. DEG10 loss-of-function mutants were impaired in root elongation, especially at elevated temperature. Quantitative proteome analysis revealed concomitant changes in the abundance of mitochondrial respiratory chain components and assembly factors, which partially appeared to depend on altered mitochondrial retrograde signaling. Under field conditions, lack of DEG10 caused a decrease in seed production. Taken together, our findings demonstrate that DEG10 affects mitochondrial proteostasis, is required for optimal root development and seed set under challenging environmental conditions, and thus contributes to stress tolerance of plants.},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Huber, Catharina V and Jakobs, Barbara D and Mishra, Laxmi S and Niedermaier, Stefan and Stift, Marc and Winter, Gudrun and Adamska, Iwona and Funk, Christiane and Huesgen, Pitter F and Funck, Dietmar},
	editor = {Bozhkov, Peter},
	month = oct,
	year = {2019},
	pages = {5423--5436},
}

Abstract Maintaining mitochondrial proteome integrity is especially important under stress conditions to ensure a continued ATP supply for protection and adaptation responses in plants. Deg/HtrA proteases are important factors in the cellular protein quality control system, but little is known about their function in mitochondria. Here we analyzed the expression pattern and physiological function of Arabidopsis thaliana DEG10, which has homologs in all photosynthetic eukaryotes. Both expression of DEG10:GFP fusion proteins and immunoblotting after cell fractionation showed an unambiguous subcellular localization exclusively in mitochondria. DEG10 promoter:GUS fusion constructs showed that DEG10 is expressed in trichomes but also in the vascular tissue of roots and aboveground organs. DEG10 loss-of-function mutants were impaired in root elongation, especially at elevated temperature. Quantitative proteome analysis revealed concomitant changes in the abundance of mitochondrial respiratory chain components and assembly factors, which partially appeared to depend on altered mitochondrial retrograde signaling. Under field conditions, lack of DEG10 caused a decrease in seed production. Taken together, our findings demonstrate that DEG10 affects mitochondrial proteostasis, is required for optimal root development and seed set under challenging environmental conditions, and thus contributes to stress tolerance of plants.

@article{fruleux_feeling_2019,
	title = {Feeling {Stressed} or {Strained}? {A} {Biophysical} {Model} for {Cell} {Wall} {Mechanosensing} in {Plants}},
	volume = {10},
	issn = {1664-462X},
	shorttitle = {Feeling {Stressed} or {Strained}?},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00757/full},
	doi = {10/gg484c},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Fruleux, Antoine and Verger, Stéphane and Boudaoud, Arezki},
	month = jun,
	year = {2019},
	pages = {757},
}

@article{grones_force-ing_2019,
	title = {{FORCE}-ing the shape},
	volume = {52},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526618301833},
	doi = {10/gjctf8},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Grones, Peter and Raggi, Sara and Robert, Stéphanie},
	month = dec,
	year = {2019},
	pages = {1--6},
}

@article{majda_mechanical_2019,
	title = {Mechanical {Asymmetry} of the {Cell} {Wall} {Predicts} {Changes} in {Pavement} {Cell} {Geometry}},
	volume = {50},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580719304873},
	doi = {10/gf6sqg},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Developmental Cell},
	author = {Majda, Mateusz and Krupinski, Pawel and Jönsson, Henrik and Hamant, Olivier and Robert, Stéphanie},
	month = jul,
	year = {2019},
	pages = {9--10},
}

@article{ranade_global_2019,
	title = {Global gene expression analysis in etiolated and de-etiolated seedlings in conifers},
	volume = {14},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0219272},
	doi = {10/gjcsvr},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, M. Rosario},
	editor = {Zhang, Jin-Song},
	month = jul,
	year = {2019},
	pages = {e0219272},
}

@article{westman_defence_2019,
	title = {Defence priming in {Arabidopsis} – a {Meta}-{Analysis}},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-49811-9},
	doi = {10/gh92kh},
	abstract = {Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Westman, Sara M. and Kloth, Karen J. and Hanson, Johannes and Ohlsson, Anna B. and Albrectsen, Benedicte R.},
	month = sep,
	year = {2019},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {13309},
}

Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.

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

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

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

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

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



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

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

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

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

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

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

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

 [1]: \#ref-1
 [2]: \#ref-3
 [3]: \#ref-4
 [4]: \#ref-5
 [5]: \#ref-6
 [6]: \#ref-7
 [7]: \#ref-8
 [8]: \#ref-9
 [9]: \#ref-10
 [10]: \#ref-11
 [11]: \#ref-12
 [12]: \#xref-ref-1-1 "View reference 1 in text"
 [13]: http://www.fao.org/3/a-i4793e.pdf
 [14]: \#xref-ref-3-1 "View reference 3 in text"
 [15]: \#xref-ref-4-1 "View reference 4 in text"
 [16]: \{openurl\}?query=rft.jtitle\%253DScience\%26rft.volume\%253D54\%26rft.spage\%253D341\%26rft.genre\%253Darticle\%26rft\_val\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Ajournal\%26ctx\_ver\%253DZ39.88-2004\%26url\_ver\%253DZ39.88-2004\%26url\_ctx\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Actx
 [17]: \#xref-ref-5-1 "View reference 5 in text"
 [18]: \#xref-ref-6-1 "View reference 6 in text"
 [19]: \{openurl\}?query=rft.jtitle\%253DScience\%26rft.volume\%253D8\%26rft.spage\%253D221\%26rft.genre\%253Darticle\%26rft\_val\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Ajournal\%26ctx\_ver\%253DZ39.88-2004\%26url\_ver\%253DZ39.88-2004\%26url\_ctx\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Actx
 [20]: \#xref-ref-7-1 "View reference 7 in text"
 [21]: \#xref-ref-8-1 "View reference 8 in text"
 [22]: \{openurl\}?query=rft.jtitle\%253DIn\%2BVitro\%2BCell.\%2BDev.\%2BBiol.\%2BPlant.\%26rft.volume\%253D54\%26rft.spage\%253D341\%26rft.genre\%253Darticle\%26rft\_val\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Ajournal\%26ctx\_ver\%253DZ39.88-2004\%26url\_ver\%253DZ39.88-2004\%26url\_ctx\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Actx
 [23]: \#xref-ref-9-1 "View reference 9 in text"
 [24]: \{openurl\}?query=rft.jtitle\%253DNature\%2Bbiotechnology\%26rft.stitle\%253DNat\%2BBiotechnol\%26rft.aulast\%253DWalter\%26rft.auinit1\%253DC.\%26rft.volume\%253D28\%26rft.issue\%253D7\%26rft.spage\%253D656\%26rft.epage\%253D658\%26rft.atitle\%253DThe\%2B20-year\%2Benvironmental\%2Bsafety\%2Brecord\%2Bof\%2BGM\%2Btrees.\%26rft\_id\%253Dinfo\%253Adoi\%252F10.1038\%252Fnbt0710-656\%26rft\_id\%253Dinfo\%253Apmid\%252F20622831\%26rft.genre\%253Darticle\%26rft\_val\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Ajournal\%26ctx\_ver\%253DZ39.88-2004\%26url\_ver\%253DZ39.88-2004\%26url\_ctx\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Actx
 [25]: /lookup/external-ref?access\_num=10.1038/nbt0710-656\&link\_type=DOI
 [26]: /lookup/external-ref?access\_num=20622831\&link\_type=MED\&atom=\%2Fsci\%2F365\%2F6455\%2F767.2.atom
 [27]: \#xref-ref-10-1 "View reference 10 in text"
 [28]: \{openurl\}?query=rft.jtitle\%253DTree\%2BGenet.\%2BGenomes\%26rft.volume\%253D8\%26rft.spage\%253D221\%26rft.genre\%253Darticle\%26rft\_val\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Ajournal\%26ctx\_ver\%253DZ39.88-2004\%26url\_ver\%253DZ39.88-2004\%26url\_ctx\_fmt\%253Dinfo\%253Aofi\%252Ffmt\%253Akev\%253Amtx\%253Actx
 [29]: \#xref-ref-11-1 "View reference 11 in text"
 [30]: http://www.pefc.co.uk/news\_articles/editorial-updates-to-chain-of-custody-standard-pefc-st-2002-2013
 [31]: \#xref-ref-12-1 "View reference 12 in text"
 [32]: http://www.nap.edu/catalog/25221/forest-health-and-biotechnology-possibilities-and-considerations},
	language = {en},
	number = {6455},
	urldate = {2021-06-07},
	journal = {Science},
	author = {Strauss, Steven H. and Boerjan, Wout and Chiang, Vincent and Costanza, Adam and Coleman, Heather and Davis, John M. and Lu, Meng-Zhu and Mansfield, Shawn D. and Merkle, Scott and Myburg, Alexander and Nilsson, Ove and Pilate, Gilles and Powell, William and Seguin, Armand and Valenzuela, Sofia},
	month = aug,
	year = {2019},
	pmid = {31439790},
	note = {Publisher: American Association for the Advancement of Science
Section: Letters},
	pages = {767--768},
}

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

@article{randewig_combining_2019,
	title = {Combining microdialysis with metabolomics to characterize the in situ composition of dissolved organic compounds in boreal forest soil},
	volume = {136},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071719301853},
	doi = {10/gjcsrk},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Randewig, Dörte and Marshall, John D. and Näsholm, Torgny and Jämtgård, Sandra},
	month = sep,
	year = {2019},
	pages = {107530},
}

@article{lakehal_dao1-mediated_2019,
	title = {A {DAO1}-{Mediated} {Circuit} {Controls} {Auxin} and {Jasmonate} {Crosstalk} {Robustness} during {Adventitious} {Root} {Initiation} in {Arabidopsis}},
	volume = {20},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/20/18/4428},
	doi = {10/gjcs2h},
	abstract = {Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {International Journal of Molecular Sciences},
	author = {Lakehal, Abdellah and Dob, Asma and Novák, Ondřej and Bellini, Catherine},
	month = sep,
	year = {2019},
	pages = {4428},
}

Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.

@article{bernackawojcik_implantable_2019,
	title = {Implantable {Organic} {Electronic} {Ion} {Pump} {Enables} {ABA} {Hormone} {Delivery} for {Control} of {Stomata} in an {Intact} {Tobacco} {Plant}},
	volume = {15},
	issn = {1613-6810, 1613-6829},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201902189},
	doi = {10/gjbhcp},
	language = {en},
	number = {43},
	urldate = {2021-06-07},
	journal = {Small},
	author = {Bernacka‐Wojcik, Iwona and Huerta, Miriam and Tybrandt, Klas and Karady, Michal and Mulla, Mohammad Yusuf and Poxson, David J. and Gabrielsson, Erik O. and Ljung, Karin and Simon, Daniel T. and Berggren, Magnus and Stavrinidou, Eleni},
	month = oct,
	year = {2019},
	pages = {1902189},
}

@article{dauphinee_chemical_2019,
	title = {Chemical {Screening} {Pipeline} for {Identification} of {Specific} {Plant} {Autophagy} {Modulators}},
	volume = {181},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/181/3/855-866/6044914},
	doi = {10/ghwwjc},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Dauphinee, Adrian N. and Cardoso, Catarina and Dalman, Kerstin and Ohlsson, Jonas A. and Fick, Stina Berglund and Robert, Stéphanie and Hicks, Glenn R. and Bozhkov, Peter V. and Minina, Elena A.},
	month = nov,
	year = {2019},
	pages = {855--866},
}

@article{ferro_statistical_2019,
	title = {Statistical {Methods} for {Rapid} {Quantification} of {Proteins}, {Lipids}, and {Carbohydrates} in {Nordic} {Microalgal} {Species} {Using} {ATR}–{FTIR} {Spectroscopy}},
	volume = {24},
	issn = {1420-3049},
	url = {https://www.mdpi.com/1420-3049/24/18/3237},
	doi = {10/ghgqcg},
	abstract = {Attenuated total reflection–Fourier transform infrared (ATR–FTIR) spectroscopy is a simple, cheap, and fast method to collect chemical compositional information from microalgae. However, (semi)quantitative evaluation of the collected data can be daunting. In this work, ATR–FTIR spectroscopy was used to monitor changes of protein, lipid, and carbohydrate content in seven green microalgae grown under nitrogen starvation. Three statistical methods—univariate linear regression analysis (ULRA), orthogonal partial least squares (OPLS), and multivariate curve resolution-alternating least squares (MCR–ALS)—were compared in their ability to model and predict the concentration of these compounds in the biomass. OPLS was found superior, since it i) included all three compounds simultaneously; ii) explained variations in the data very well; iii) had excellent prediction accuracy for proteins and lipids, and acceptable for carbohydrates; and iv) was able to discriminate samples based on cultivation stage and type of storage compounds accumulated in the cells. ULRA models worked well for the determination of proteins and lipids, but carbohydrates could only be estimated if already determined protein contents were used for scaling. Results obtained by MCR–ALS were similar to ULRA, however, this method is considerably easier to perform and interpret than the more abstract statistical/chemometric methods. FTIR-spectroscopy-based models allow high-throughput, cost-effective, and rapid estimation of biomass composition of green microalgae.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Molecules},
	author = {Ferro, Lorenza and Gojkovic, Zivan and Gorzsás, András and Funk, Christiane},
	month = sep,
	year = {2019},
	pages = {3237},
}

Attenuated total reflection–Fourier transform infrared (ATR–FTIR) spectroscopy is a simple, cheap, and fast method to collect chemical compositional information from microalgae. However, (semi)quantitative evaluation of the collected data can be daunting. In this work, ATR–FTIR spectroscopy was used to monitor changes of protein, lipid, and carbohydrate content in seven green microalgae grown under nitrogen starvation. Three statistical methods—univariate linear regression analysis (ULRA), orthogonal partial least squares (OPLS), and multivariate curve resolution-alternating least squares (MCR–ALS)—were compared in their ability to model and predict the concentration of these compounds in the biomass. OPLS was found superior, since it i) included all three compounds simultaneously; ii) explained variations in the data very well; iii) had excellent prediction accuracy for proteins and lipids, and acceptable for carbohydrates; and iv) was able to discriminate samples based on cultivation stage and type of storage compounds accumulated in the cells. ULRA models worked well for the determination of proteins and lipids, but carbohydrates could only be estimated if already determined protein contents were used for scaling. Results obtained by MCR–ALS were similar to ULRA, however, this method is considerably easier to perform and interpret than the more abstract statistical/chemometric methods. FTIR-spectroscopy-based models allow high-throughput, cost-effective, and rapid estimation of biomass composition of green microalgae.

@article{myburg_systems_2019,
	title = {Systems and {Synthetic} {Biology} of {Forest} {Trees}: {A} {Bioengineering} {Paradigm} for {Woody} {Biomass} {Feedstocks}},
	volume = {10},
	issn = {1664-462X},
	shorttitle = {Systems and {Synthetic} {Biology} of {Forest} {Trees}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.00775/full},
	doi = {10/gjdzht},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Myburg, Alexander A. and Hussey, Steven G. and Wang, Jack P. and Street, Nathaniel R. and Mizrachi, Eshchar},
	month = jun,
	year = {2019},
	pages = {775},
}

@article{bogaert_auxin_2019,
	title = {Auxin {Function} in the {Brown} {Alga} \textit{{Dictyota} dichotoma}},
	volume = {179},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/179/1/280-299/6116458},
	doi = {10/gjcrcp},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Bogaert, Kenny A. and Blommaert, Lander and Ljung, Karin and Beeckman, Tom and De Clerck, Olivier},
	month = jan,
	year = {2019},
	pages = {280--299},
}

@article{nielsen_transcription-driven_2019,
	title = {Transcription-driven chromatin repression of {Intragenic} transcription start sites},
	volume = {15},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1007969},
	doi = {10/gh9djk},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Nielsen, Mathias and Ard, Ryan and Leng, Xueyuan and Ivanov, Maxim and Kindgren, Peter and Pelechano, Vicent and Marquardt, Sebastian},
	editor = {Köhler, Claudia},
	month = feb,
	year = {2019},
	pages = {e1007969},
}

@article{mishra_reduced_2019,
	title = {Reduced expression of the proteolytically inactive {FtsH} members has impacts on the {Darwinian} fitness of {Arabidopsis} thaliana},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/7/2173/5289174},
	doi = {10/gjdxdd},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Mishra, Laxmi S and Mielke, Kati and Wagner, Raik and Funk, Christiane},
	month = apr,
	year = {2019},
	pages = {2173--2184},
}

@article{lage_microalgae_2019,
	title = {Microalgae {Cultivation} for the {Biotransformation} of {Birch} {Wood} {Hydrolysate} and {Dairy} {Effluent}},
	volume = {9},
	issn = {2073-4344},
	url = {http://www.mdpi.com/2073-4344/9/2/150},
	doi = {10/gjb3cx},
	abstract = {In order to investigate environmentally sustainable sources of organic carbon and nutrients, four Nordic green microalgal strains, Chlorella sorokiniana, Chlorella saccharophila, Chlorella vulgaris, and Coelastrella sp., were grown on a wood (Silver birch, Betula pendula) hydrolysate and dairy effluent mixture. The biomass and lipid production were analysed under mixotrophic, as well as two-stage mixotrophic/heterotrophic regimes. Of all of the species, Coelastrella sp. produced the most total lipids per dry weight ({\textasciitilde}40\%) in the mixture of birch hydrolysate and dairy effluent without requiring nutrient (nitrogen, phosphorus, and potassium—NPK) supplementation. Overall, in the absence of NPK, the two-stage mixotrophic/heterotrophic cultivation enhanced the lipid concentration, but reduced the amount of biomass. Culturing microalgae in integrated waste streams under mixotrophic growth regimes is a promising approach for sustainable biofuel production, especially in regions with large seasonal variation in daylight, like northern Sweden. To the best of our knowledge, this is the first report of using a mixture of wood hydrolysate and dairy effluent for the growth and lipid production of microalgae in the literature.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Catalysts},
	author = {Lage, Sandra and Kudahettige, Nirupa and Ferro, Lorenza and Matsakas, Leonidas and Funk, Christiane and Rova, Ulrika and Gentili, Francesco},
	month = feb,
	year = {2019},
	pages = {150},
}

In order to investigate environmentally sustainable sources of organic carbon and nutrients, four Nordic green microalgal strains, Chlorella sorokiniana, Chlorella saccharophila, Chlorella vulgaris, and Coelastrella sp., were grown on a wood (Silver birch, Betula pendula) hydrolysate and dairy effluent mixture. The biomass and lipid production were analysed under mixotrophic, as well as two-stage mixotrophic/heterotrophic regimes. Of all of the species, Coelastrella sp. produced the most total lipids per dry weight (~40%) in the mixture of birch hydrolysate and dairy effluent without requiring nutrient (nitrogen, phosphorus, and potassium—NPK) supplementation. Overall, in the absence of NPK, the two-stage mixotrophic/heterotrophic cultivation enhanced the lipid concentration, but reduced the amount of biomass. Culturing microalgae in integrated waste streams under mixotrophic growth regimes is a promising approach for sustainable biofuel production, especially in regions with large seasonal variation in daylight, like northern Sweden. To the best of our knowledge, this is the first report of using a mixture of wood hydrolysate and dairy effluent for the growth and lipid production of microalgae in the literature.

@article{you_phloem_2019,
	title = {Phloem {Companion} {Cell}-{Specific} {Transcriptomic} and {Epigenomic} {Analyses} {Identify} {MRF1}, a {Regulator} of {Flowering}},
	volume = {31},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/31/2/325-345/5985421},
	doi = {10/gjdw33},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {You, Yuan and Sawikowska, Aneta and Lee, Joanne E. and Benstein, Ruben M. and Neumann, Manuela and Krajewski, Paweł and Schmid, Markus},
	month = feb,
	year = {2019},
	pages = {325--345},
}

@article{aubry_lateral_2019,
	title = {Lateral {Transport} of {Organic} and {Inorganic} {Solutes}},
	volume = {8},
	issn = {2223-7747},
	url = {http://www.mdpi.com/2223-7747/8/1/20},
	doi = {10/gjdwmf},
	abstract = {Organic (e.g., sugars and amino acids) and inorganic (e.g., K+, Na+, PO42−, and SO42−) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plants},
	author = {Aubry, Emilie and Dinant, Sylvie and Vilaine, Françoise and Bellini, Catherine and Le Hir, Rozenn},
	month = jan,
	year = {2019},
	pages = {20},
}

Organic (e.g., sugars and amino acids) and inorganic (e.g., K+, Na+, PO42−, and SO42−) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.

@article{ferro_elucidating_2019,
	title = {Elucidating the symbiotic interactions between a locally isolated microalga {Chlorella} vulgaris and its co-occurring bacterium {Rhizobium} sp. in synthetic municipal wastewater},
	volume = {31},
	issn = {0921-8971, 1573-5176},
	url = {http://link.springer.com/10.1007/s10811-019-1741-1},
	doi = {10/gjdzrk},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Journal of Applied Phycology},
	author = {Ferro, L. and Colombo, M. and Posadas, E. and Funk, C. and Muñoz, R.},
	month = aug,
	year = {2019},
	pages = {2299--2310},
}

@article{decker_udp-sugar_2019,
	title = {{UDP}-{Sugar} {Producing} {Pyrophosphorylases}: {Distinct} and {Essential} {Enzymes} {With} {Overlapping} {Substrate} {Specificities}, {Providing} de novo {Precursors} for {Glycosylation} {Reactions}},
	volume = {9},
	issn = {1664-462X},
	shorttitle = {{UDP}-{Sugar} {Producing} {Pyrophosphorylases}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.01822/full},
	doi = {10/gjdwdm},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Decker, Daniel and Kleczkowski, Leszek A.},
	month = jan,
	year = {2019},
	pages = {1822},
}

@article{karan_green_2019,
	title = {Green {Bioplastics} as {Part} of a {Circular} {Bioeconomy}},
	volume = {24},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138518302723},
	doi = {10/gfw5hg},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Trends in Plant Science},
	author = {Karan, Hakan and Funk, Christiane and Grabert, Martin and Oey, Melanie and Hankamer, Ben},
	month = mar,
	year = {2019},
	pages = {237--249},
}

@article{escamez_extracellular_2019,
	title = {Extracellular peptide {Kratos} restricts cell death during vascular development and stress in {Arabidopsis}},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/7/2199/5308826},
	doi = {10/gjd42p},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Escamez, Sacha and Stael, Simon and Vainonen, Julia P and Willems, Patrick and Jin, Huiting and Kimura, Sachie and Van Breusegem, Frank and Gevaert, Kris and Wrzaczek, Michael and Tuominen, Hannele},
	month = apr,
	year = {2019},
	pages = {2199--2210},
}

@article{cui_interaction_2019,
	title = {Interaction of methyl viologen-induced chloroplast and mitochondrial signalling in {Arabidopsis}},
	volume = {134},
	issn = {08915849},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0891584918323116},
	doi = {10/gkf56j},
	language = {en},
	urldate = {2021-06-07},
	journal = {Free Radical Biology and Medicine},
	author = {Cui, Fuqiang and Brosché, Mikael and Shapiguzov, Alexey and He, Xin-Qiang and Vainonen, Julia P. and Leppälä, Johanna and Trotta, Andrea and Kangasjärvi, Saijaliisa and Salojärvi, Jarkko and Kangasjärvi, Jaakko and Overmyer, Kirk},
	month = apr,
	year = {2019},
	pages = {555--566},
}

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

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

@article{vico_can_2019,
	title = {Can leaf net photosynthesis acclimate to rising and more variable temperatures?},
	volume = {42},
	issn = {0140-7791, 1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13525},
	doi = {10/gjcr7x},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Vico, Giulia and Way, Danielle A. and Hurry, Vaughan and Manzoni, Stefano},
	month = jun,
	year = {2019},
	pages = {1913--1928},
}

@article{bergman_heterologous_2019,
	title = {Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in {Saccharomyces} cerevisiae},
	volume = {18},
	issn = {1475-2859},
	url = {https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-019-1072-6},
	doi = {10/gh8zrg},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Microbial Cell Factories},
	author = {Bergman, Alexandra and Hellgren, John and Moritz, Thomas and Siewers, Verena and Nielsen, Jens and Chen, Yun},
	month = dec,
	year = {2019},
	pages = {25},
}

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

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

@article{vain_selective_2019,
	title = {Selective auxin agonists induce specific {AUX}/{IAA} protein degradation to modulate plant development},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1809037116},
	doi = {10/gfxjp6},
	abstract = {Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCF
              TIR1/AFB
              functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Vain, Thomas and Raggi, Sara and Ferro, Noel and Barange, Deepak Kumar and Kieffer, Martin and Ma, Qian and Doyle, Siamsa M. and Thelander, Mattias and Pařízková, Barbora and Novák, Ondřej and Ismail, Alexandre and Enquist, Per-Anders and Rigal, Adeline and Łangowska, Małgorzata and Ramans Harborough, Sigurd and Zhang, Yi and Ljung, Karin and Callis, Judy and Almqvist, Fredrik and Kepinski, Stefan and Estelle, Mark and Pauwels, Laurens and Robert, Stéphanie},
	month = mar,
	year = {2019},
	pages = {6463--6472},
}

Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCF TIR1/AFB functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.

@article{carius_dynamic_2019,
	title = {Dynamic {pH}‐induced conformational changes of the {PsbO} protein in the fluctuating acidity of the thylakoid lumen},
	volume = {166},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.12948},
	doi = {10/gjdxbj},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Carius, Anke B. and Rogne, Per and Duchoslav, Miloš and Wolf‐Watz, Magnus and Samuelsson, Göran and Shutova, Tatyana},
	month = may,
	year = {2019},
	pages = {288--299},
}

@article{bieleszova_new_2019,
	title = {New fluorescently labeled auxins exhibit promising anti-auxin activity},
	volume = {48},
	issn = {18716784},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1871678417305721},
	doi = {10.1016/j.nbt.2018.06.003},
	language = {en},
	urldate = {2021-06-07},
	journal = {New Biotechnology},
	author = {Bieleszová, Kristýna and Pařízková, Barbora and Kubeš, Martin and Husičková, Alexandra and Kubala, Martin and Ma, Qian and Sedlářová, Michaela and Robert, Stéphanie and Doležal, Karel and Strnad, Miroslav and Novák, Ondřej and Žukauskaitė, Asta},
	month = jan,
	year = {2019},
	pages = {44--52},
}

@article{brunoni_control_2019,
	title = {Control of root meristem establishment in conifers},
	volume = {165},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12783},
	doi = {10.1111/ppl.12783},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Brunoni, Federica and Ljung, Karin and Bellini, Catherine},
	month = jan,
	year = {2019},
	pages = {81--89},
}

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

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

@article{chen_combining_2019,
	title = {Combining retinal-based and chlorophyll-based (oxygenic) photosynthesis: {Proteorhodopsin} expression increases growth rate and fitness of a ∆{PSI} strain of {Synechocystis} sp. {PCC6803}},
	volume = {52},
	issn = {10967176},
	shorttitle = {Combining retinal-based and chlorophyll-based (oxygenic) photosynthesis},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1096717618303161},
	doi = {10.1016/j.ymben.2018.11.002},
	language = {en},
	urldate = {2021-06-07},
	journal = {Metabolic Engineering},
	author = {Chen, Que and Arents, Jos and Schuurmans, J. Merijn and Ganapathy, Srividya and de Grip, Willem J. and Cheregi, Otilia and Funk, Christiane and dos Santos, Filipe Branco and Hellingwerf, Klaas J.},
	month = mar,
	year = {2019},
	pages = {68--76},
}

@article{de_zio_tissue-specific_2019,
	title = {Tissue-specific hormone profiles from woody poplar roots under bending stress},
	volume = {165},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12830},
	doi = {10.1111/ppl.12830},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {De Zio, Elena and Trupiano, Dalila and Karady, Michal and Antoniadi, Ioanna and Montagnoli, Antonio and Terzaghi, Mattia and Chiatante, Donato and Ljung, Karin and Scippa, Gabriella S.},
	month = jan,
	year = {2019},
	pages = {101--113},
}

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

@article{gojkovic_northern_2019,
	title = {Northern green algae have the capacity to remove active pharmaceutical ingredients},
	volume = {170},
	issn = {01476513},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0147651318313198},
	doi = {10.1016/j.ecoenv.2018.12.032},
	language = {en},
	urldate = {2021-06-07},
	journal = {Ecotoxicology and Environmental Safety},
	author = {Gojkovic, Zivan and Lindberg, Richard H. and Tysklind, Mats and Funk, Christiane},
	month = apr,
	year = {2019},
	pages = {644--656},
}

@article{igamberdiev_thermodynamic_2019,
	title = {Thermodynamic buffering, stable non-equilibrium and establishment of the computable structure of plant metabolism},
	volume = {146},
	issn = {00796107},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0079610718302037},
	doi = {10.1016/j.pbiomolbio.2018.11.005},
	language = {en},
	urldate = {2021-06-07},
	journal = {Progress in Biophysics and Molecular Biology},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = sep,
	year = {2019},
	pages = {23--36},
}

@article{johnsson_plant_2019,
	title = {The plant hormone auxin directs timing of xylem development by inhibition of secondary cell wall deposition through repression of secondary wall {NAC}‐domain transcription factors},
	volume = {165},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.12766},
	doi = {10.1111/ppl.12766},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Johnsson, Christoffer and Jin, Xu and Xue, Weiya and Dubreuil, Carole and Lezhneva, Lina and Fischer, Urs},
	month = apr,
	year = {2019},
	pages = {673--689},
}

@article{kawde_microstructured_2019,
	title = {A microstructured p-{Si} photocathode outcompetes {Pt} as a counter electrode to hematite in photoelectrochemical water splitting},
	volume = {48},
	issn = {1477-9226, 1477-9234},
	url = {http://xlink.rsc.org/?DOI=C8DT03653E},
	doi = {10.1039/C8DT03653E},
	abstract = {Herein we demonstrate that an earth-abundant semiconductor photocathode (p-Si/TiO
              2
              /NiO
              x
              ) out-competes rare and expensive Pt as counter electrode to Fe-oxide for overall photoelectrochemical water splitting.
            
          , 
            
              Herein, we communicate about an Earth-abundant semiconductor photocathode (p-Si/TiO
              2
              /NiO
              x
              ) as an alternative for the rare and expensive Pt as a counter electrode for overall photoelectrochemical water splitting. The proposed photoelectrochemical (PEC) water-splitting device mimics the “Z”-scheme observed in natural photosynthesis by combining two photoelectrodes in a parallel-illumination mode. A nearly 60\% increase in the photocurrent density (
              J
              ph
              ) for pristine α-Fe
              2
              O
              3
              and a 77\% increase in the applied bias photocurrent efficiency (ABPE) were achieved by replacing the conventionally used Pt cathode with an efficient, cost effective p-Si/TiO
              2
              /NiO
              x
              photocathode under parallel illumination. The resulting photocurrent density of 1.26 mA cm
              −2
              at 1.23
              V
              RHE
              represents a new record performance for hydrothermally grown pristine α-Fe
              2
              O
              3
              nanorod photoanodes in combination with a photocathode, which opens the prospect for further improvement by doping α-Fe
              2
              O
              3
              or by its decoration with co-catalysts. Electrochemical impedance spectroscopy measurements suggest that this significant performance increase is due to the enhancement of the space-charge field in α-Fe
              2
              O
              3
              .},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Dalton Transactions},
	author = {Kawde, Anurag and Annamalai, Alagappan and Sellstedt, Anita and Glatzel, Pieter and Wågberg, Thomas and Messinger, Johannes},
	year = {2019},
	pages = {1166--1170},
}

Herein we demonstrate that an earth-abundant semiconductor photocathode (p-Si/TiO 2 /NiO x ) out-competes rare and expensive Pt as counter electrode to Fe-oxide for overall photoelectrochemical water splitting. , Herein, we communicate about an Earth-abundant semiconductor photocathode (p-Si/TiO 2 /NiO x ) as an alternative for the rare and expensive Pt as a counter electrode for overall photoelectrochemical water splitting. The proposed photoelectrochemical (PEC) water-splitting device mimics the “Z”-scheme observed in natural photosynthesis by combining two photoelectrodes in a parallel-illumination mode. A nearly 60% increase in the photocurrent density ( J ph ) for pristine α-Fe 2 O 3 and a 77% increase in the applied bias photocurrent efficiency (ABPE) were achieved by replacing the conventionally used Pt cathode with an efficient, cost effective p-Si/TiO 2 /NiO x photocathode under parallel illumination. The resulting photocurrent density of 1.26 mA cm −2 at 1.23 V RHE represents a new record performance for hydrothermally grown pristine α-Fe 2 O 3 nanorod photoanodes in combination with a photocathode, which opens the prospect for further improvement by doping α-Fe 2 O 3 or by its decoration with co-catalysts. Electrochemical impedance spectroscopy measurements suggest that this significant performance increase is due to the enhancement of the space-charge field in α-Fe 2 O 3 .

@article{lakehal_control_2019,
	title = {Control of adventitious root formation: insights into synergistic and antagonistic hormonal interactions},
	volume = {165},
	issn = {00319317},
	shorttitle = {Control of adventitious root formation},
	url = {http://doi.wiley.com/10.1111/ppl.12823},
	doi = {10.1111/ppl.12823},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Lakehal, Abdellah and Bellini, Catherine},
	month = jan,
	year = {2019},
	pages = {90--100},
}

@article{ruwe_e_2019,
	title = {The {E} domain of {CRR2} participates in sequence‐specific recognition of {RNA} in plastids},
	volume = {222},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15578},
	doi = {10.1111/nph.15578},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Ruwe, Hannes and Gutmann, Bernard and Schmitz‐Linneweber, Christian and Small, Ian and Kindgren, Peter},
	month = apr,
	year = {2019},
	pages = {218--229},
}

@article{singh_tree_2019,
	title = {A {Tree} {Ortholog} of {SHORT} {VEGETATIVE} {PHASE} {Floral} {Repressor} {Mediates} {Photoperiodic} {Control} of {Bud} {Dormancy}},
	volume = {29},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982218314726},
	doi = {10.1016/j.cub.2018.11.006},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Singh, Rajesh Kumar and Miskolczi, Pal and Maurya, Jay P. and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2019},
	pages = {128--133.e2},
}

@article{vaattovaara_high-throughput_2019,
	title = {High-throughput sequencing data and the impact of plant gene annotation quality},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/4/1069/5259105},
	doi = {10.1093/jxb/ery434},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Vaattovaara, Aleksia and Leppälä, Johanna and Salojärvi, Jarkko and Wrzaczek, Michael},
	month = feb,
	year = {2019},
	pages = {1069--1076},
}

@article{van_der_horst_novel_2019,
	title = {Novel pipeline identifies new upstream {ORFs} and non-{AUG} initiating main {ORFs} with conserved amino acid sequences in the 5′ leader of {mRNAs} in \textit{{Arabidopsis} thaliana}},
	volume = {25},
	issn = {1355-8382, 1469-9001},
	url = {http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.067983.118},
	doi = {10.1261/rna.067983.118},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {RNA},
	author = {van der Horst, Sjors and Snel, Berend and Hanson, Johannes and Smeekens, Sjef},
	month = mar,
	year = {2019},
	pages = {292--304},
}

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

@article{blanco_dual_2019,
	title = {Dual and dynamic intracellular localization of {Arabidopsis} thaliana {SnRK1}.1},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/8/2325/5308885},
	doi = {10.1093/jxb/erz023},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Blanco, Nicolás E and Liebsch, Daniela and Guinea Díaz, Manuel and Strand, Åsa and Whelan, James},
	month = apr,
	year = {2019},
	pages = {2325--2338},
}

@article{holbein_root_2019,
	title = {Root endodermal barrier system contributes to defence against plant‐parasitic cyst and root‐knot nematodes},
	volume = {100},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14459},
	doi = {10.1111/tpj.14459},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Holbein, Julia and Franke, Rochus B. and Marhavý, Peter and Fujita, Satoshi and Górecka, Mirosława and Sobczak, Mirosław and Geldner, Niko and Schreiber, Lukas and Grundler, Florian M. W. and Siddique, Shahid},
	month = oct,
	year = {2019},
	pages = {221--236},
}

@incollection{street_genomics_2019,
	title = {Genomics of forest trees},
	volume = {89},
	isbn = {978-0-12-815465-6},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0065229618300867},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Advances in {Botanical} {Research}},
	publisher = {Elsevier},
	author = {Street, Nathaniel Robert},
	year = {2019},
	doi = {10.1016/bs.abr.2018.11.001},
	pages = {1--37},
}

@article{palmroth_nitrogen_2019,
	title = {Nitrogen supply and other controls of carbon uptake of understory vegetation in a boreal {Picea} abies forest},
	volume = {276-277},
	issn = {01681923},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S016819231930228X},
	doi = {10.1016/j.agrformet.2019.107620},
	language = {en},
	urldate = {2021-06-07},
	journal = {Agricultural and Forest Meteorology},
	author = {Palmroth, Sari and Bach, Lisbet H. and Lindh, Marie and Kolari, Pasi and Nordin, Annika and Palmqvist, Kristin},
	month = oct,
	year = {2019},
	pages = {107620},
}

@article{bjarstig_struggling_2019,
	title = {A struggling collaborative process – revisiting the woodland key habitat concept in {Swedish} forests},
	volume = {34},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827581.2019.1674916},
	doi = {10.1080/02827581.2019.1674916},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Bjärstig, Therese and Sandström, Camilla and Sjögren, Jörgen and Soneson, Johan and Nordin, Annika},
	month = nov,
	year = {2019},
	pages = {699--708},
}

@article{van_der_woude_histone_2019,
	title = {{HISTONE} {DEACETYLASE} 9 stimulates auxin-dependent thermomorphogenesis in \textit{{Arabidopsis} thaliana} by mediating {H2A}.{Z} depletion},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1911694116},
	doi = {10.1073/pnas.1911694116},
	abstract = {Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the
              YUCCA8
              locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with
              YUCCA8
              , allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.},
	language = {en},
	number = {50},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {van der Woude, Lennard C. and Perrella, Giorgio and Snoek, Basten L. and van Hoogdalem, Mark and Novák, Ondřej and van Verk, Marcel C. and van Kooten, Heleen N. and Zorn, Lennert E. and Tonckens, Rolf and Dongus, Joram A. and Praat, Myrthe and Stouten, Evelien A. and Proveniers, Marcel C. G. and Vellutini, Elisa and Patitaki, Eirini and Shapulatov, Umidjon and Kohlen, Wouter and Balasubramanian, Sureshkumar and Ljung, Karin and van der Krol, Alexander R. and Smeekens, Sjef and Kaiserli, Eirini and van Zanten, Martijn},
	month = dec,
	year = {2019},
	pages = {25343--25354},
}

Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8 , allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.

@article{hajheidari_autoregulation_2019,
	title = {Autoregulation of {RCO} by {Low}-{Affinity} {Binding} {Modulates} {Cytokinin} {Action} and {Shapes} {Leaf} {Diversity}},
	volume = {29},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219313806},
	doi = {10.1016/j.cub.2019.10.040},
	language = {en},
	number = {24},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Hajheidari, Mohsen and Wang, Yi and Bhatia, Neha and Vuolo, Francesco and Franco-Zorrilla, José Manuel and Karady, Michal and Mentink, Remco A. and Wu, Anhui and Oluwatobi, Bello Rilwan and Müller, Bruno and Dello Ioio, Raffaele and Laurent, Stefan and Ljung, Karin and Huijser, Peter and Gan, Xiangchao and Tsiantis, Miltos},
	month = dec,
	year = {2019},
	pages = {4183--4192.e6},
}

@article{skokan_pin-driven_2019,
	title = {{PIN}-driven auxin transport emerged early in streptophyte evolution},
	volume = {5},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-019-0542-5},
	doi = {10.1038/s41477-019-0542-5},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Skokan, Roman and Medvecká, Eva and Viaene, Tom and Vosolsobě, Stanislav and Zwiewka, Marta and Müller, Karel and Skůpa, Petr and Karady, Michal and Zhang, Yuzhou and Janacek, Dorina P. and Hammes, Ulrich Z. and Ljung, Karin and Nodzyński, Tomasz and Petrášek, Jan and Friml, Jiří},
	month = nov,
	year = {2019},
	pages = {1114--1119},
}

@article{brunoni_bacterial_2019,
	title = {A bacterial assay for rapid screening of {IAA} catabolic enzymes},
	volume = {15},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0509-6},
	doi = {10.1186/s13007-019-0509-6},
	abstract = {Abstract
            
              Background
              
                Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-
                l
                -aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and
                in planta
                feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.
              
            
            
              Results
              In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.
            
            
              Conclusions
              This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Methods},
	author = {Brunoni, Federica and Collani, Silvio and Šimura, Jan and Schmid, Markus and Bellini, Catherine and Ljung, Karin},
	month = dec,
	year = {2019},
	pages = {126},
}

Abstract Background Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl- l -aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays. Results In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein. Conclusions This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.

@article{rende_two-step_2019,
	title = {Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry},
	volume = {15},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0514-9},
	doi = {10.1186/s13007-019-0514-9},
	abstract = {Abstract
            
              Background
              Sugar phosphates are important intermediates of central carbon metabolism in biological systems, with roles in glycolysis, the pentose–phosphate pathway, tricarboxylic acid (TCA) cycle, and many other biosynthesis pathways. Understanding central carbon metabolism requires a simple, robust and comprehensive analytical method. However, sugar phosphates are notoriously difficult to analyze by traditional reversed phase liquid chromatography.
            
            
              Results
              
                Here, we show a two-step derivatization of sugar phosphates by methoxylamine and propionic acid anhydride after chloroform/methanol (3:7) extraction from
                Populus
                leaf and developing wood that improves separation, identification and quantification of sugar phosphates by ultra high performance liquid chromatography–electrospray ionization–mass spectrometry (UHPLC–ESI–MS). Standard curves of authentic sugar phosphates were generated for concentrations from pg to ng/μl with a correlation coefficient
                R
                2
                 {\textgreater} 0.99. The method showed high sensitivity and repeatability with relative standard deviation (RSD) {\textless} 20\% based on repeated extraction, derivatization and detection. The analytical accuracy for
                Populus
                leaf extracts, determined by a two-level spiking approach of selected metabolites, was 79–107\%.
              
            
            
              Conclusion
              
                The results show the reliability of combined reversed phase liquid chromatography–tandem mass spectrometry for sugar phosphate analysis and demonstrate the presence of two unknown sugar phosphates in
                Populus
                extracts.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Methods},
	author = {Rende, Umut and Niittylä, Totte and Moritz, Thomas},
	month = dec,
	year = {2019},
	pages = {127},
}

Abstract Background Sugar phosphates are important intermediates of central carbon metabolism in biological systems, with roles in glycolysis, the pentose–phosphate pathway, tricarboxylic acid (TCA) cycle, and many other biosynthesis pathways. Understanding central carbon metabolism requires a simple, robust and comprehensive analytical method. However, sugar phosphates are notoriously difficult to analyze by traditional reversed phase liquid chromatography. Results Here, we show a two-step derivatization of sugar phosphates by methoxylamine and propionic acid anhydride after chloroform/methanol (3:7) extraction from Populus leaf and developing wood that improves separation, identification and quantification of sugar phosphates by ultra high performance liquid chromatography–electrospray ionization–mass spectrometry (UHPLC–ESI–MS). Standard curves of authentic sugar phosphates were generated for concentrations from pg to ng/μl with a correlation coefficient R 2  \textgreater 0.99. The method showed high sensitivity and repeatability with relative standard deviation (RSD) \textless 20% based on repeated extraction, derivatization and detection. The analytical accuracy for Populus leaf extracts, determined by a two-level spiking approach of selected metabolites, was 79–107%. Conclusion The results show the reliability of combined reversed phase liquid chromatography–tandem mass spectrometry for sugar phosphate analysis and demonstrate the presence of two unknown sugar phosphates in Populus extracts.

@article{zhu_targeted_2019,
	title = {Targeted {Multiple} {Reaction} {Monitoring} {Analysis} of {CSF} {Identifies} {UCHL1} and {GPNMB} as {Candidate} {Biomarkers} for {ALS}},
	volume = {69},
	issn = {0895-8696, 1559-1166},
	url = {http://link.springer.com/10.1007/s12031-019-01411-y},
	doi = {10.1007/s12031-019-01411-y},
	abstract = {Abstract
            The neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) share some common molecular deficits including disruption of protein homeostasis leading to disease-specific protein aggregation. While insoluble protein aggregates are the defining pathological confirmation of diagnosis, patient stratification based on early molecular etiologies may identify distinct subgroups within a clinical diagnosis that would respond differently in therapeutic development programs. We are developing targeted multiple reaction monitoring (MRM) mass spectrometry methods to rigorously quantify CSF proteins from known disease genes involved in lysosomal, ubiquitin-proteasomal, and autophagy pathways. Analysis of CSF from 21 PD, 21 ALS, and 25 control patients, rigorously matched for gender, age, and age of sample, revealed significant changes in peptide levels between PD, ALS, and control. In patients with PD, levels of two peptides for chromogranin B (CHGB, secretogranin 1) were significantly reduced. In CSF of patients with ALS, levels of two peptides from ubiquitin carboxy-terminal hydrolase like protein 1 (UCHL1) and one peptide each for glycoprotein non-metastatic melanoma protein B (GPNMB) and cathepsin D (CTSD) were all increased. Analysis of patients with ALS separated into two groups based on length of survival after CSF sampling revealed that the increases in GPNMB and UCHL1 were specific for short-lived ALS patients. While analysis of additional cohorts is required to validate these candidate biomarkers, this study suggests methods for stratification of ALS patients for clinical trials and identifies targets for drug efficacy measurements during therapeutic development.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Journal of Molecular Neuroscience},
	author = {Zhu, Shaochun and Wuolikainen, Anna and Wu, Junfang and Öhman, Anders and Wingsle, Gunnar and Moritz, Thomas and Andersen, Peter M. and Forsgren, Lars and Trupp, Miles},
	month = dec,
	year = {2019},
	pages = {643--657},
}

Abstract The neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) share some common molecular deficits including disruption of protein homeostasis leading to disease-specific protein aggregation. While insoluble protein aggregates are the defining pathological confirmation of diagnosis, patient stratification based on early molecular etiologies may identify distinct subgroups within a clinical diagnosis that would respond differently in therapeutic development programs. We are developing targeted multiple reaction monitoring (MRM) mass spectrometry methods to rigorously quantify CSF proteins from known disease genes involved in lysosomal, ubiquitin-proteasomal, and autophagy pathways. Analysis of CSF from 21 PD, 21 ALS, and 25 control patients, rigorously matched for gender, age, and age of sample, revealed significant changes in peptide levels between PD, ALS, and control. In patients with PD, levels of two peptides for chromogranin B (CHGB, secretogranin 1) were significantly reduced. In CSF of patients with ALS, levels of two peptides from ubiquitin carboxy-terminal hydrolase like protein 1 (UCHL1) and one peptide each for glycoprotein non-metastatic melanoma protein B (GPNMB) and cathepsin D (CTSD) were all increased. Analysis of patients with ALS separated into two groups based on length of survival after CSF sampling revealed that the increases in GPNMB and UCHL1 were specific for short-lived ALS patients. While analysis of additional cohorts is required to validate these candidate biomarkers, this study suggests methods for stratification of ALS patients for clinical trials and identifies targets for drug efficacy measurements during therapeutic development.

@article{skrobonja_uptake_2019,
	title = {Uptake {Kinetics} of {Methylmercury} in a {Freshwater} {Alga} {Exposed} to {Methylmercury} {Complexes} with {Environmentally} {Relevant} {Thiols}},
	volume = {53},
	issn = {0013-936X, 1520-5851},
	url = {https://pubs.acs.org/doi/10.1021/acs.est.9b05164},
	doi = {10.1021/acs.est.9b05164},
	language = {en},
	number = {23},
	urldate = {2021-06-07},
	journal = {Environmental Science \& Technology},
	author = {Skrobonja, Aleksandra and Gojkovic, Zivan and Soerensen, Anne L. and Westlund, Per-Olof and Funk, Christiane and Björn, Erik},
	month = dec,
	year = {2019},
	pages = {13757--13766},
}

@article{van_moerkercke_myc2myc3myc4-dependent_2019,
	title = {A {MYC2}/{MYC3}/{MYC4}-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1911758116},
	doi = {10.1073/pnas.1911758116},
	abstract = {Mechanical stimuli, such as wind, rain, and touch affect plant development, growth, pest resistance, and ultimately reproductive success. Using water spray to simulate rain, we demonstrate that jasmonic acid (JA) signaling plays a key role in early gene-expression changes, well before it leads to developmental changes in flowering and plant architecture. The JA-activated transcription factors MYC2/MYC3/MYC4 modulate transiently induced expression of 266 genes, most of which peak within 30 min, and control 52\% of genes induced {\textgreater}100-fold. Chromatin immunoprecipitation-sequencing analysis indicates that MYC2 dynamically binds {\textgreater}1,300 promoters and
              trans
              -activation assays show that MYC2 activates these promoters. By mining our multiomic datasets, we identified a core MYC2/MYC3/MYC4-dependent “regulon” of 82 genes containing many previously unknown MYC2 targets, including transcription factors
              bHLH19
              and
              ERF109
              . bHLH19 can in turn directly activate the
              ORA47
              promoter, indicating that MYC2/MYC3/MYC4 initiate a hierarchical network of downstream transcription factors. Finally, we also reveal that rapid water spray-induced accumulation of JA and JA-isoleucine is directly controlled by MYC2/MYC3/MYC4 through a positive amplification loop that regulates JA-biosynthesis genes.},
	language = {en},
	number = {46},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Van Moerkercke, Alex and Duncan, Owen and Zander, Mark and Šimura, Jan and Broda, Martyna and Vanden Bossche, Robin and Lewsey, Mathew G. and Lama, Sbatie and Singh, Karam B. and Ljung, Karin and Ecker, Joseph R. and Goossens, Alain and Millar, A. Harvey and Van Aken, Olivier},
	month = nov,
	year = {2019},
	pages = {23345--23356},
}

Mechanical stimuli, such as wind, rain, and touch affect plant development, growth, pest resistance, and ultimately reproductive success. Using water spray to simulate rain, we demonstrate that jasmonic acid (JA) signaling plays a key role in early gene-expression changes, well before it leads to developmental changes in flowering and plant architecture. The JA-activated transcription factors MYC2/MYC3/MYC4 modulate transiently induced expression of 266 genes, most of which peak within 30 min, and control 52% of genes induced \textgreater100-fold. Chromatin immunoprecipitation-sequencing analysis indicates that MYC2 dynamically binds \textgreater1,300 promoters and trans -activation assays show that MYC2 activates these promoters. By mining our multiomic datasets, we identified a core MYC2/MYC3/MYC4-dependent “regulon” of 82 genes containing many previously unknown MYC2 targets, including transcription factors bHLH19 and ERF109 . bHLH19 can in turn directly activate the ORA47 promoter, indicating that MYC2/MYC3/MYC4 initiate a hierarchical network of downstream transcription factors. Finally, we also reveal that rapid water spray-induced accumulation of JA and JA-isoleucine is directly controlled by MYC2/MYC3/MYC4 through a positive amplification loop that regulates JA-biosynthesis genes.

@article{ferro_growth_2019,
	title = {Growth performance and nutrient removal of a {Chlorella} vulgaris-{Rhizobium} sp. co-culture during mixotrophic feed-batch cultivation in synthetic wastewater},
	volume = {44},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926419305107},
	doi = {10.1016/j.algal.2019.101690},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Ferro, Lorenza and Gojkovic, Zivan and Muñoz, Raul and Funk, Christiane},
	month = dec,
	year = {2019},
	pages = {101690},
}

@article{bonner_why_2019,
	title = {Why does nitrogen addition to forest soils inhibit decomposition?},
	volume = {137},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071719302342},
	doi = {10.1016/j.soilbio.2019.107570},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Bonner, Mark TL. and Castro, David and Schneider, Andreas N. and Sundström, Görel and Hurry, Vaughan and Street, Nathaniel R. and Näsholm, Torgny},
	month = oct,
	year = {2019},
	pages = {107570},
}

@article{mateo-bonmati_epigenetic_2019,
	title = {Epigenetic {Regulation} of {Auxin} {Homeostasis}},
	volume = {9},
	issn = {2218-273X},
	url = {https://www.mdpi.com/2218-273X/9/10/623},
	doi = {10.3390/biom9100623},
	abstract = {Epigenetic regulation involves a myriad of mechanisms that regulate the expression of loci without altering the DNA sequence. These different mechanisms primarily result in modifications of the chromatin topology or DNA chemical structure that can be heritable or transient as a dynamic response to environmental cues. The phytohormone auxin plays an important role in almost every aspect of plant life via gradient formation. Auxin maxima/minima result from a complex balance of metabolism, transport, and signaling. Although epigenetic regulation of gene expression during development has been known for decades, the specific mechanisms behind the spatiotemporal dynamics of auxin levels in plants are only just being elucidated. In this review, we gather current knowledge on the epigenetic mechanisms regulating the expression of genes for indole-3-acetic acid (IAA) metabolism and transport in Arabidopsis and discuss future perspectives of this emerging field.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Biomolecules},
	author = {Mateo-Bonmatí, Eduardo and Casanova-Sáez, Rubén and Ljung, Karin},
	month = oct,
	year = {2019},
	pages = {623},
}

Epigenetic regulation involves a myriad of mechanisms that regulate the expression of loci without altering the DNA sequence. These different mechanisms primarily result in modifications of the chromatin topology or DNA chemical structure that can be heritable or transient as a dynamic response to environmental cues. The phytohormone auxin plays an important role in almost every aspect of plant life via gradient formation. Auxin maxima/minima result from a complex balance of metabolism, transport, and signaling. Although epigenetic regulation of gene expression during development has been known for decades, the specific mechanisms behind the spatiotemporal dynamics of auxin levels in plants are only just being elucidated. In this review, we gather current knowledge on the epigenetic mechanisms regulating the expression of genes for indole-3-acetic acid (IAA) metabolism and transport in Arabidopsis and discuss future perspectives of this emerging field.

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

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

@article{seyfferth_ethylene_2019,
	title = {Ethylene {Signaling} {Is} {Required} for {Fully} {Functional} {Tension} {Wood} in {Hybrid} {Aspen}},
	volume = {10},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2019.01101/full},
	doi = {10.3389/fpls.2019.01101},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Seyfferth, Carolin and Wessels, Bernard A. and Gorzsás, András and Love, Jonathan W. and Rüggeberg, Markus and Delhomme, Nicolas and Vain, Thomas and Antos, Kamil and Tuominen, Hannele and Sundberg, Björn and Felten, Judith},
	month = sep,
	year = {2019},
	pages = {1101},
}

@article{papazian_leaf_2019,
	title = {Leaf metabolic signatures induced by real and simulated herbivory in black mustard ({Brassica} nigra)},
	volume = {15},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-019-1592-4},
	doi = {10.1007/s11306-019-1592-4},
	abstract = {Abstract
            
              Introduction
              The oxylipin methyl jasmonate (MeJA) is a plant hormone active in response signalling and defence against herbivores. Although MeJA is applied experimentally to mimic herbivory and induce plant defences, its downstream effects on the plant metabolome are largely uncharacterized, especially in the context of primary growth and tissue-specificity of the response.
            
            
              Objectives
              
                We investigated the effects of MeJA-simulated and real caterpillar herbivory on the foliar metabolome of the wild plant
                Brassica nigra
                and monitored the herbivore-induced responses in relation to leaf ontogeny.
              
            
            
              Methods
              As single or multiple herbivory treatments, MeJA- and mock-sprayed plants were consecutively exposed to caterpillars or left untreated. Gas chromatography (GC) and liquid chromatography (LC) time-of-flight mass-spectrometry (TOF-MS) were combined to analyse foliar compounds, including central primary and specialized defensive plant metabolites.
            
            
              Results
              Plant responses were stronger in young leaves, which simultaneously induced higher chlorophyll levels. Both MeJA and caterpillar herbivory induced similar, but not identical, accumulation of tricarboxylic acids (TCAs), glucosinolates (GSLs) and phenylpropanoids (PPs), but only caterpillar feeding led to depletion of amino acids. MeJA followed by caterpillars caused higher induction of defence compounds, including a three-fold increase in the major defence compound allyl-GSL (sinigrin). When feeding on MeJA-treated plants, caterpillars gained less weight indicative of the reduced host-plant quality and enhanced resistance.
            
            
              Conclusions
              The metabolomics approach showed that plant responses induced by herbivory extend beyond the regulation of defence metabolism and are tightly modulated throughout leaf development. This leads to a new understanding of the plant metabolic potential that can be exploited for future plant protection strategies.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Papazian, Stefano and Girdwood, Tristan and Wessels, Bernard A. and Poelman, Erik H. and Dicke, Marcel and Moritz, Thomas and Albrectsen, Benedicte R.},
	month = oct,
	year = {2019},
	pages = {130},
}

Abstract Introduction The oxylipin methyl jasmonate (MeJA) is a plant hormone active in response signalling and defence against herbivores. Although MeJA is applied experimentally to mimic herbivory and induce plant defences, its downstream effects on the plant metabolome are largely uncharacterized, especially in the context of primary growth and tissue-specificity of the response. Objectives We investigated the effects of MeJA-simulated and real caterpillar herbivory on the foliar metabolome of the wild plant Brassica nigra and monitored the herbivore-induced responses in relation to leaf ontogeny. Methods As single or multiple herbivory treatments, MeJA- and mock-sprayed plants were consecutively exposed to caterpillars or left untreated. Gas chromatography (GC) and liquid chromatography (LC) time-of-flight mass-spectrometry (TOF-MS) were combined to analyse foliar compounds, including central primary and specialized defensive plant metabolites. Results Plant responses were stronger in young leaves, which simultaneously induced higher chlorophyll levels. Both MeJA and caterpillar herbivory induced similar, but not identical, accumulation of tricarboxylic acids (TCAs), glucosinolates (GSLs) and phenylpropanoids (PPs), but only caterpillar feeding led to depletion of amino acids. MeJA followed by caterpillars caused higher induction of defence compounds, including a three-fold increase in the major defence compound allyl-GSL (sinigrin). When feeding on MeJA-treated plants, caterpillars gained less weight indicative of the reduced host-plant quality and enhanced resistance. Conclusions The metabolomics approach showed that plant responses induced by herbivory extend beyond the regulation of defence metabolism and are tightly modulated throughout leaf development. This leads to a new understanding of the plant metabolic potential that can be exploited for future plant protection strategies.

@article{kloth_pectin_2019,
	title = {{PECTIN} {ACETYLESTERASE9} {Affects} the {Transcriptome} and {Metabolome} and {Delays} {Aphid} {Feeding}},
	volume = {181},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/181/4/1704-1720/6000543},
	doi = {10.1104/pp.19.00635},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Kloth, Karen J. and Abreu, Ilka N. and Delhomme, Nicolas and Petřík, Ivan and Villard, Cloé and Ström, Cecilia and Amini, Fariba and Novák, Ondřej and Moritz, Thomas and Albrectsen, Benedicte R.},
	month = dec,
	year = {2019},
	pages = {1704--1720},
}

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

@article{stens_ecological_2019,
	title = {From ecological knowledge to conservation policy: a case study on green tree retention and continuous-cover forestry in {Sweden}},
	volume = {28},
	issn = {0960-3115, 1572-9710},
	shorttitle = {From ecological knowledge to conservation policy},
	url = {http://link.springer.com/10.1007/s10531-019-01836-2},
	doi = {10.1007/s10531-019-01836-2},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Biodiversity and Conservation},
	author = {Sténs, Anna and Roberge, Jean-Michel and Löfmarck, Erik and Beland Lindahl, Karin and Felton, Adam and Widmark, Camilla and Rist, Lucy and Johansson, Johanna and Nordin, Annika and Nilsson, Urban and Laudon, Hjalmar and Ranius, Thomas},
	month = nov,
	year = {2019},
	pages = {3547--3574},
}

@article{blokhina_ray_2019,
	title = {Ray {Parenchymal} {Cells} {Contribute} to {Lignification} of {Tracheids} in {Developing} {Xylem} of {Norway} {Spruce}},
	volume = {181},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/181/4/1552-1572/6000532},
	doi = {10.1104/pp.19.00743},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Blokhina, Olga and Laitinen, Teresa and Hatakeyama, Yuto and Delhomme, Nicolas and Paasela, Tanja and Zhao, Lei and Street, Nathaniel R. and Wada, Hiroshi and Kärkönen, Anna and Fagerstedt, Kurt},
	month = dec,
	year = {2019},
	pages = {1552--1572},
}

@article{lee_crispr-based_2019,
	title = {{CRISPR}-based tools for targeted transcriptional and epigenetic regulation in plants},
	volume = {14},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0222778},
	doi = {10.1371/journal.pone.0222778},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Lee, Joanne E. and Neumann, Manuela and Duro, Daniel Iglesias and Schmid, Markus},
	editor = {Candela, Hector},
	month = sep,
	year = {2019},
	pages = {e0222778},
}