Publications 2010

@article{nookaraju_molecular_2010,
	title = {Molecular approaches for enhancing sweetness in fruits and vegetables},
	volume = {127},
	issn = {0304-4238},
	url = {https://www.sciencedirect.com/science/article/pii/S030442381000422X},
	doi = {10.1016/j.scienta.2010.09.014},
	abstract = {The quality of fruits and vegetables is mainly dependant on the sweetness determined by the level of soluble sugars such as glucose, fructose and sucrose. Other fruit quality parameters include Brix content, acidity, aroma, color, size and shape. Total sugar content in fruits and vegetables is a function of genetic, nutritional, environmental and developmental factors. Understanding the factors controlling sweetness is important to design strategies for enhancing quality of fruits and vegetables. Modifying the activity of enzymes in carbohydrate metabolism such as sucrose synthase (SuSy), acid invertase, ADP-glucose pyrophosphorylase (AGPase), sucrose phosphate synthase (SPS) and sucrose transporters were found to influence carbohydrate partitioning and sucrose accumulation in sink tissues of several food crops. Plant based taste-modifying sweet proteins such as brazzein, cucurmin, mabinlin, monellin, miraculin, neoculin and thaumatin have potential application for developing transgenic plants to improve the sweetness and quality of fruits and vegetables. The present review envisages various cultural, breeding and molecular approaches used for enhancing sugar content and sweetness in fruits and vegetables.},
	number = {1},
	urldate = {2023-11-14},
	journal = {Scientia Horticulturae},
	author = {Nookaraju, Akula and Upadhyaya, Chandrama P. and Pandey, Shashank K. and Young, Ko Eun and Hong, Se Jin and Park, Suk Keun and Park, Se Won},
	month = nov,
	year = {2010},
	keywords = {Carbohydrate partitioning, Flavor, Metabolic engineering, Sucrose, Sweet proteins},
	pages = {1--15},
}

The quality of fruits and vegetables is mainly dependant on the sweetness determined by the level of soluble sugars such as glucose, fructose and sucrose. Other fruit quality parameters include Brix content, acidity, aroma, color, size and shape. Total sugar content in fruits and vegetables is a function of genetic, nutritional, environmental and developmental factors. Understanding the factors controlling sweetness is important to design strategies for enhancing quality of fruits and vegetables. Modifying the activity of enzymes in carbohydrate metabolism such as sucrose synthase (SuSy), acid invertase, ADP-glucose pyrophosphorylase (AGPase), sucrose phosphate synthase (SPS) and sucrose transporters were found to influence carbohydrate partitioning and sucrose accumulation in sink tissues of several food crops. Plant based taste-modifying sweet proteins such as brazzein, cucurmin, mabinlin, monellin, miraculin, neoculin and thaumatin have potential application for developing transgenic plants to improve the sweetness and quality of fruits and vegetables. The present review envisages various cultural, breeding and molecular approaches used for enhancing sugar content and sweetness in fruits and vegetables.

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

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

@article{wilczynski_computer_2010,
	title = {A {Computer} {Scientist}'s {Guide} to the {Regulatory} {Genome}},
	volume = {103},
	issn = {0169-2968},
	url = {https://content.iospress.com/articles/fundamenta-informaticae/fi103-1-4-17},
	doi = {10/gkgft6},
	abstract = {Recent years have seen a wealth of computational methods applied to problems stemming from molecular biology. In particular, with the completion of many new full genome sequences, great advances have been made in studying the role of non-protein-codi},
	language = {en},
	number = {1-4},
	urldate = {2021-06-08},
	journal = {Fundamenta Informaticae},
	author = {Wilczyński, Bartek and Hvidsten, Torgeir R.},
	month = jan,
	year = {2010},
	pages = {323--332},
}

Recent years have seen a wealth of computational methods applied to problems stemming from molecular biology. In particular, with the completion of many new full genome sequences, great advances have been made in studying the role of non-protein-codi

@article{pracharoenwattana_arabidopsis_2010,
	title = {Arabidopsis has a cytosolic fumarase required for the massive allocation of photosynthate into fumaric acid and for rapid plant growth on high nitrogen},
	volume = {62},
	copyright = {© 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2010.04189.x},
	doi = {10/bpcb9c},
	abstract = {The Arabidopsis genome has two fumarase genes, one of which encodes a protein with mitochondrial targeting information (FUM1) while the other (FUM2) does not. We show that a FUM1–green fluorescent protein fusion is directed to mitochondria while FUM2–red fluorescent protein remains in the cytosol. While mitochondrial FUM1 is an essential gene, cytosolic FUM2 is not required for plant growth. However FUM2 is required for the massive accumulation of carbon into fumarate that occurs in Arabidopsis leaves during the day. In fum2 knock-out mutants, fumarate levels remain low while malate increases, and these changes can be reversed with a FUM2 transgene. The fum2 mutant has lower levels of many amino acids in leaves during the day compared with the wild type, but higher levels at night, consistent with a link between fumarate and amino acid metabolism. To further test this relationship we grew plants in the absence or presence of nitrogen fertilizer. The amount of fumarate in leaves increased several fold in response to nitrogen in wild-type plants, but not in fum2. Malate increased to a small extent in the wild type but to a greater extent in fum2. Growth of fum2 plants was similar to that of the wild type in low nitrogen but much slower in the presence of high nitrogen. Activities of key enzymes of nitrogen assimilation were similar in both genotypes. We conclude that FUM2 is required for the accumulation of fumarate in leaves, which is in turn required for rapid nitrogen assimilation and growth on high nitrogen.},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Pracharoenwattana, Itsara and Zhou, Wenxu and Keech, Olivier and Francisco, Perigio B. and Udomchalothorn, Thanikan and Tschoep, Hendrik and Stitt, Mark and Gibon, Yves and Smith, Steven M.},
	year = {2010},
	keywords = {Arabidopsis thaliana, fumarase, fumaric acid, nitrogen assimilation, photosynthate allocation, plant growth},
	pages = {785--795},
}

The Arabidopsis genome has two fumarase genes, one of which encodes a protein with mitochondrial targeting information (FUM1) while the other (FUM2) does not. We show that a FUM1–green fluorescent protein fusion is directed to mitochondria while FUM2–red fluorescent protein remains in the cytosol. While mitochondrial FUM1 is an essential gene, cytosolic FUM2 is not required for plant growth. However FUM2 is required for the massive accumulation of carbon into fumarate that occurs in Arabidopsis leaves during the day. In fum2 knock-out mutants, fumarate levels remain low while malate increases, and these changes can be reversed with a FUM2 transgene. The fum2 mutant has lower levels of many amino acids in leaves during the day compared with the wild type, but higher levels at night, consistent with a link between fumarate and amino acid metabolism. To further test this relationship we grew plants in the absence or presence of nitrogen fertilizer. The amount of fumarate in leaves increased several fold in response to nitrogen in wild-type plants, but not in fum2. Malate increased to a small extent in the wild type but to a greater extent in fum2. Growth of fum2 plants was similar to that of the wild type in low nitrogen but much slower in the presence of high nitrogen. Activities of key enzymes of nitrogen assimilation were similar in both genotypes. We conclude that FUM2 is required for the accumulation of fumarate in leaves, which is in turn required for rapid nitrogen assimilation and growth on high nitrogen.

@article{ohberg_biological_2010,
	title = {Biological control of clover rot on red clover by \textit{{Coniothyrium} minitans} under natural and controlled climatic conditions},
	volume = {20},
	issn = {0958-3157, 1360-0478},
	url = {http://www.tandfonline.com/doi/abs/10.1080/09583150903337805},
	doi = {10/b74tzp},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Biocontrol Science and Technology},
	author = {Öhberg, Helena and Bång, Ulla},
	month = jan,
	year = {2010},
	pages = {25--36},
}

@article{metcalfe_impacts_2010,
	title = {Impacts of experimentally imposed drought on leaf respiration and morphology in an {Amazon} rain forest: {Drought} affects rain forest leaf respiration},
	volume = {24},
	issn = {02698463},
	shorttitle = {Impacts of experimentally imposed drought on leaf respiration and morphology in an {Amazon} rain forest},
	url = {http://doi.wiley.com/10.1111/j.1365-2435.2009.01683.x},
	doi = {10/cpr644},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Functional Ecology},
	author = {Metcalfe, Daniel B. and Lobo-do-Vale, Raquel and Chaves, Manuela M. and Maroco, Joao P. and C Aragão, Luiz E. O. and Malhi, Yadvinder and Da Costa, Antonio L. and Braga, Alan P. and Gonçalves, Paulo L. and De Athaydes, Joao and Da Costa, Mauricio and Almeida, Samuel S. and Campbell, Catherine and Hurry, Vaughan and Williams, Mathew and Meir, Patrick},
	month = jun,
	year = {2010},
	pages = {524--533},
}

@article{karlberg_analysis_2010,
	title = {Analysis of global changes in gene expression during activity-dormancy cycle in hybrid aspen apex},
	volume = {27},
	doi = {10/frkc7v},
	abstract = {Perennial plants such as the long-lived trees of boreal forest cycle between periods of active growth and dormancy. Transition from active growth to dormancy is induced by short day (SD) signal. Once dormancy is established, prolonged exposure to low temperature is required for breaking dormancy before warm temperatures can induce growth. We have studied global changes in gene expression in the apex of model plant hybrid aspen during the distinct stages of activity-dormancy cycle. Our data shows that all stages of activity-dormancy cycle in the apex are associated with substantial modulation of the transcriptome. Detailed analysis of core cell cycle genes indicates that with the exception of plant specific B-type CDKs, all of the other CDKs are regulated post-transcriptionally during growth cessation. SD signal appears to target the expression of cyclin genes that are down regulated during growth arrest. Several of the cold hardiness related genes e. g. dehydrins are induced during transition to dormancy although temperature is not reduced and the up-regulation of the expression of these genes does not appear to rely on SD mediated induction of classical CBF transcription factors. Our results suggest that transcriptional control plays a key role in modulation of hormones such as ABA and GA that are known to play a central role in various processes during activity-dormancy cycle. Analysis of histone and DNA modification genes indicates that chromatin remodeling could be involved in coordinating global changes in gene expression during activity-dormancy cycle.},
	number = {1},
	journal = {Plant Biotechnology},
	author = {Karlberg, Anna and Englund, Madeleine and Petterle, Anna and Molnar, Gergely and Sjödin, Andreas and Bakó, Laszlo and Bhalerao, Rishikesh P.},
	year = {2010},
	keywords = {Cell cycle, dormancy, hormone, microarray, poplar},
	pages = {1--16},
}

Perennial plants such as the long-lived trees of boreal forest cycle between periods of active growth and dormancy. Transition from active growth to dormancy is induced by short day (SD) signal. Once dormancy is established, prolonged exposure to low temperature is required for breaking dormancy before warm temperatures can induce growth. We have studied global changes in gene expression in the apex of model plant hybrid aspen during the distinct stages of activity-dormancy cycle. Our data shows that all stages of activity-dormancy cycle in the apex are associated with substantial modulation of the transcriptome. Detailed analysis of core cell cycle genes indicates that with the exception of plant specific B-type CDKs, all of the other CDKs are regulated post-transcriptionally during growth cessation. SD signal appears to target the expression of cyclin genes that are down regulated during growth arrest. Several of the cold hardiness related genes e. g. dehydrins are induced during transition to dormancy although temperature is not reduced and the up-regulation of the expression of these genes does not appear to rely on SD mediated induction of classical CBF transcription factors. Our results suggest that transcriptional control plays a key role in modulation of hormones such as ABA and GA that are known to play a central role in various processes during activity-dormancy cycle. Analysis of histone and DNA modification genes indicates that chromatin remodeling could be involved in coordinating global changes in gene expression during activity-dormancy cycle.

@article{ge_arabidopsis_2010,
	title = {Arabidopsis {ROOT} {UVB} {SENSITIVE2}/{WEAK} {AUXIN} {RESPONSE1} {Is} {Required} for {Polar} {Auxin} {Transport}},
	volume = {22},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.110.074195},
	doi = {10/brs5hr},
	abstract = {Auxin is an essential phytohormone that regulates many aspects of plant development. To identify new genes that function in auxin signaling, we performed a genetic screen for Arabidopsis thaliana mutants with an alteration in the expression of the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One of the mutants recovered in this screen, called weak auxin response1 (wxr1), has a defect in auxin response and exhibits a variety of auxin-related growth defects in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels in the root apex. In addition, the levels of the PIN auxin transport proteins are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2), a member of the broadly conserved DUF647 domain protein family found in diverse eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport and to maintain the normal levels of PIN proteins in the root.},
	number = {6},
	urldate = {2021-06-21},
	journal = {The Plant Cell},
	author = {Ge, L. and Peer, W. and Robert, S. and Swarup, R. and Ye, S. and Prigge, M. and Cohen, J.D. and Friml, J. and Murphy, A. and Tang, D. and Estelle, M.},
	month = jun,
	year = {2010},
	pages = {1749--1761},
}

Auxin is an essential phytohormone that regulates many aspects of plant development. To identify new genes that function in auxin signaling, we performed a genetic screen for Arabidopsis thaliana mutants with an alteration in the expression of the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One of the mutants recovered in this screen, called weak auxin response1 (wxr1), has a defect in auxin response and exhibits a variety of auxin-related growth defects in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels in the root apex. In addition, the levels of the PIN auxin transport proteins are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2), a member of the broadly conserved DUF647 domain protein family found in diverse eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport and to maintain the normal levels of PIN proteins in the root.

@article{lan_extensive_2010,
	title = {Extensive {Functional} {Diversification} of the \textit{{Populus}} {Glutathione} \textit{{S}} -{Transferase} {Supergene} {Family}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/12/3749/6096103},
	doi = {10/fjhnrx},
	abstract = {Abstract
            Identifying how genes and their functions evolve after duplication is central to understanding gene family radiation. In this study, we systematically examined the functional diversification of the glutathione S-transferase (GST) gene family in Populus trichocarpa by integrating phylogeny, expression, substrate specificity, and enzyme kinetic data. GSTs are ubiquitous proteins in plants that play important roles in stress tolerance and detoxification metabolism. Genome annotation identified 81 GST genes in Populus that were divided into eight classes with distinct divergence in their evolutionary rate, gene structure, expression responses to abiotic stressors, and enzymatic properties of encoded proteins. In addition, when all the functional parameters were examined, clear divergence was observed within tandem clusters and between paralogous gene pairs, suggesting that subfunctionalization has taken place among duplicate genes. The two domains of GST proteins appear to have evolved under differential selective pressures. The C-terminal domain seems to have been subject to more relaxed functional constraints or divergent directional selection, which may have allowed rapid changes in substrate specificity, affinity, and activity, while maintaining the primary function of the enzyme. Our findings shed light on mechanisms that facilitate the retention of duplicate genes, which can result in a large gene family with a broad substrate spectrum and a wide range of reactivity toward different substrates.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Lan, Ting and Yang, Zhi-Ling and Yang, Xue and Liu, Yan-Jing and Wang, Xiao-Ru and Zeng, Qing-Yin},
	month = jan,
	year = {2010},
	pages = {3749--3766},
}

Abstract Identifying how genes and their functions evolve after duplication is central to understanding gene family radiation. In this study, we systematically examined the functional diversification of the glutathione S-transferase (GST) gene family in Populus trichocarpa by integrating phylogeny, expression, substrate specificity, and enzyme kinetic data. GSTs are ubiquitous proteins in plants that play important roles in stress tolerance and detoxification metabolism. Genome annotation identified 81 GST genes in Populus that were divided into eight classes with distinct divergence in their evolutionary rate, gene structure, expression responses to abiotic stressors, and enzymatic properties of encoded proteins. In addition, when all the functional parameters were examined, clear divergence was observed within tandem clusters and between paralogous gene pairs, suggesting that subfunctionalization has taken place among duplicate genes. The two domains of GST proteins appear to have evolved under differential selective pressures. The C-terminal domain seems to have been subject to more relaxed functional constraints or divergent directional selection, which may have allowed rapid changes in substrate specificity, affinity, and activity, while maintaining the primary function of the enzyme. Our findings shed light on mechanisms that facilitate the retention of duplicate genes, which can result in a large gene family with a broad substrate spectrum and a wide range of reactivity toward different substrates.

@article{gapare_genetic_2010,
	title = {Genetic stability of wood density and diameter in {Pinus} radiata {D}. {Don} plantation estate across {Australia}},
	volume = {6},
	copyright = {2009 Springer-Verlag},
	issn = {1614-2950},
	url = {https://link.springer.com/article/10.1007/s11295-009-0233-x},
	doi = {10/dg26z4},
	abstract = {Genetic variation for wood quality traits and diameter growth for radiata pine (Pinus radiata D. Don) at age 20/21 years was estimated from eight trials in Australia. The traits studied were wood density, acoustic time-of-flight (an indirect measure of stiffness) and diameter at breast height (DBH). Wood density and DBH exhibited significant additive genetic variation whereas non-additive effects were not significantly different from zero. Time of flight was also not significantly different from zero for both additive and non-additive effects, respectively. Average single-site heritability estimates (±SE) for wood density and DBH were 0.38 ± 0.10 and 0.16 ± 0.08, respectively. Pooled-site heritability estimates for wood density and DBH were 0.38 ± 0.10 and 0.08 ± 0.10, respectively. For density, there was little evidence of genotype-by-environment interaction (GEI) across the eight trials at the additive level (type B additive genetic correlation; r BADD = 0.73 ± 0.08) and type B genetic correlation for full-sib families (r BFS = 0.64 ± 0.08). In contrast, the type B additive genetic correlation for DBH was lower, (r BADD = 0.51 ± 0.14), suggesting evidence of GEI. However, type B genetic correlation for full-sib families was moderate (0.63 ± 0.11) for DBH, suggesting that there may be some stable full-sib families. On the basis of the results of this study, GEI should be considered in order to optimise deployment of improved germplasm in Australia.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gapare, Washington J. and Ivković, Miloš and Baltunis, Brian S. and Matheson, Colin A. and Wu, Harry X.},
	month = jan,
	year = {2010},
	note = {Company: Springer
Distributor: Springer
Institution: Springer
Label: Springer
Number: 1
Publisher: Springer-Verlag},
	pages = {113--125},
}

Genetic variation for wood quality traits and diameter growth for radiata pine (Pinus radiata D. Don) at age 20/21 years was estimated from eight trials in Australia. The traits studied were wood density, acoustic time-of-flight (an indirect measure of stiffness) and diameter at breast height (DBH). Wood density and DBH exhibited significant additive genetic variation whereas non-additive effects were not significantly different from zero. Time of flight was also not significantly different from zero for both additive and non-additive effects, respectively. Average single-site heritability estimates (±SE) for wood density and DBH were 0.38 ± 0.10 and 0.16 ± 0.08, respectively. Pooled-site heritability estimates for wood density and DBH were 0.38 ± 0.10 and 0.08 ± 0.10, respectively. For density, there was little evidence of genotype-by-environment interaction (GEI) across the eight trials at the additive level (type B additive genetic correlation; r BADD = 0.73 ± 0.08) and type B genetic correlation for full-sib families (r BFS = 0.64 ± 0.08). In contrast, the type B additive genetic correlation for DBH was lower, (r BADD = 0.51 ± 0.14), suggesting evidence of GEI. However, type B genetic correlation for full-sib families was moderate (0.63 ± 0.11) for DBH, suggesting that there may be some stable full-sib families. On the basis of the results of this study, GEI should be considered in order to optimise deployment of improved germplasm in Australia.

@article{li_use_2010,
	title = {Use of chromosome walking in discovery of single-nucleotide polymorphism in noncoding regions of a candidate actin gene in {Pinus} radiata},
	volume = {51},
	issn = {2190-3883},
	doi = {10/d5385t},
	abstract = {Untranslated regions (UTRs) of eukaryotic mRNAs play crucial roles in post-transcriptional regulation of gene expression via the modulation of nucleocytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Single-nucleotide polymorphisms (SNPs) in UTRs of a candidate gene may also change the post-transcriptional regulation of a gene or function by nucleotide mutation. For species that have not been entirely sequenced genomically, new methods need to be devised to discover SNPs in noncoding regions of candidate genes. In this study, based on the expressed sequence tag (EST) of Pinus radiata (Monterey pine), we obtained all the sequences of UTRs of the actin gene by using a chromosome walking method. We also detected all the SNPs in and around the coding region of the actin gene. In this way, the full genomic sequence (2154 bp) of the actin gene was identified, including the 5\’UTR, introns, the coding sequence, and the 3\’UTR. PCR amplification and DNA fragment sequencing from 200 unrelated P. radiata trees revealed a total of 21 SNPs in the actin gene, of which 3 were located in the 5\’UTR, 3 in the introns, 10 in the coding sequence, and 5 in the 3\’UTR. We show that chromosome walking can be used for obtaining the sequence of UTRs, and then, based on this sequence, to discover SNPs in the noncoding regions of candidate genes from this species without an entire genomic sequence.},
	language = {eng},
	number = {3},
	journal = {Journal of Applied Genetics},
	author = {Li, W. and Li, H. and Wu, H. and Chen, X.-Y.},
	year = {2010},
	pmid = {20720301},
	keywords = {Actins, Base Sequence, Chromosome Walking, Expressed Sequence Tags, Genes, Plant, Genome, Plant, Molecular Sequence Data, Pinus, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Untranslated Regions},
	pages = {275--281},
}

Untranslated regions (UTRs) of eukaryotic mRNAs play crucial roles in post-transcriptional regulation of gene expression via the modulation of nucleocytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Single-nucleotide polymorphisms (SNPs) in UTRs of a candidate gene may also change the post-transcriptional regulation of a gene or function by nucleotide mutation. For species that have not been entirely sequenced genomically, new methods need to be devised to discover SNPs in noncoding regions of candidate genes. In this study, based on the expressed sequence tag (EST) of Pinus radiata (Monterey pine), we obtained all the sequences of UTRs of the actin gene by using a chromosome walking method. We also detected all the SNPs in and around the coding region of the actin gene. In this way, the full genomic sequence (2154 bp) of the actin gene was identified, including the 5’UTR, introns, the coding sequence, and the 3’UTR. PCR amplification and DNA fragment sequencing from 200 unrelated P. radiata trees revealed a total of 21 SNPs in the actin gene, of which 3 were located in the 5’UTR, 3 in the introns, 10 in the coding sequence, and 5 in the 3’UTR. We show that chromosome walking can be used for obtaining the sequence of UTRs, and then, based on this sequence, to discover SNPs in the noncoding regions of candidate genes from this species without an entire genomic sequence.

@article{robert_abp1_2010,
	title = {{ABP1} mediates auxin inhibition of clathrin-dependent endocytosis in {Arabidopsis}},
	volume = {143},
	issn = {1097-4172},
	doi = {10/b86r8c},
	abstract = {Spatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.},
	language = {eng},
	number = {1},
	journal = {Cell},
	author = {Robert, Stéphanie and Kleine-Vehn, Jürgen and Barbez, Elke and Sauer, Michael and Paciorek, Tomasz and Baster, Pawel and Vanneste, Steffen and Zhang, Jing and Simon, Sibu and Čovanová, Milada and Hayashi, Kenichiro and Dhonukshe, Pankaj and Yang, Zhenbiao and Bednarek, Sebastian Y. and Jones, Alan M. and Luschnig, Christian and Aniento, Fernando and Zažímalová, Eva and Friml, Jiří},
	month = oct,
	year = {2010},
	pmid = {20887896},
	pmcid = {PMC3503507},
	keywords = {Arabidopsis, Arabidopsis Proteins, Cell Membrane, Clathrin, Endocytosis, Indoleacetic Acids, Membrane Transport Proteins, Plant Proteins, Receptors, Cell Surface},
	pages = {111--121},
}

Spatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.

@article{pacak_investigations_2010,
	title = {Investigations of barley stripe mosaic virus as a gene silencing vector in barley roots and in {Brachypodium} distachyon and oat},
	volume = {6},
	issn = {1746-4811},
	url = {http://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-6-26},
	doi = {10/dsq4sr},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Methods},
	author = {Pacak, Andrzej and Geisler, Katrin and Jørgensen, Bodil and Barciszewska-Pacak, Maria and Nilsson, Lena and Nielsen, Tom and Johansen, Elisabeth and Grønlund, Mette and Jakobsen, Iver and Albrechtsen, Merete},
	year = {2010},
	pages = {26},
}

@article{johansson_responses_2010,
	title = {Responses of epiphytic lichens to an experimental whole‐tree nitrogen‐deposition gradient},
	volume = {188},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03426.x},
	doi = {10/b58824},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Johansson, Otilia and Nordin, Annika and Olofsson, Johan and Palmqvist, Kristin},
	month = dec,
	year = {2010},
	pages = {1075--1084},
}

@article{wind_sucrose_2010,
	title = {Sucrose: metabolite and signaling molecule},
	volume = {71},
	issn = {1873-3700},
	shorttitle = {Sucrose},
	doi = {10/bcnsm2},
	abstract = {Sucrose is a molecule that is synthesized only by oxygenic photosynthetic organisms. In plants, sucrose is synthesized in source tissues and then can be transported to sink tissues, where it is utilized or stored. Interestingly, sucrose is both a metabolite and a signaling molecule. Manipulating the rate of the synthesis, transport or degradation of sucrose affects plant growth, development and physiology. Altered sucrose levels changes the quantity of sucrose derived metabolites and sucrose-specific signaling. In this paper, these changes are summarized. Better understanding of sucrose metabolism and sucrose sensing systems in plants will lead to opportunities to adapt plant metabolism and growth.},
	language = {eng},
	number = {14-15},
	journal = {Phytochemistry},
	author = {Wind, Julia and Smeekens, Sjef and Hanson, Johannes},
	month = oct,
	year = {2010},
	pmid = {20696445},
	keywords = {Arabidopsis, Molecular Structure, Photosynthesis, Plant Development, Plants, Signal Transduction, Sucrose},
	pages = {1610--1614},
}

Sucrose is a molecule that is synthesized only by oxygenic photosynthetic organisms. In plants, sucrose is synthesized in source tissues and then can be transported to sink tissues, where it is utilized or stored. Interestingly, sucrose is both a metabolite and a signaling molecule. Manipulating the rate of the synthesis, transport or degradation of sucrose affects plant growth, development and physiology. Altered sucrose levels changes the quantity of sucrose derived metabolites and sucrose-specific signaling. In this paper, these changes are summarized. Better understanding of sucrose metabolism and sucrose sensing systems in plants will lead to opportunities to adapt plant metabolism and growth.

@article{ivkovic_bio-economic_2010,
	title = {Bio-economic {Modelling} as a {Method} for {Determining} {Economic} {Weights} for {Optimal} {Multiple}-{Trait} {Tree} {Selection}},
	volume = {59},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2010-0010},
	doi = {10/gkgftk},
	abstract = {Abstract
            A bio-economic model provides a framework for simultaneously considering breeding, management, and production decisions. Such a model should result in optimal breeding (and silvicultural) objectives if main goals of a production system are well defined. Historically estimation of economic weights for breeding-objective traits has been based on partial regressions and profit functions relating only to certain parts of the production system. A bio-economic model includes effects of growth rate, branching, form, and wood quality on all production system components and on overall profitability of an integrated production system. However, long rotation cycles in forestry make determination of relative economic values for the breeding-objective traits particularly difficult. When modelling complex systems under uncertainty about future production goals, there are necessary trade offs between the complexity of the model and the use of simplifying assumptions.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Ivković, M. and Wu, H. and Kumar, S.},
	month = dec,
	year = {2010},
	pages = {77--90},
}

Abstract A bio-economic model provides a framework for simultaneously considering breeding, management, and production decisions. Such a model should result in optimal breeding (and silvicultural) objectives if main goals of a production system are well defined. Historically estimation of economic weights for breeding-objective traits has been based on partial regressions and profit functions relating only to certain parts of the production system. A bio-economic model includes effects of growth rate, branching, form, and wood quality on all production system components and on overall profitability of an integrated production system. However, long rotation cycles in forestry make determination of relative economic values for the breeding-objective traits particularly difficult. When modelling complex systems under uncertainty about future production goals, there are necessary trade offs between the complexity of the model and the use of simplifying assumptions.

@article{baltunis_genotype_2010,
	title = {Genotype by {Environmental} {Interaction} for {DBH}, {Wood} {Density}, {Branch} {Angle}, {Branch} {Size}, and {Stem} {Straightness} in {Eight} {Young} {Pinus} radiata {D}. {Don} {Trials} in {Australia}},
	journal = {Silvae Genetica},
	author = {Baltunis, Brian and Gapare, Washington and {WJ} and Wu, Harry},
	month = jan,
	year = {2010},
	keywords = {⛔ No DOI found},
}

@article{keech_leaf_2010,
	title = {Leaf {Senescence} {Is} {Accompanied} by an {Early} {Disruption} of the {Microtubule} {Network} in {Arabidopsis}},
	volume = {154},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/154/4/1710/6108651},
	doi = {10/cp2qs5},
	abstract = {Abstract
            The dynamic assembly and disassembly of microtubules (MTs) is essential for cell function. Although leaf senescence is a well-documented process, the role of the MT cytoskeleton during senescence in plants remains unknown. Here, we show that both natural leaf senescence and senescence of individually darkened Arabidopsis (Arabidopsis thaliana) leaves are accompanied by early degradation of the MT network in epidermis and mesophyll cells, whereas guard cells, which do not senesce, retain their MT network. Similarly, entirely darkened plants, which do not senesce, retain their MT network. While genes encoding the tubulin subunits and the bundling/stabilizing MT-associated proteins (MAPs) MAP65 and MAP70-1 were repressed in both natural senescence and dark-induced senescence, we found strong induction of the gene encoding the MT-destabilizing protein MAP18. However, induction of MAP18 gene expression was also observed in leaves from entirely darkened plants, showing that its expression is not sufficient to induce MT disassembly and is more likely to be part of a Ca2+-dependent signaling mechanism. Similarly, genes encoding the MT-severing protein katanin p60 and two of the four putative regulatory katanin p80s were repressed in the dark, but their expression did not correlate with degradation of the MT network during leaf senescence. Taken together, these results highlight the earliness of the degradation of the cortical MT array during leaf senescence and lead us to propose a model in which suppression of tubulin and MAP genes together with induction of MAP18 play key roles in MT disassembly during senescence.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Keech, Olivier and Pesquet, Edouard and Gutierrez, Laurent and Ahad, Abdul and Bellini, Catherine and Smith, Steven M. and Gardeström, Per},
	month = dec,
	year = {2010},
	pages = {1710--1720},
}

Abstract The dynamic assembly and disassembly of microtubules (MTs) is essential for cell function. Although leaf senescence is a well-documented process, the role of the MT cytoskeleton during senescence in plants remains unknown. Here, we show that both natural leaf senescence and senescence of individually darkened Arabidopsis (Arabidopsis thaliana) leaves are accompanied by early degradation of the MT network in epidermis and mesophyll cells, whereas guard cells, which do not senesce, retain their MT network. Similarly, entirely darkened plants, which do not senesce, retain their MT network. While genes encoding the tubulin subunits and the bundling/stabilizing MT-associated proteins (MAPs) MAP65 and MAP70-1 were repressed in both natural senescence and dark-induced senescence, we found strong induction of the gene encoding the MT-destabilizing protein MAP18. However, induction of MAP18 gene expression was also observed in leaves from entirely darkened plants, showing that its expression is not sufficient to induce MT disassembly and is more likely to be part of a Ca2+-dependent signaling mechanism. Similarly, genes encoding the MT-severing protein katanin p60 and two of the four putative regulatory katanin p80s were repressed in the dark, but their expression did not correlate with degradation of the MT network during leaf senescence. Taken together, these results highlight the earliness of the degradation of the cortical MT array during leaf senescence and lead us to propose a model in which suppression of tubulin and MAP genes together with induction of MAP18 play key roles in MT disassembly during senescence.

@article{li_seasonal_2010,
	title = {Seasonal reorganization of the xylem transcriptome at different tree ages reveals novel insights into wood formation in {Pinus} radiata},
	volume = {187},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/j.1469-8137.2010.03333.x},
	doi = {10/bhvgjx},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Li, Xinguo and Wu, Harry X. and Southerton, Simon G.},
	month = aug,
	year = {2010},
	pages = {764--776},
}

@article{li_comparative_2010,
	title = {Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants},
	volume = {10},
	issn = {1471-2148},
	url = {http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-190},
	doi = {10/bwhkfp},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Evolutionary Biology},
	author = {Li, Xinguo and Wu, Harry X and Southerton, Simon G},
	year = {2010},
	pages = {190},
}

@article{ivkovic_breeding_2010,
	title = {Breeding against dothistroma needle blight of radiata pine in {Australia}},
	volume = {40},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/X10-097},
	doi = {10/b72bt5},
	abstract = {Pine needle blight, caused by Dothistroma septosporum (Dorog.) M. Morelet, is one of the most serious foliar diseases of Pinus spp. in Australia and New Zealand. In 16 Pinus radiata (D.Don.) progeny trials in northeastern Victoria, Australia, Dothistroma-caused defoliation varied widely among trials and assessment years, ranging from 5\% to 65\%. The estimated narrow sense heritability ranged from nonsignificant to as high as 0.69 with a median of 0.36. Spatial autocorrelation of residuals accounted for a significant proportion of residual variance, and that increased heritability estimates. Genetic correlation between defoliation scores at an early age and growth at a later age was negative with a median value of –0.39. Phenotypic correlation between defoliation and survival was low and negative with a median value of –0.11. Economic analyses indicated that at sites with a high risk of infection, the effect of reducing defoliation on profitability was comparable with that of increasing growth at sites free from infection. The genetic parameters and economic impacts of Dothistroma were used to derive selection indices and include resistance to defoliation into the current breeding objective for radiata pine.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Canadian Journal of Forest Research},
	author = {Ivković, Miloš and Baltunis, Brian and Gapare, Washington and Sasse, Jo and Dutkowski, Gregory and Elms, Stephen and Wu, Harry},
	month = aug,
	year = {2010},
	pages = {1653--1660},
}

Pine needle blight, caused by Dothistroma septosporum (Dorog.) M. Morelet, is one of the most serious foliar diseases of Pinus spp. in Australia and New Zealand. In 16 Pinus radiata (D.Don.) progeny trials in northeastern Victoria, Australia, Dothistroma-caused defoliation varied widely among trials and assessment years, ranging from 5% to 65%. The estimated narrow sense heritability ranged from nonsignificant to as high as 0.69 with a median of 0.36. Spatial autocorrelation of residuals accounted for a significant proportion of residual variance, and that increased heritability estimates. Genetic correlation between defoliation scores at an early age and growth at a later age was negative with a median value of –0.39. Phenotypic correlation between defoliation and survival was low and negative with a median value of –0.11. Economic analyses indicated that at sites with a high risk of infection, the effect of reducing defoliation on profitability was comparable with that of increasing growth at sites free from infection. The genetic parameters and economic impacts of Dothistroma were used to derive selection indices and include resistance to defoliation into the current breeding objective for radiata pine.

@article{dillon_allelic_2010,
	title = {Allelic {Variation} in {Cell} {Wall} {Candidate} {Genes} {Affecting} {Solid} {Wood} {Properties} in {Natural} {Populations} and {Land} {Races} of \textit{{Pinus} radiata}},
	volume = {185},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/185/4/1477/6063711},
	doi = {10/fdj9jt},
	abstract = {Abstract
            Forest trees are ideally suited to association mapping due to their high levels of diversity and low genomic linkage disequilibrium. Using an association mapping approach, single-nucleotide polymorphism (SNP) markers influencing quantitative variation in wood quality were identified in a natural population of Pinus radiata. Of 149 sites examined, 10 demonstrated significant associations (P \< 0.05, q \< 0.1) with one or more traits after accounting for population structure and experimentwise error. Without accounting for marker interactions, phenotypic variation attributed to individual SNPs ranged from 2 to 6.5\%. Undesirable negative correlations between wood quality and growth were not observed, indicating potential to break negative correlations by selecting for individual SNPs in breeding programs. Markers that yielded significant associations were reexamined in an Australian land race. SNPs from three genes (PAL1, PCBER, and SUSY) yielded significant associations. Importantly, associations with two of these genes validated associations with density previously observed in the discovery population. In both cases, decreased wood density was associated with the minor allele, suggesting that these SNPs may be under weak negative purifying selection for density in the natural populations. These results demonstrate the utility of LD mapping to detect associations, even when the power to detect SNPs with small effect is anticipated to be low.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Genetics},
	author = {Dillon, S K and Nolan, M and Li, W and Bell, C and Wu, H X and Southerton, S G},
	month = aug,
	year = {2010},
	pages = {1477--1487},
}

Abstract Forest trees are ideally suited to association mapping due to their high levels of diversity and low genomic linkage disequilibrium. Using an association mapping approach, single-nucleotide polymorphism (SNP) markers influencing quantitative variation in wood quality were identified in a natural population of Pinus radiata. Of 149 sites examined, 10 demonstrated significant associations (P < 0.05, q < 0.1) with one or more traits after accounting for population structure and experimentwise error. Without accounting for marker interactions, phenotypic variation attributed to individual SNPs ranged from 2 to 6.5%. Undesirable negative correlations between wood quality and growth were not observed, indicating potential to break negative correlations by selecting for individual SNPs in breeding programs. Markers that yielded significant associations were reexamined in an Australian land race. SNPs from three genes (PAL1, PCBER, and SUSY) yielded significant associations. Importantly, associations with two of these genes validated associations with density previously observed in the discovery population. In both cases, decreased wood density was associated with the minor allele, suggesting that these SNPs may be under weak negative purifying selection for density in the natural populations. These results demonstrate the utility of LD mapping to detect associations, even when the power to detect SNPs with small effect is anticipated to be low.

@article{hallingback_which_2010,
	title = {Which annual rings to assess grain angles in breeding of {Scots} pine for improved shape stability of sawn timber?},
	volume = {44},
	issn = {22424075},
	url = {http://www.silvafennica.fi/article/154},
	doi = {10/gjcmkk},
	number = {2},
	urldate = {2021-06-08},
	journal = {Silva Fennica},
	author = {Hallingbäck, Henrik and Jansson, Gunnar and Hannrup, Björn and Fries, Anders},
	year = {2010},
}

@article{bentsink_natural_2010,
	title = {Natural variation for seed dormancy in {Arabidopsis} is regulated by additive genetic and molecular pathways},
	volume = {107},
	issn = {1091-6490},
	doi = {10/c2gjzz},
	abstract = {Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.},
	language = {eng},
	number = {9},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Bentsink, Leónie and Hanson, Johannes and Hanhart, Corrie J. and Blankestijn-de Vries, Hetty and Coltrane, Colin and Keizer, Paul and El-Lithy, Mohamed and Alonso-Blanco, Carlos and de Andrés, M. Teresa and Reymond, Matthieu and van Eeuwijk, Fred and Smeekens, Sjef and Koornneef, Maarten},
	month = mar,
	year = {2010},
	pmid = {20145108},
	pmcid = {PMC2840098},
	keywords = {Arabidopsis, Arabidopsis Proteins, Gene Expression Profiling, Genetic Variation, Quantitative Trait Loci, Seeds},
	pages = {4264--4269},
}

Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.

@article{smeekens_sugar_2010,
	title = {Sugar signals and molecular networks controlling plant growth},
	volume = {13},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526609001782},
	doi = {10/d9t45g},
	abstract = {In recent years, several regulatory systems that link carbon nutrient status to plant growth and development have emerged. In this paper, we discuss the growth promoting functions of the hexokinase (HXK) glucose sensor, the trehalose 6-phosphate (T6P) signal and the Target of Rapamycin (TOR) kinase pathway, and the growth inhibitory function of the SNF1-related Protein Kinase1 (SnRK1) and the C/S1 bZIP transcription factor network. It is crucial that these systems interact closely in regulating growth and in several cases crosstalk has been demonstrated. Importantly, these nutrient controlled systems must interact with other growth regulatory pathways.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Smeekens, Sjef and Ma, Jingkun and Hanson, Johannes and Rolland, Filip},
	month = jun,
	year = {2010},
	pages = {273--278},
}

In recent years, several regulatory systems that link carbon nutrient status to plant growth and development have emerged. In this paper, we discuss the growth promoting functions of the hexokinase (HXK) glucose sensor, the trehalose 6-phosphate (T6P) signal and the Target of Rapamycin (TOR) kinase pathway, and the growth inhibitory function of the SNF1-related Protein Kinase1 (SnRK1) and the C/S1 bZIP transcription factor network. It is crucial that these systems interact closely in regulating growth and in several cases crosstalk has been demonstrated. Importantly, these nutrient controlled systems must interact with other growth regulatory pathways.

@article{resman_components_2010,
	title = {Components {Acting} {Downstream} of {Short} {Day} {Perception} {Regulate} {Differential} {Cessation} of {Cambial} {Activity} and {Associated} {Responses} in {Early} and {Late} {Clones} of {Hybrid} {Poplar}},
	volume = {154},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/154/3/1294/6111326},
	doi = {10/dhnvbh},
	abstract = {Abstract
            Short days (SDs) in autumn induce growth cessation, bud set, cold acclimation, and dormancy in trees of boreal and temperate forests, and these responses occur earlier in northern than in southern genotypes. Nevertheless, we know little about whether this variation results from differential perception of SDs or differential downstream responses to the SD signal or a combination of the two. We compared global patterns of SD-regulated gene expression in the stems of hybrid poplar (Populus trichocarpa × Populus deltoides) clones that differ in their SD-induced growth cessation in order to address this question. The timing of cessation of cambial cell division caused by SDs differed between the clones and was coincident with the change in the pattern of expression of the auxin-regulated genes. The clones also differed in the timing of their SD-regulated changes in the transcript abundance of genes associated with cold tolerance, starch breakdown, and storage protein accumulation. By analyzing the expression of homologs of FLOWERING LOCUS T, we demonstrated that the clones differed little in their perception of SDs under the growth conditions applied but differed substantially in the downstream responses manifested in the timing and magnitude of gene expression after SD treatment. These results demonstrate the existence of factors that act downstream of SD perception and can contribute to variation in SD-regulated adaptive photoperiodic responses in trees.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Resman, Lars and Howe, Glenn and Jonsen, David and Englund, Madeleine and Druart, Nathalie and Schrader, Jarmo and Antti, Henrik and Skinner, Jeff and Sjödin, Andreas and Chen, Tony and Bhalerao, Rishikesh P.},
	month = nov,
	year = {2010},
	pages = {1294--1303},
}

Abstract Short days (SDs) in autumn induce growth cessation, bud set, cold acclimation, and dormancy in trees of boreal and temperate forests, and these responses occur earlier in northern than in southern genotypes. Nevertheless, we know little about whether this variation results from differential perception of SDs or differential downstream responses to the SD signal or a combination of the two. We compared global patterns of SD-regulated gene expression in the stems of hybrid poplar (Populus trichocarpa × Populus deltoides) clones that differ in their SD-induced growth cessation in order to address this question. The timing of cessation of cambial cell division caused by SDs differed between the clones and was coincident with the change in the pattern of expression of the auxin-regulated genes. The clones also differed in the timing of their SD-regulated changes in the transcript abundance of genes associated with cold tolerance, starch breakdown, and storage protein accumulation. By analyzing the expression of homologs of FLOWERING LOCUS T, we demonstrated that the clones differed little in their perception of SDs under the growth conditions applied but differed substantially in the downstream responses manifested in the timing and magnitude of gene expression after SD treatment. These results demonstrate the existence of factors that act downstream of SD perception and can contribute to variation in SD-regulated adaptive photoperiodic responses in trees.

@article{bjurhager_ultrastructure_2010,
	title = {Ultrastructure and {Mechanical} {Properties} of {Populus} {Wood} with {Reduced} {Lignin} {Content} {Caused} by {Transgenic} {Down}-{Regulation} of {Cinnamate} 4-{Hydroxylase}},
	volume = {11},
	issn = {1525-7797, 1526-4602},
	url = {https://pubs.acs.org/doi/10.1021/bm100487e},
	doi = {10/cc8zgg},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Biomacromolecules},
	author = {Bjurhager, Ingela and Olsson, Anne-Mari and Zhang, Bo and Gerber, Lorenz and Kumar, Manoj and Berglund, Lars A. and Burgert, Ingo and Sundberg, Björn and Salmén, Lennart},
	month = sep,
	year = {2010},
	pages = {2359--2365},
}

@article{freyhult_challenges_2010,
	title = {Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering},
	volume = {11},
	issn = {1471-2105},
	shorttitle = {Challenges in microarray class discovery},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-503},
	doi = {10/dx8xmb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Bioinformatics},
	author = {Freyhult, Eva and Landfors, Mattias and Önskog, Jenny and Hvidsten, Torgeir R and Rydén, Patrik},
	month = dec,
	year = {2010},
	pages = {503},
}

@article{tomaz_mitochondrial_2010,
	title = {Mitochondrial {Malate} {Dehydrogenase} {Lowers} {Leaf} {Respiration} and {Alters} {Photorespiration} and {Plant} {Growth} in {Arabidopsis}},
	volume = {154},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/154/3/1143/6111237},
	doi = {10/c7j4h7},
	abstract = {Abstract
            Malate dehydrogenase (MDH) catalyzes a reversible NAD+-dependent-dehydrogenase reaction involved in central metabolism and redox homeostasis between organelle compartments. To explore the role of mitochondrial MDH (mMDH) in Arabidopsis (Arabidopsis thaliana), knockout single and double mutants for the highly expressed mMDH1 and lower expressed mMDH2 isoforms were constructed and analyzed. A mmdh1mmdh2 mutant has no detectable mMDH activity but is viable, albeit small and slow growing. Quantitative proteome analysis of mitochondria shows changes in other mitochondrial NAD-linked dehydrogenases, indicating a reorganization of such enzymes in the mitochondrial matrix. The slow-growing mmdh1mmdh2 mutant has elevated leaf respiration rate in the dark and light, without loss of photosynthetic capacity, suggesting that mMDH normally uses NADH to reduce oxaloacetate to malate, which is then exported to the cytosol, rather than to drive mitochondrial respiration. Increased respiratory rate in leaves can account in part for the low net CO2 assimilation and slow growth rate of mmdh1mmdh2. Loss of mMDH also affects photorespiration, as evidenced by a lower postillumination burst, alterations in CO2 assimilation/intercellular CO2 curves at low CO2, and the light-dependent elevated concentration of photorespiratory metabolites. Complementation of mmdh1mmdh2 with an mMDH cDNA recovered mMDH activity, suppressed respiratory rate, ameliorated changes to photorespiration, and increased plant growth. A previously established inverse correlation between mMDH and ascorbate content in tomato (Solanum lycopersicum) has been consolidated in Arabidopsis and may potentially be linked to decreased galactonolactone dehydrogenase content in mitochondria in the mutant. Overall, a central yet complex role for mMDH emerges in the partitioning of carbon and energy in leaves, providing new directions for bioengineering of plant growth rate and a new insight into the molecular mechanisms linking respiration and photosynthesis in plants.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Tomaz, Tiago and Bagard, Matthieu and Pracharoenwattana, Itsara and Lindén, Pernilla and Lee, Chun Pong and Carroll, Adam J. and Ströher, Elke and Smith, Steven M. and Gardeström, Per and Millar, A. Harvey},
	month = nov,
	year = {2010},
	pages = {1143--1157},
}

Abstract Malate dehydrogenase (MDH) catalyzes a reversible NAD+-dependent-dehydrogenase reaction involved in central metabolism and redox homeostasis between organelle compartments. To explore the role of mitochondrial MDH (mMDH) in Arabidopsis (Arabidopsis thaliana), knockout single and double mutants for the highly expressed mMDH1 and lower expressed mMDH2 isoforms were constructed and analyzed. A mmdh1mmdh2 mutant has no detectable mMDH activity but is viable, albeit small and slow growing. Quantitative proteome analysis of mitochondria shows changes in other mitochondrial NAD-linked dehydrogenases, indicating a reorganization of such enzymes in the mitochondrial matrix. The slow-growing mmdh1mmdh2 mutant has elevated leaf respiration rate in the dark and light, without loss of photosynthetic capacity, suggesting that mMDH normally uses NADH to reduce oxaloacetate to malate, which is then exported to the cytosol, rather than to drive mitochondrial respiration. Increased respiratory rate in leaves can account in part for the low net CO2 assimilation and slow growth rate of mmdh1mmdh2. Loss of mMDH also affects photorespiration, as evidenced by a lower postillumination burst, alterations in CO2 assimilation/intercellular CO2 curves at low CO2, and the light-dependent elevated concentration of photorespiratory metabolites. Complementation of mmdh1mmdh2 with an mMDH cDNA recovered mMDH activity, suppressed respiratory rate, ameliorated changes to photorespiration, and increased plant growth. A previously established inverse correlation between mMDH and ascorbate content in tomato (Solanum lycopersicum) has been consolidated in Arabidopsis and may potentially be linked to decreased galactonolactone dehydrogenase content in mitochondria in the mutant. Overall, a central yet complex role for mMDH emerges in the partitioning of carbon and energy in leaves, providing new directions for bioengineering of plant growth rate and a new insight into the molecular mechanisms linking respiration and photosynthesis in plants.

@article{ma_genetic_2010,
	title = {Genetic {Differentiation}, {Clinal} {Variation} and {Phenotypic} {Associations} {With} {Growth} {Cessation} {Across} the \textit{{Populus} tremula} {Photoperiodic} {Pathway}},
	volume = {186},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/186/3/1033/6063664},
	doi = {10/c7k7hc},
	abstract = {Abstract
            Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P. tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10–15\% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5–7\% of the phenotypic variation in growth cessation.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Genetics},
	author = {Ma, Xiao-Fei and Hall, David and Onge, Katherine R St and Jansson, Stefan and Ingvarsson, Pär K},
	month = nov,
	year = {2010},
	pages = {1033--1044},
}

Abstract Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P. tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10–15% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5–7% of the phenotypic variation in growth cessation.

@article{contesto_auxin-signaling_2010,
	title = {The auxin-signaling pathway is required for the lateral root response of {Arabidopsis} to the rhizobacterium {Phyllobacterium} brassicacearum},
	volume = {232},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-010-1264-0},
	doi = {10/c99m2s},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Contesto, Céline and Milesi, Sandrine and Mantelin, Sophie and Zancarini, Anouk and Desbrosses, Guilhem and Varoquaux, Fabrice and Bellini, Catherine and Kowalczyk, Mariusz and Touraine, Bruno},
	month = nov,
	year = {2010},
	pages = {1455--1470},
}

@article{ivkovic_risks_2010,
	title = {Risks affecting breeding objectives for radiata pine in {Australia}},
	volume = {73},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2010.10676338},
	doi = {10/gkgfsd},
	abstract = {This paper examines the effects of climatic and biotic risks—drought, Essigella aphid, Dothistroma needle blight and Fusarium pitch canker—on the Pinus radiata production system in Australia. These risks were examined in relation to climatic variables in order to develop ‘hazard ratings’ for planting sites. Bio-economic models were developed to link the risks with the established breeding objective for solid wood production. Economic weights were derived for resistance traits that can be used in index selection for breeding and deployment. Under one scenario, drought-affected sites can achieve an internal rate of return of {\textgreater}7.0\% only if the land rental is sufficiently low, that is {\textgreater}\$25 ha−1 y−1, but replanting costs and volume losses due to mortality can be significant. An average of 13.5\% defoliation caused by Essigella aphid would reduce volume growth over a rotation period by about 10\%. A modest increase in profitability can be achieved through deployment of Essigella-resistant genotypes. Reduction of volume growth by Dothistroma defoliation at an early age (4–10 y) had a relatively small effect on subsequent yield reduction. At a site with a high level of infection, however, the profitability of improving Dothistroma resistance was similar to that for improving growth on uninfected sites. The economic importance of risk traits relative to MAI over the entire radiata pine plantation estate was generally low: 4\% for pine aphid, 0.6\% for needle blight and 1.3\% for pitch canker resistance. Essigella pine aphid is the most important pest currently affecting the productivity of radiata pine plantations in Australia.},
	number = {4},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	author = {Ivković, M. and Gapare, W. J. and Wharton, T. and Jovanovic, T. and Elms, S. and McRae, T. A. and Wu, H. X.},
	month = jan,
	year = {2010},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/00049158.2010.10676338},
	keywords = {Dothistroma septosporum, Essigella californica, Fusarium circinatum, Pinus radiata, breeding, diseases, economic analysis, insect pests, objectives, risk assessment},
	pages = {265--278},
}

This paper examines the effects of climatic and biotic risks—drought, Essigella aphid, Dothistroma needle blight and Fusarium pitch canker—on the Pinus radiata production system in Australia. These risks were examined in relation to climatic variables in order to develop ‘hazard ratings’ for planting sites. Bio-economic models were developed to link the risks with the established breeding objective for solid wood production. Economic weights were derived for resistance traits that can be used in index selection for breeding and deployment. Under one scenario, drought-affected sites can achieve an internal rate of return of \textgreater7.0% only if the land rental is sufficiently low, that is \textgreater$25 ha−1 y−1, but replanting costs and volume losses due to mortality can be significant. An average of 13.5% defoliation caused by Essigella aphid would reduce volume growth over a rotation period by about 10%. A modest increase in profitability can be achieved through deployment of Essigella-resistant genotypes. Reduction of volume growth by Dothistroma defoliation at an early age (4–10 y) had a relatively small effect on subsequent yield reduction. At a site with a high level of infection, however, the profitability of improving Dothistroma resistance was similar to that for improving growth on uninfected sites. The economic importance of risk traits relative to MAI over the entire radiata pine plantation estate was generally low: 4% for pine aphid, 0.6% for needle blight and 1.3% for pitch canker resistance. Essigella pine aphid is the most important pest currently affecting the productivity of radiata pine plantations in Australia.

@article{baltunis_genetic_2010,
	title = {Genetic {Parameters} and {Genotype} by {Environment} {Interaction} in {Radiata} {Pine} for {Growth} and {Wood} {Quality} {Traits} in {Australia}},
	volume = {59},
	issn = {2509-8934},
	url = {https://www.sciendo.com/article/10.1515/sg-2010-0014},
	doi = {10/gkgfsb},
	abstract = {Abstract
            
              The phenotypic response of genotypes across different environments can be quantified by estimating the genotype by environment interaction (GxE). In a practical sense, GxE means that the relative performance of genotypes does not remain constant under all test conditions. Genetic parameters and genotype by environment interactions for wood density, growth, branching characteristics and stem straightness were investigated in eight radiata pine progeny trials derived from a second generation breeding population in Australia. Five trials were on the mainland, while three trials were in Tasmania. Generally, ĥ
              2
              for density {\textgreater} branch angle {\textgreater} stem straightness {\textgreater} tree diameter {\textgreater} branch size; and significant ĥ
              2
              was observed for all traits and at all trials with only two exceptions. Genetic correlations were estimated among the five traits, and a large negative genetic correlation observed between wood density and tree diameter indicated that a selection strategy should be developed in dealing with this adverse genetic correlation in advanced generations of breeding for radiata pine. Interactions for density, branch angle, and stem straightness were small within the two regions. Overall, branch angle had the least GxE, followed by density and stem straightness. Growth traits (tree diameter and branch size) tended to be the most interactive with substantial GxE present. Genotype by regional interactions (Mainland versus Tasmania) revealed that density and branch angle had the least interactions (ȓ
              B
              = 0.98 and ȓ
              B
              = 0.95, respectively). Branch size and tree diameter had the highest interactions among the two regions (ȓ
              B
              = 0.55 and ȓ
              B
              = 0.63, respectively). Within Tasmania, only branch size and tree diameter had a sizable interaction within the three sites. In contrast, there was little interaction for tree diameter among the Mainland trials. Branch size in the Mainland trials had a similar size of interaction as in Tasmania. Further research is recommended in identifying the cause of GxE for tree diameter and branch size in radiata pine across the entire radiata pine estate in Australia.},
	language = {en},
	number = {1-6},
	urldate = {2021-06-08},
	journal = {Silvae Genetica},
	author = {Baltunis, Brian. S. and Gapare, W. J. and Wu, H. X.},
	month = dec,
	year = {2010},
	pages = {113--124},
}

Abstract The phenotypic response of genotypes across different environments can be quantified by estimating the genotype by environment interaction (GxE). In a practical sense, GxE means that the relative performance of genotypes does not remain constant under all test conditions. Genetic parameters and genotype by environment interactions for wood density, growth, branching characteristics and stem straightness were investigated in eight radiata pine progeny trials derived from a second generation breeding population in Australia. Five trials were on the mainland, while three trials were in Tasmania. Generally, ĥ 2 for density \textgreater branch angle \textgreater stem straightness \textgreater tree diameter \textgreater branch size; and significant ĥ 2 was observed for all traits and at all trials with only two exceptions. Genetic correlations were estimated among the five traits, and a large negative genetic correlation observed between wood density and tree diameter indicated that a selection strategy should be developed in dealing with this adverse genetic correlation in advanced generations of breeding for radiata pine. Interactions for density, branch angle, and stem straightness were small within the two regions. Overall, branch angle had the least GxE, followed by density and stem straightness. Growth traits (tree diameter and branch size) tended to be the most interactive with substantial GxE present. Genotype by regional interactions (Mainland versus Tasmania) revealed that density and branch angle had the least interactions (ȓ B = 0.98 and ȓ B = 0.95, respectively). Branch size and tree diameter had the highest interactions among the two regions (ȓ B = 0.55 and ȓ B = 0.63, respectively). Within Tasmania, only branch size and tree diameter had a sizable interaction within the three sites. In contrast, there was little interaction for tree diameter among the Mainland trials. Branch size in the Mainland trials had a similar size of interaction as in Tasmania. Further research is recommended in identifying the cause of GxE for tree diameter and branch size in radiata pine across the entire radiata pine estate in Australia.

@article{ranocha_walls_2010,
	title = {Walls are thin 1 ({WAT1}), an {Arabidopsis} homolog of {Medicago} truncatula {NODULIN21}, is a tonoplast-localized protein required for secondary wall formation in fibers: {Tonoplastic} {WAT1} and secondary wall formation},
	volume = {63},
	issn = {09607412},
	shorttitle = {Walls are thin 1 ({WAT1}), an {Arabidopsis} homolog of {Medicago} truncatula {NODULIN21}, is a tonoplast-localized protein required for secondary wall formation in fibers},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2010.04256.x},
	doi = {10/bhpctv},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Ranocha, Philippe and Denancé, Nicolas and Vanholme, Ruben and Freydier, Amandine and Martinez, Yves and Hoffmann, Laurent and Köhler, Lothar and Pouzet, Cécile and Renou, Jean-Pierre and Sundberg, Björn and Boerjan, Wout and Goffner, Deborah},
	month = aug,
	year = {2010},
	pages = {469--483},
}

@article{hallander_bayesian_2010,
	title = {Bayesian {Inference} of {Genetic} {Parameters} {Based} on {Conditional} {Decompositions} of {Multivariate} {Normal} {Distributions}},
	volume = {185},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/185/2/645/6096932},
	doi = {10/bt2hhr},
	abstract = {Abstract
            It is widely recognized that the mixed linear model is an important tool for parameter estimation in the analysis of complex pedigrees, which includes both pedigree and genomic information, and where mutually dependent genetic factors are often assumed to follow multivariate normal distributions of high dimension. We have developed a Bayesian statistical method based on the decomposition of the multivariate normal prior distribution into products of conditional univariate distributions. This procedure permits computationally demanding genetic evaluations of complex pedigrees, within the user-friendly computer package WinBUGS. To demonstrate and evaluate the flexibility of the method, we analyzed two example pedigrees: a large noninbred pedigree of Scots pine (Pinus sylvestris L.) that includes additive and dominance polygenic relationships and a simulated pedigree where genomic relationships have been calculated on the basis of a dense marker map. The analysis showed that our method was fast and provided accurate estimates and that it should therefore be a helpful tool for estimating genetic parameters of complex pedigrees quickly and reliably.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Genetics},
	author = {Hallander, Jon and Waldmann, Patrik and Wang, Chunkao and Sillanpää, Mikko J},
	month = jun,
	year = {2010},
	pages = {645--654},
}

Abstract It is widely recognized that the mixed linear model is an important tool for parameter estimation in the analysis of complex pedigrees, which includes both pedigree and genomic information, and where mutually dependent genetic factors are often assumed to follow multivariate normal distributions of high dimension. We have developed a Bayesian statistical method based on the decomposition of the multivariate normal prior distribution into products of conditional univariate distributions. This procedure permits computationally demanding genetic evaluations of complex pedigrees, within the user-friendly computer package WinBUGS. To demonstrate and evaluate the flexibility of the method, we analyzed two example pedigrees: a large noninbred pedigree of Scots pine (Pinus sylvestris L.) that includes additive and dominance polygenic relationships and a simulated pedigree where genomic relationships have been calculated on the basis of a dense marker map. The analysis showed that our method was fast and provided accurate estimates and that it should therefore be a helpful tool for estimating genetic parameters of complex pedigrees quickly and reliably.

@article{szal_influence_2010,
	title = {Influence of mitochondrial genome rearrangement on cucumber leaf carbon and nitrogen metabolism},
	volume = {232},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-010-1261-3},
	doi = {10/fdzxxf},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Szal, Bożena and Jastrzębska, Agata and Kulka, Marek and Leśniak, Karolina and Podgórska, Anna and Pärnik, Tiit and Ivanova, Hiie and Keerberg, Olav and Gardeström, Per and Rychter, Anna M.},
	month = nov,
	year = {2010},
	pages = {1371--1382},
}

@article{liu_modelling_2010,
	title = {Modelling and experimental analysis of hormonal crosstalk in \textit{{Arabidopsis}}},
	volume = {6},
	issn = {1744-4292, 1744-4292},
	url = {https://onlinelibrary.wiley.com/doi/10.1038/msb.2010.26},
	doi = {10/cwkvtp},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Molecular Systems Biology},
	author = {Liu, Junli and Mehdi, Saher and Topping, Jennifer and Tarkowski, Petr and Lindsey, Keith},
	month = jan,
	year = {2010},
	pages = {373},
}

@article{danielsson_development_2010,
	title = {Development and optimization of a metabolomic method for analysis of adherent cell cultures},
	volume = {404},
	issn = {00032697},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0003269710002502},
	doi = {10/fhmpbx},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Analytical Biochemistry},
	author = {Danielsson, Anders P.H. and Moritz, Thomas and Mulder, Hindrik and Spégel, Peter},
	month = sep,
	year = {2010},
	pages = {30--39},
}

@article{banerjee_hierarchical_2010,
	title = {Hierarchical {Spatial} {Process} {Models} for {Multiple} {Traits} in {Large} {Genetic} {Trials}},
	volume = {105},
	issn = {0162-1459, 1537-274X},
	url = {http://www.tandfonline.com/doi/abs/10.1198/jasa.2009.ap09068},
	doi = {10/frh2ds},
	language = {en},
	number = {490},
	urldate = {2021-06-08},
	journal = {Journal of the American Statistical Association},
	author = {Banerjee, Sudipto and Finley, Andrew O. and Waldmann, Patrik and Ericsson, Tore},
	month = jun,
	year = {2010},
	pages = {506--521},
}

@article{takata_phylogenetic_2010,
	title = {Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of {Pseudo}-{Response} {Regulators}},
	volume = {10},
	issn = {1471-2148},
	shorttitle = {Phylogenetic footprint of the plant clock system in angiosperms},
	url = {http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-126},
	doi = {10/c92zxh},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Evolutionary Biology},
	author = {Takata, Naoki and Saito, Shigeru and Saito, Claire and Uemura, Matsuo},
	year = {2010},
	pages = {126},
}

@article{vera-sirera_role_2010,
	title = {Role of polyamines in plant vascular development},
	volume = {48},
	issn = {09819428},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942810000173},
	doi = {10/c429rn},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Plant Physiology and Biochemistry},
	author = {Vera-Sirera, Francisco and Minguet, Eugenio G. and Singh, Sunil Kumar and Ljung, Karin and Tuominen, Hannele and Blázquez, Miguel A. and Carbonell, Juan},
	month = jul,
	year = {2010},
	pages = {534--539},
}

@article{dillon_association_2010,
	title = {Association genetics reveal candidate gene {SNPs} affecting wood properties in {Pinus} radiata},
	volume = {73},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2010.10676326},
	doi = {10/gkgfrf},
	abstract = {Association or linkage disequilibrium (LD) mapping is an emerging approach for identifying molecular markers linked to phenotypic variation. Forest trees are ideally suited to association mapping due to their low genomic LD which permits highresolution mapping of marker associations. Using this approach several single-nucleotide polymorphisms (SNPs) potentially influencing economically important wood traits (density, cellulose microfibril angle and modulus of elasticity) were identified in a Pinus radiata provenance trial. One hundred and forty-nine SNP markers from 44 cell wall candidate genes were examined. After accounting for population structure and multiple testing, 15 SNPs demonstrated significant associations at P {\textless} 0.05. We have demonstrated that linkage disequilibrium in the native populations of P. radiata decays within the length of a gene. Therefore, the identified associations may result from the SNP under examination, or at least a linked SNP within the same gene. Without accounting for multi-colinearity between markers, the proportion of trait variance attributed to individual SNPs ranged from 1.5\% to 6.5\%. SNP associations are presently undergoing validation in a second-generation Southern Tree Breeding Association progeny trial. The small proportion of total quantitative variation contributed by individual SNPs indicates molecular breeding strategies would achieve greatest gains using combinations of SNPs for marker-assisted selection. Establishing methods for efficient transfer of validated SNPs into breeding selection models is essential for the uptake of the marker technology identified here, and is the focus of ongoing research.},
	number = {3},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	author = {Dillon, S. K. and Nolan, M. F. and Wu, H. and Southerton, S. G.},
	month = jan,
	year = {2010},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/00049158.2010.10676326},
	keywords = {Pinus radiata, genetic variation, marker-aided selection, molecular markers, phenotypic variation, wood properties},
	pages = {185--190},
}

Association or linkage disequilibrium (LD) mapping is an emerging approach for identifying molecular markers linked to phenotypic variation. Forest trees are ideally suited to association mapping due to their low genomic LD which permits highresolution mapping of marker associations. Using this approach several single-nucleotide polymorphisms (SNPs) potentially influencing economically important wood traits (density, cellulose microfibril angle and modulus of elasticity) were identified in a Pinus radiata provenance trial. One hundred and forty-nine SNP markers from 44 cell wall candidate genes were examined. After accounting for population structure and multiple testing, 15 SNPs demonstrated significant associations at P \textless 0.05. We have demonstrated that linkage disequilibrium in the native populations of P. radiata decays within the length of a gene. Therefore, the identified associations may result from the SNP under examination, or at least a linked SNP within the same gene. Without accounting for multi-colinearity between markers, the proportion of trait variance attributed to individual SNPs ranged from 1.5% to 6.5%. SNP associations are presently undergoing validation in a second-generation Southern Tree Breeding Association progeny trial. The small proportion of total quantitative variation contributed by individual SNPs indicates molecular breeding strategies would achieve greatest gains using combinations of SNPs for marker-assisted selection. Establishing methods for efficient transfer of validated SNPs into breeding selection models is essential for the uptake of the marker technology identified here, and is the focus of ongoing research.

@article{chen_transfer_2010,
	title = {Transfer {RNA} modifications and genes for modifying enzymes in {Arabidopsis} thaliana},
	volume = {10},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-10-201},
	doi = {10/dc7jmm},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Chen, Peng and Jäger, Gunilla and Zheng, Bo},
	year = {2010},
	pages = {201},
}

@article{pietra_auxin_2010,
	title = {Auxin {Paves} the {Way} for {Planar} {Morphogenesis}},
	volume = {143},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867410010779},
	doi = {10/c3rh33},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Cell},
	author = {Pietra, Stefano and Grebe, Markus},
	month = oct,
	year = {2010},
	pages = {29--31},
}

@article{renberg_metabolomic_2010,
	title = {A {Metabolomic} {Approach} to {Study} {Major} {Metabolite} {Changes} during {Acclimation} to {Limiting} {CO2} in \textit{{Chlamydomonas} reinhardtii}},
	volume = {154},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/154/1/187/6111228},
	doi = {10/b3xzqv},
	abstract = {Abstract
            Using a gas chromatography-mass spectrometry-time of flight technique, we determined major metabolite changes during induction of the carbon-concentrating mechanism in the unicellular green alga Chlamydomonas reinhardtii. In total, 128 metabolites with significant differences between high- and low-CO2-grown cells were detected, of which 82 were wholly or partially identified, including amino acids, lipids, and carbohydrates. In a 24-h time course experiment, we show that the amino acids serine and phenylalanine increase transiently while aspartate and glutamate decrease after transfer to low CO2. The biggest differences were typically observed 3 h after transfer to low-CO2 conditions. Therefore, we made a careful metabolomic examination at the 3-h time point, comparing low-CO2 treatment to high-CO2 control. Five metabolites involved in photorespiration, 11 amino acids, and one lipid were increased, while six amino acids and, interestingly, 21 lipids were significantly lower. Our conclusion is that the metabolic pattern during early induction of the carbon-concentrating mechanism fit a model where photorespiration is increasing.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Renberg, Linda and Johansson, Annika I. and Shutova, Tatiana and Stenlund, Hans and Aksmann, Anna and Raven, John A. and Gardeström, Per and Moritz, Thomas and Samuelsson, Göran},
	month = sep,
	year = {2010},
	pages = {187--196},
}

Abstract Using a gas chromatography-mass spectrometry-time of flight technique, we determined major metabolite changes during induction of the carbon-concentrating mechanism in the unicellular green alga Chlamydomonas reinhardtii. In total, 128 metabolites with significant differences between high- and low-CO2-grown cells were detected, of which 82 were wholly or partially identified, including amino acids, lipids, and carbohydrates. In a 24-h time course experiment, we show that the amino acids serine and phenylalanine increase transiently while aspartate and glutamate decrease after transfer to low CO2. The biggest differences were typically observed 3 h after transfer to low-CO2 conditions. Therefore, we made a careful metabolomic examination at the 3-h time point, comparing low-CO2 treatment to high-CO2 control. Five metabolites involved in photorespiration, 11 amino acids, and one lipid were increased, while six amino acids and, interestingly, 21 lipids were significantly lower. Our conclusion is that the metabolic pattern during early induction of the carbon-concentrating mechanism fit a model where photorespiration is increasing.

@article{savitch_regulation_2010,
	title = {Regulation of {Energy} {Partitioning} and {Alternative} {Electron} {Transport} {Pathways} {During} {Cold} {Acclimation} of {Lodgepole} {Pine} is {Oxygen} {Dependent}},
	volume = {51},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcq101},
	doi = {10/cdrdzh},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {Savitch, Leonid V. and Ivanov, Alexander G. and Krol, Marianna and Sprott, David P. and Öquist, Gunnar and Huner, Norman P. A.},
	month = sep,
	year = {2010},
	pages = {1555--1570},
}

@article{hogberg_quantification_2010,
	title = {Quantification of effects of season and nitrogen supply on tree below‐ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest},
	volume = {187},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03274.x},
	doi = {10/b9nhbk},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Högberg, Mona N. and Briones, Maria J. I. and Keel, Sonja G. and Metcalfe, Daniel B. and Campbell, Catherine and Midwood, Andrew J. and Thornton, Barry and Hurry, Vaughan and Linder, Sune and Näsholm, Torgny and Högberg, Peter},
	month = jul,
	year = {2010},
	pages = {485--493},
}

@article{atkinson_impact_2010,
	title = {Impact of growth temperature on scaling relationships linking photosynthetic metabolism to leaf functional traits: {Impacts} of growth temperature on scaling relationships},
	volume = {24},
	issn = {02698463},
	shorttitle = {Impact of growth temperature on scaling relationships linking photosynthetic metabolism to leaf functional traits},
	url = {http://doi.wiley.com/10.1111/j.1365-2435.2010.01758.x},
	doi = {10/dmdkm7},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Functional Ecology},
	author = {Atkinson, Lindsey J. and Campbell, Catherine D. and Zaragoza-Castells, Joana and Hurry, Vaughan and Atkin, Owen K.},
	month = dec,
	year = {2010},
	pages = {1181--1191},
}

@article{jones_cytokinin_2010,
	title = {Cytokinin {Regulation} of {Auxin} {Synthesis} in \textit{{Arabidopsis}} {Involves} a {Homeostatic} {Feedback} {Loop} {Regulated} via {Auxin} and {Cytokinin} {Signal} {Transduction}},
	volume = {22},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/22/9/2956/6096141},
	doi = {10/dszfmr},
	abstract = {Abstract
            Together, auxin and cytokinin regulate many of the processes that are critical to plant growth, development, and environmental responsiveness. We have previously shown that exogenous auxin regulates cytokinin biosynthesis in Arabidopsis thaliana. In this work, we show that, conversely, the application or induced ectopic biosynthesis of cytokinin leads to a rapid increase in auxin biosynthesis in young, developing root and shoot tissues. We also show that reducing endogenous cytokinin levels, either through the induction of CYTOKININ OXIDASE expression or the mutation of one or more of the cytokinin biosynthetic ISOPENTENYLTRANSFERASE genes leads to a reduction in auxin biosynthesis. Cytokinin modifies the abundance of transcripts for several putative auxin biosynthetic genes, suggesting a direct induction of auxin biosynthesis by cytokinin. Our data indicate that cytokinin is essential, not only to maintain basal levels of auxin biosynthesis in developing root and shoot tissues but also for the dynamic regulation of auxin biosynthesis in response to changing developmental or environmental conditions. In combination with our previous work, the data suggest that a homeostatic feedback regulatory loop involving both auxin and cytokinin signaling acts to maintain appropriate auxin and cytokinin concentrations in developing root and shoot tissues.},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Jones, Brian and Gunnerås, Sara Andersson and Petersson, Sara V. and Tarkowski, Petr and Graham, Neil and May, Sean and Dolezal, Karel and Sandberg, Göran and Ljung, Karin},
	month = oct,
	year = {2010},
	pages = {2956--2969},
}

Abstract Together, auxin and cytokinin regulate many of the processes that are critical to plant growth, development, and environmental responsiveness. We have previously shown that exogenous auxin regulates cytokinin biosynthesis in Arabidopsis thaliana. In this work, we show that, conversely, the application or induced ectopic biosynthesis of cytokinin leads to a rapid increase in auxin biosynthesis in young, developing root and shoot tissues. We also show that reducing endogenous cytokinin levels, either through the induction of CYTOKININ OXIDASE expression or the mutation of one or more of the cytokinin biosynthetic ISOPENTENYLTRANSFERASE genes leads to a reduction in auxin biosynthesis. Cytokinin modifies the abundance of transcripts for several putative auxin biosynthetic genes, suggesting a direct induction of auxin biosynthesis by cytokinin. Our data indicate that cytokinin is essential, not only to maintain basal levels of auxin biosynthesis in developing root and shoot tissues but also for the dynamic regulation of auxin biosynthesis in response to changing developmental or environmental conditions. In combination with our previous work, the data suggest that a homeostatic feedback regulatory loop involving both auxin and cytokinin signaling acts to maintain appropriate auxin and cytokinin concentrations in developing root and shoot tissues.

@article{krouk_nitrate-regulated_2010,
	title = {Nitrate-{Regulated} {Auxin} {Transport} by {NRT1}.1 {Defines} a {Mechanism} for {Nutrient} {Sensing} in {Plants}},
	volume = {18},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580710002169},
	doi = {10/dq3gjd},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Developmental Cell},
	author = {Krouk, Gabriel and Lacombe, Benoît and Bielach, Agnieszka and Perrine-Walker, Francine and Malinska, Katerina and Mounier, Emmanuelle and Hoyerova, Klara and Tillard, Pascal and Leon, Sarah and Ljung, Karin and Zazimalova, Eva and Benkova, Eva and Nacry, Philippe and Gojon, Alain},
	month = jun,
	year = {2010},
	pages = {927--937},
}

@article{kleczkowski_mechanisms_2010,
	title = {Mechanisms of {UDP}-{Glucose} {Synthesis} in {Plants}},
	volume = {29},
	issn = {0735-2689, 1549-7836},
	url = {https://www.tandfonline.com/doi/full/10.1080/07352689.2010.483578},
	doi = {10/fdfr4g},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Critical Reviews in Plant Sciences},
	author = {Kleczkowski, Leszek A. and Kunz, Sabine and Wilczynska, Malgorzata},
	month = jul,
	year = {2010},
	pages = {191--203},
}

@article{jansson_cohort-structured_2010,
	title = {Cohort-structured tree populations},
	volume = {105},
	issn = {0018-067X, 1365-2540},
	url = {http://www.nature.com/articles/hdy2010101},
	doi = {10/ckkxzd},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Heredity},
	author = {Jansson, S and Ingvarsson, P K},
	month = oct,
	year = {2010},
	pages = {331--332},
}

@article{hedwall_compositional_2010,
	title = {Compositional changes of forest-floor vegetation in young stands of {Norway} spruce as an effect of repeated fertilisation},
	volume = {259},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112710001714},
	doi = {10/fv8s3x},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Forest Ecology and Management},
	author = {Hedwall, Per-Ola and Nordin, Annika and Brunet, Jörg and Bergh, Johan},
	month = may,
	year = {2010},
	pages = {2418--2425},
}

@article{zhao_hormonal_2010,
	title = {Hormonal control of the shoot stem-cell niche},
	volume = {465},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature09126},
	doi = {10/bq25jx},
	language = {en},
	number = {7301},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Zhao, Zhong and Andersen, Stig U. and Ljung, Karin and Dolezal, Karel and Miotk, Andrej and Schultheiss, Sebastian J. and Lohmann, Jan U.},
	month = jun,
	year = {2010},
	pages = {1089--1092},
}

@article{bergemalm_superoxide_2010,
	title = {Superoxide dismutase-1 and other proteins in inclusions from transgenic amyotrophic lateral sclerosis model mice: {SOD1} inclusions in {ALS} transgenic mice},
	volume = {114},
	issn = {00223042},
	shorttitle = {Superoxide dismutase-1 and other proteins in inclusions from transgenic amyotrophic lateral sclerosis model mice},
	url = {http://doi.wiley.com/10.1111/j.1471-4159.2010.06753.x},
	doi = {10/fdbwxp},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Neurochemistry},
	author = {Bergemalm, Daniel and Forsberg, Karin and Srivastava, Vaibhav and Graffmo, Karin S. and Andersen, Peter M. and Brännström, Thomas and Wingsle, Gunnar and Marklund, Stefan L.},
	month = jul,
	year = {2010},
	pages = {408--418},
}

@article{mikami_dibasic_2010,
	title = {A {Dibasic} {Amino} {Acid} {Pair} {Conserved} in the {Activation} {Loop} {Directs} {Plasma} {Membrane} {Localization} and {Is} {Necessary} for {Activity} of {Plant} {Type} {I}/{II} {Phosphatidylinositol} {Phosphate} {Kinase}},
	volume = {153},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/153/3/1004/6109401},
	doi = {10/dzmkwn},
	abstract = {Abstract
            Phosphatidylinositol phosphate kinase (PIPK) is an enzyme involved in the regulation of cellular levels of phosphoinositides involved in various physiological processes, such as cytoskeletal organization, ion channel activation, and vesicle trafficking. In animals, research has focused on the modes of activation and function of PIPKs, providing an understanding of the importance of plasma membrane localization. However, it still remains unclear how this issue is regulated in plant PIPKs. Here, we demonstrate that the carboxyl-terminal catalytic domain, which contains the activation loop, is sufficient for plasma membrane localization of PpPIPK1, a type I/II B PIPK from the moss Physcomitrella patens. The importance of the carboxyl-terminal catalytic domain for plasma membrane localization was confirmed with Arabidopsis (Arabidopsis thaliana) AtPIP5K1. Our findings, in which substitution of a conserved dibasic amino acid pair in the activation loop of PpPIPK1 completely prevented plasma membrane targeting and abolished enzymatic activity, demonstrate its critical role in these processes. Placing our results in the context of studies of eukaryotic PIPKs led us to conclude that the function of the dibasic amino acid pair in the activation loop in type I/II PIPKs is plant specific.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Mikami, Koji and Saavedra, Laura and Hiwatashi, Yuji and Uji, Toshiki and Hasebe, Mitsuyasu and Sommarin, Marianne},
	month = jul,
	year = {2010},
	pages = {1004--1015},
}

Abstract Phosphatidylinositol phosphate kinase (PIPK) is an enzyme involved in the regulation of cellular levels of phosphoinositides involved in various physiological processes, such as cytoskeletal organization, ion channel activation, and vesicle trafficking. In animals, research has focused on the modes of activation and function of PIPKs, providing an understanding of the importance of plasma membrane localization. However, it still remains unclear how this issue is regulated in plant PIPKs. Here, we demonstrate that the carboxyl-terminal catalytic domain, which contains the activation loop, is sufficient for plasma membrane localization of PpPIPK1, a type I/II B PIPK from the moss Physcomitrella patens. The importance of the carboxyl-terminal catalytic domain for plasma membrane localization was confirmed with Arabidopsis (Arabidopsis thaliana) AtPIP5K1. Our findings, in which substitution of a conserved dibasic amino acid pair in the activation loop of PpPIPK1 completely prevented plasma membrane targeting and abolished enzymatic activity, demonstrate its critical role in these processes. Placing our results in the context of studies of eukaryotic PIPKs led us to conclude that the function of the dibasic amino acid pair in the activation loop in type I/II PIPKs is plant specific.

@article{christensen_higher_2010,
	title = {Higher {Plant} {Calreticulins} {Have} {Acquired} {Specialized} {Functions} in {Arabidopsis}},
	volume = {5},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0011342},
	doi = {10/dp7zwx},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Christensen, Anna and Svensson, Karin and Thelin, Lisa and Zhang, Wenjing and Tintor, Nico and Prins, Daniel and Funke, Norma and Michalak, Marek and Schulze-Lefert, Paul and Saijo, Yusuke and Sommarin, Marianne and Widell, Susanne and Persson, Staffan},
	editor = {Bassham, Diane},
	month = jun,
	year = {2010},
	pages = {e11342},
}

@article{ruta_collocations_2010,
	title = {Collocations of {QTLs} for {Seedling} {Traits} and {Yield} {Components} of {Tropical} {Maize} under {Water} {Stress} {Conditions}},
	volume = {50},
	issn = {0011183X},
	url = {http://doi.wiley.com/10.2135/cropsci2009.01.0036},
	doi = {10/fnwsjk},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Crop Science},
	author = {Ruta, Nathinee and Stamp, Peter and Liedgens, Markus and Fracheboud, Yvan and Hund, Andreas},
	month = jul,
	year = {2010},
	pages = {1385--1392},
}

@article{krus_pyruvate_2010,
	title = {Pyruvate dehydrogenase kinase 1 controls mitochondrial metabolism and insulin secretion in {INS}-1 832/13 clonal β-cells},
	volume = {429},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/429/1/205/45438/Pyruvate-dehydrogenase-kinase-1-controls},
	doi = {10/d2d23m},
	abstract = {Tight coupling between cytosolic and mitochondrial metabolism is key for GSIS (glucose-stimulated insulin secretion). In the present study we examined the regulatory contribution of PDH (pyruvate dehydrogenase) kinase 1, a negative regulator of PDH, to metabolic coupling in 832/13 clonal β-cells. Knockdown of PDH kinase 1 with siRNA (small interfering RNA) reduced its mRNA ({\textgreater}80\%) and protein level ({\textgreater}40\%) after 72 h. PDH activity, glucose-stimulated cellular oxygen consumption and pyruvate-stimulated mitochondrial oxygen consumption increased 1.7- (P{\textless}0.05), 1.6- (P{\textless}0.05) and 1.6-fold (P{\textless}0.05) respectively. Gas chromatography/MS revealed an altered metabolite profile upon silencing of PDH kinase 1, determined by increased levels of the tricarboxylic acid cycle intermediates malate, fumarate and α-ketoglutarate. These metabolic alterations were associated with exaggerated GSIS (5-fold compared with 3.1-fold in control cells; P{\textless}0.01). Insulin secretion, provoked by leucine and dimethylsuccinate, which feed into the tricarboxylic acid cycle bypassing PDH, was unaffected. The oxygen consumption and metabolic data strongly suggest that knockdown of PDH kinase 1 in β-cells permits increased metabolic flux of glucose-derived carbons into the tricarboxylic acid cycle via PDH. Enhanced insulin secretion is probably caused by increased generation of tricarboxylic acid cycle-derived reducing equivalents for mitochondrial electron transport to generate ATP and/or stimulatory metabolic intermediates. On the basis of these findings, we suggest that PDH kinase 1 is an important regulator of PDH in clonal β-cells and that PDH kinase 1 and PDH are important for efficient metabolic coupling. Maintaining low PDH kinase 1 expression/activity, keeping PDH in a dephosphorylated and active state, may be important for β-cells to achieve the metabolic flux rates necessary for maximal GSIS.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Krus, Ulrika and Kotova, Olga and Spégel, Peter and Hallgard, Elna and Sharoyko, Vladimir V. and Vedin, Anna and Moritz, Thomas and Sugden, Mary C. and Koeck, Thomas and Mulder, Hindrik},
	month = jul,
	year = {2010},
	pages = {205--213},
}

Tight coupling between cytosolic and mitochondrial metabolism is key for GSIS (glucose-stimulated insulin secretion). In the present study we examined the regulatory contribution of PDH (pyruvate dehydrogenase) kinase 1, a negative regulator of PDH, to metabolic coupling in 832/13 clonal β-cells. Knockdown of PDH kinase 1 with siRNA (small interfering RNA) reduced its mRNA (\textgreater80%) and protein level (\textgreater40%) after 72 h. PDH activity, glucose-stimulated cellular oxygen consumption and pyruvate-stimulated mitochondrial oxygen consumption increased 1.7- (P\textless0.05), 1.6- (P\textless0.05) and 1.6-fold (P\textless0.05) respectively. Gas chromatography/MS revealed an altered metabolite profile upon silencing of PDH kinase 1, determined by increased levels of the tricarboxylic acid cycle intermediates malate, fumarate and α-ketoglutarate. These metabolic alterations were associated with exaggerated GSIS (5-fold compared with 3.1-fold in control cells; P\textless0.01). Insulin secretion, provoked by leucine and dimethylsuccinate, which feed into the tricarboxylic acid cycle bypassing PDH, was unaffected. The oxygen consumption and metabolic data strongly suggest that knockdown of PDH kinase 1 in β-cells permits increased metabolic flux of glucose-derived carbons into the tricarboxylic acid cycle via PDH. Enhanced insulin secretion is probably caused by increased generation of tricarboxylic acid cycle-derived reducing equivalents for mitochondrial electron transport to generate ATP and/or stimulatory metabolic intermediates. On the basis of these findings, we suggest that PDH kinase 1 is an important regulator of PDH in clonal β-cells and that PDH kinase 1 and PDH are important for efficient metabolic coupling. Maintaining low PDH kinase 1 expression/activity, keeping PDH in a dephosphorylated and active state, may be important for β-cells to achieve the metabolic flux rates necessary for maximal GSIS.

@article{ibanez_circadian_2010,
	title = {Circadian {Clock} {Components} {Regulate} {Entry} and {Affect} {Exit} of {Seasonal} {Dormancy} as {Well} as {Winter} {Hardiness} in \textit{{Populus}} {Trees}},
	volume = {153},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/153/4/1823/6111276},
	doi = {10/dzmr76},
	abstract = {Abstract
            This study addresses the role of the circadian clock in the seasonal growth cycle of trees: growth cessation, bud set, freezing tolerance, and bud burst. Populus tremula × Populus tremuloides (Ptt) LATE ELONGATED HYPOCOTYL1 (PttLHY1), PttLHY2, and TIMING OF CAB EXPRESSION1 constitute regulatory clock components because down-regulation by RNA interference of these genes leads to altered phase and period of clock-controlled gene expression as compared to the wild type. Also, both RNA interference lines show about 1-h-shorter critical daylength for growth cessation as compared to the wild type, extending their period of growth. During winter dormancy, when the diurnal variation in clock gene expression stops altogether, down-regulation of PttLHY1 and PttLHY2 expression compromises freezing tolerance and the expression of C-REPEAT BINDING FACTOR1, suggesting a role of these genes in cold hardiness. Moreover, down-regulation of PttLHY1 and PttLHY2 causes a delay in bud burst. This evidence shows that in addition to a role in daylength-controlled processes, PttLHY plays a role in the temperature-dependent processes of dormancy in Populus such as cold hardiness and bud burst.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {IbÁñez, Cristian and Kozarewa, Iwanka and Johansson, Mikael and Ögren, Erling and Rohde, Antje and Eriksson, Maria E.},
	month = aug,
	year = {2010},
	pages = {1823--1833},
}

Abstract This study addresses the role of the circadian clock in the seasonal growth cycle of trees: growth cessation, bud set, freezing tolerance, and bud burst. Populus tremula × Populus tremuloides (Ptt) LATE ELONGATED HYPOCOTYL1 (PttLHY1), PttLHY2, and TIMING OF CAB EXPRESSION1 constitute regulatory clock components because down-regulation by RNA interference of these genes leads to altered phase and period of clock-controlled gene expression as compared to the wild type. Also, both RNA interference lines show about 1-h-shorter critical daylength for growth cessation as compared to the wild type, extending their period of growth. During winter dormancy, when the diurnal variation in clock gene expression stops altogether, down-regulation of PttLHY1 and PttLHY2 expression compromises freezing tolerance and the expression of C-REPEAT BINDING FACTOR1, suggesting a role of these genes in cold hardiness. Moreover, down-regulation of PttLHY1 and PttLHY2 causes a delay in bud burst. This evidence shows that in addition to a role in daylength-controlled processes, PttLHY plays a role in the temperature-dependent processes of dormancy in Populus such as cold hardiness and bud burst.

@incollection{buschmann_chapter_2010,
	series = {Microtubules: in vivo},
	title = {Chapter 20 - {Microtubule} {Dynamics} in {Plant} {Cells}},
	volume = {97},
	url = {https://www.sciencedirect.com/science/article/pii/S0091679X10970209},
	abstract = {This chapter describes some of the choices and unavoidable compromises to be made when studying microtubule dynamics in plant cells. The choice of species still depends very much on the ability to produce transgenic plants and most work has been done in the relatively small cells of Arabidopsis plants or in tobacco BY-2 suspension cells. Fluorescence-tagged microtubule proteins have been used to label entire microtubules, or their plus ends, but there are still few minus-end markers for these acentrosomal cells. Pragmatic decisions have to be made about probes, balancing the efficacy of microtubule labeling against a tendency to overstabilize and bundle the microtubules and even induce helical plant growth. A key limitation in visualizing plant microtubules is the ability to keep plants alive for long periods under the microscope and we describe a biochamber that allows for plant cell growth and development while allowing gas exchange and reducing evaporation. Another major difficulty is the limited fluorescence lifetime and we describe imaging strategies to reduce photobleaching in long-term imaging. We also discuss methods of measuring microtubule dynamics, with emphasis on the behavior of plant-specific microtubule arrays.},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {Methods in {Cell} {Biology}},
	publisher = {Academic Press},
	author = {Buschmann, Henrik and Sambade, Adrian and Pesquet, Edouard and Calder, Grant and Lloyd, Clive W.},
	editor = {Cassimeris, Lynne and Tran, Phong},
	month = jan,
	year = {2010},
	doi = {10.1016/S0091-679X(10)97020-9},
	pages = {373--400},
}

This chapter describes some of the choices and unavoidable compromises to be made when studying microtubule dynamics in plant cells. The choice of species still depends very much on the ability to produce transgenic plants and most work has been done in the relatively small cells of Arabidopsis plants or in tobacco BY-2 suspension cells. Fluorescence-tagged microtubule proteins have been used to label entire microtubules, or their plus ends, but there are still few minus-end markers for these acentrosomal cells. Pragmatic decisions have to be made about probes, balancing the efficacy of microtubule labeling against a tendency to overstabilize and bundle the microtubules and even induce helical plant growth. A key limitation in visualizing plant microtubules is the ability to keep plants alive for long periods under the microscope and we describe a biochamber that allows for plant cell growth and development while allowing gas exchange and reducing evaporation. Another major difficulty is the limited fluorescence lifetime and we describe imaging strategies to reduce photobleaching in long-term imaging. We also discuss methods of measuring microtubule dynamics, with emphasis on the behavior of plant-specific microtubule arrays.

@article{grebe_cell_2010,
	title = {Cell {Polarity}: {Lateral} {Perspectives}},
	volume = {20},
	issn = {09609822},
	shorttitle = {Cell {Polarity}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S096098221000360X},
	doi = {10/bv2mz7},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Grebe, Markus},
	month = may,
	year = {2010},
	pages = {R446--R448},
}

@article{hobson_gene_2010,
	title = {Gene expression in tension wood and bast fibres},
	volume = {57},
	issn = {1021-4437, 1608-3407},
	url = {http://link.springer.com/10.1134/S1021443710030039},
	doi = {10/ft9vng},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Russian Journal of Plant Physiology},
	author = {Hobson, N. and Roach, M. J. and Deyholos, M. K.},
	month = may,
	year = {2010},
	pages = {321--327},
}

@article{gundale_variation_2010,
	title = {Variation in protein complexation capacity among and within six plant species across a boreal forest chronosequence},
	volume = {211},
	issn = {1385-0237, 1573-5052},
	url = {http://link.springer.com/10.1007/s11258-010-9787-9},
	doi = {10/fb7xxd},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Ecology},
	author = {Gundale, Michael J. and Sverker, Jennie and Albrectsen, Benedicte R. and Nilsson, Marie-Charlotte and Wardle, David A.},
	month = dec,
	year = {2010},
	pages = {253--266},
}

@article{le_bail_auxin_2010,
	title = {Auxin {Metabolism} and {Function} in the {Multicellular} {Brown} {Alga} \textit{{Ectocarpus} siliculosus}},
	volume = {153},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/153/1/128/6108337},
	doi = {10/dsq4bg},
	abstract = {Abstract
            Ectocarpus siliculosus is a small brown alga that has recently been developed as a genetic model. Its thallus is filamentous, initially organized as a main primary filament composed of elongated cells and round cells, from which branches differentiate. Modeling of its early development suggests the involvement of very local positional information mediated by cell-cell recognition. However, this model also indicates that an additional mechanism is required to ensure proper organization of the branching pattern. In this paper, we show that auxin indole-3-acetic acid (IAA) is detectable in mature E. siliculosus organisms and that it is present mainly at the apices of the filaments in the early stages of development. An in silico survey of auxin biosynthesis, conjugation, response, and transport genes showed that mainly IAA biosynthesis genes from land plants have homologs in the E. siliculosus genome. In addition, application of exogenous auxins and 2,3,5-triiodobenzoic acid had different effects depending on the developmental stage of the organism, and we propose a model in which auxin is involved in the negative control of progression in the developmental program. Furthermore, we identified an auxin-inducible gene called EsGRP1 from a small-scale microarray experiment and showed that its expression in a series of morphogenetic mutants was positively correlated with both their elongated-to-round cell ratio and their progression in the developmental program. Altogether, these data suggest that IAA is used by the brown alga Ectocarpus to relay cell-cell positional information and induces a signaling pathway different from that known in land plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Le Bail, Aude and Billoud, Bernard and Kowalczyk, Nathalie and Kowalczyk, Mariusz and Gicquel, Morgane and Le Panse, Sophie and Stewart, Sarah and Scornet, Delphine and Cock, Jeremy Mark and Ljung, Karin and Charrier, Bénédicte},
	month = may,
	year = {2010},
	pages = {128--144},
}

Abstract Ectocarpus siliculosus is a small brown alga that has recently been developed as a genetic model. Its thallus is filamentous, initially organized as a main primary filament composed of elongated cells and round cells, from which branches differentiate. Modeling of its early development suggests the involvement of very local positional information mediated by cell-cell recognition. However, this model also indicates that an additional mechanism is required to ensure proper organization of the branching pattern. In this paper, we show that auxin indole-3-acetic acid (IAA) is detectable in mature E. siliculosus organisms and that it is present mainly at the apices of the filaments in the early stages of development. An in silico survey of auxin biosynthesis, conjugation, response, and transport genes showed that mainly IAA biosynthesis genes from land plants have homologs in the E. siliculosus genome. In addition, application of exogenous auxins and 2,3,5-triiodobenzoic acid had different effects depending on the developmental stage of the organism, and we propose a model in which auxin is involved in the negative control of progression in the developmental program. Furthermore, we identified an auxin-inducible gene called EsGRP1 from a small-scale microarray experiment and showed that its expression in a series of morphogenetic mutants was positively correlated with both their elongated-to-round cell ratio and their progression in the developmental program. Altogether, these data suggest that IAA is used by the brown alga Ectocarpus to relay cell-cell positional information and induces a signaling pathway different from that known in land plants.

@article{danusevicius_efficiency_2010,
	title = {Efficiency of breeding strategy where grandparents — but not parents — contribute equally to the breeding population},
	volume = {67},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1051/forest/2009124},
	doi = {10/d56qth},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Danusevičius, Darius and Lindgren, Dag},
	month = jan,
	year = {2010},
	pages = {404--404},
}

@article{waldenstrom_ischaemic_2010,
	title = {Ischaemic preconditioning is related to decreasing levels of extracellular adenosine that may be metabolically useful in the at-risk myocardium: an experimental study in the pig},
	volume = {199},
	issn = {17481708, 17481716},
	shorttitle = {Ischaemic preconditioning is related to decreasing levels of extracellular adenosine that may be metabolically useful in the at-risk myocardium},
	url = {http://doi.wiley.com/10.1111/j.1748-1716.2009.02071.x},
	doi = {10/dsp97q},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Acta Physiologica},
	author = {Waldenström, A. and Haney, M. and Biber, B. and Kavianipour, M. and Moritz, T. and Strandén, P. and Wikström, G. and Ronquist, G.},
	month = may,
	year = {2010},
	pages = {1--9},
}

@article{dillon_association_2010,
	title = {Association genetics reveal candidate gene {SNPs} affecting wood properties in \textit{{Pinus} radiata}},
	volume = {73},
	issn = {0004-9158, 2325-6087},
	url = {https://www.tandfonline.com/doi/full/10.1080/00049158.2010.10676326},
	doi = {10/gkgfrf},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Australian Forestry},
	author = {Dillon, S. K. and Nolan, M. F. and Wu, H. and Southerton, S. G.},
	month = jan,
	year = {2010},
	pages = {185--190},
}

@article{pesquet_microtubule-associated_2010,
	title = {The {Microtubule}-{Associated} {Protein} {AtMAP70}-5 {Regulates} {Secondary} {Wall} {Patterning} in {Arabidopsis} {Wood} {Cells}},
	volume = {20},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982210003301},
	doi = {10/bq2d82},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Pesquet, Edouard and Korolev, Andrey V. and Calder, Grant and Lloyd, Clive W.},
	month = apr,
	year = {2010},
	pages = {744--749},
}

@article{schlereth_monopteros_2010,
	title = {{MONOPTEROS} controls embryonic root initiation by regulating a mobile transcription factor},
	volume = {464},
	issn = {1476-4687},
	doi = {10/fvkmp7},
	abstract = {Acquisition of cell identity in plants relies strongly on positional information, hence cell-cell communication and inductive signalling are instrumental for developmental patterning. During Arabidopsis embryogenesis, an extra-embryonic cell is specified to become the founder cell of the primary root meristem, hypophysis, in response to signals from adjacent embryonic cells. The auxin-dependent transcription factor MONOPTEROS (MP) drives hypophysis specification by promoting transport of the hormone auxin from the embryo to the hypophysis precursor. However, auxin accumulation is not sufficient for hypophysis specification, indicating that additional MP-dependent signals are required. Here we describe the microarray-based isolation of MP target genes that mediate signalling from embryo to hypophysis. Of three direct transcriptional target genes, TARGET OF MP 5 (TMO5) and TMO7 encode basic helix-loop-helix (bHLH) transcription factors that are expressed in the hypophysis-adjacent embryo cells, and are required and partially sufficient for MP-dependent root initiation. Importantly, the small TMO7 transcription factor moves from its site of synthesis in the embryo to the hypophysis precursor, thus representing a novel MP-dependent intercellular signal in embryonic root specification.},
	language = {eng},
	number = {7290},
	journal = {Nature},
	author = {Schlereth, Alexandra and Möller, Barbara and Liu, Weilin and Kientz, Marika and Flipse, Jacky and Rademacher, Eike H. and Schmid, Markus and Jürgens, Gerd and Weijers, Dolf},
	month = apr,
	year = {2010},
	pmid = {20220754},
	keywords = {Arabidopsis, Arabidopsis Proteins, Basic Helix-Loop-Helix Transcription Factors, DNA-Binding Proteins, Embryonic Development, Gene Expression Regulation, Plant, Genes, Plant, Indoleacetic Acids, Meristem, Oligonucleotide Array Sequence Analysis, Plant Roots, Signal Transduction, Transcription Factors},
	pages = {913--916},
}

Acquisition of cell identity in plants relies strongly on positional information, hence cell-cell communication and inductive signalling are instrumental for developmental patterning. During Arabidopsis embryogenesis, an extra-embryonic cell is specified to become the founder cell of the primary root meristem, hypophysis, in response to signals from adjacent embryonic cells. The auxin-dependent transcription factor MONOPTEROS (MP) drives hypophysis specification by promoting transport of the hormone auxin from the embryo to the hypophysis precursor. However, auxin accumulation is not sufficient for hypophysis specification, indicating that additional MP-dependent signals are required. Here we describe the microarray-based isolation of MP target genes that mediate signalling from embryo to hypophysis. Of three direct transcriptional target genes, TARGET OF MP 5 (TMO5) and TMO7 encode basic helix-loop-helix (bHLH) transcription factors that are expressed in the hypophysis-adjacent embryo cells, and are required and partially sufficient for MP-dependent root initiation. Importantly, the small TMO7 transcription factor moves from its site of synthesis in the embryo to the hypophysis precursor, thus representing a novel MP-dependent intercellular signal in embryonic root specification.

@article{koo_control_2010,
	title = {Control of lateral organ development and flowering time by the {Arabidopsis} thaliana {MADS}-box {Gene} {AGAMOUS}-{LIKE6}},
	volume = {62},
	issn = {1365-313X},
	doi = {10/d7dmk9},
	abstract = {MADS-domain transcription factors play pivotal roles in various developmental processes. The lack of simple loss-of-function phenotypes provides impediments to understand the biological function of some of the MADS-box transcription factors. Here we have characterized the potential role of the Arabidopsis thaliana AGAMOUS-LIKE6 (AGL6) gene by fusing full-length coding sequence with transcriptional activator and repressor domains and suggest a role for AGL6 in lateral organ development and flowering. Upon photoperiodic induction of flowering, AGL6 becomes expressed in abaxial and proximal regions of cauline leaf primordia, as well as the cryptic bracts subtending flowers. In developing flowers, AGL6 is detected in the proximal regions of all floral organs and in developing ovules. Converting AGL6 into a strong activator through fusion to the VP16 domain triggers bract outgrowth, implicating AGL6 in the development of bractless flowers in Arabidopsis. In addition, ectopic reproductive structures form on both bracts and flowers in gAGL6::VP16 transgenic plants, which is dependent on B and C class homeotic genes, but independent of LEAFY. Overexpression of both AGL6 and its transcriptional repressor form, AGL6::EAR, causes precocious flowering and terminal flower formation, suggesting that AGL6 suppresses the function of a floral repressor.},
	language = {eng},
	number = {5},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Koo, Sung C. and Bracko, Oliver and Park, Mi S. and Schwab, Rebecca and Chun, Hyun J. and Park, Kyoung M. and Seo, Jun S. and Grbic, Vojislava and Balasubramanian, Sureshkumar and Schmid, Markus and Godard, François and Yun, Dae-Jin and Lee, Sang Y. and Cho, Moo J. and Weigel, Detlef and Kim, Min C.},
	month = jun,
	year = {2010},
	pmid = {20230491},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, MADS Domain Proteins, Microscopy, Electron, Scanning, Ovule, Plants, Genetically Modified, RNA, Plant},
	pages = {807--816},
}

MADS-domain transcription factors play pivotal roles in various developmental processes. The lack of simple loss-of-function phenotypes provides impediments to understand the biological function of some of the MADS-box transcription factors. Here we have characterized the potential role of the Arabidopsis thaliana AGAMOUS-LIKE6 (AGL6) gene by fusing full-length coding sequence with transcriptional activator and repressor domains and suggest a role for AGL6 in lateral organ development and flowering. Upon photoperiodic induction of flowering, AGL6 becomes expressed in abaxial and proximal regions of cauline leaf primordia, as well as the cryptic bracts subtending flowers. In developing flowers, AGL6 is detected in the proximal regions of all floral organs and in developing ovules. Converting AGL6 into a strong activator through fusion to the VP16 domain triggers bract outgrowth, implicating AGL6 in the development of bractless flowers in Arabidopsis. In addition, ectopic reproductive structures form on both bracts and flowers in gAGL6::VP16 transgenic plants, which is dependent on B and C class homeotic genes, but independent of LEAFY. Overexpression of both AGL6 and its transcriptional repressor form, AGL6::EAR, causes precocious flowering and terminal flower formation, suggesting that AGL6 suppresses the function of a floral repressor.

@article{yant_orchestration_2010,
	title = {Orchestration of the floral transition and floral development in {Arabidopsis} by the bifunctional transcription factor {APETALA2}},
	volume = {22},
	issn = {1532-298X},
	doi = {10/bqpgn4},
	abstract = {The Arabidopsis thaliana transcription factor APETALA2 (AP2) has numerous functions, including roles in seed development, stem cell maintenance, and specification of floral organ identity. To understand the relationship between these different roles, we mapped direct targets of AP2 on a genome-wide scale in two tissue types. We find that AP2 binds to thousands of loci in the developing flower, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two microRNA genes that influence AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We compare the genome-wide direct target repertoire of AP2 with that of SCHLAFMUTZE, a closely related transcription factor that also represses the transition to flowering. We detect clear similarities and important differences in the direct target repertoires that are also tissue specific. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions as both a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE15 and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1.},
	language = {eng},
	number = {7},
	journal = {The Plant Cell},
	author = {Yant, Levi and Mathieu, Johannes and Dinh, Thanh Theresa and Ott, Felix and Lanz, Christa and Wollmann, Heike and Chen, Xuemei and Schmid, Markus},
	month = jul,
	year = {2010},
	pmid = {20675573},
	pmcid = {PMC2929098},
	keywords = {Arabidopsis, Arabidopsis Proteins, Binding Sites, Flowers, Gene Expression, Genome, Plant, Homeodomain Proteins, Mutation, Nuclear Proteins},
	pages = {2156--2170},
}

The Arabidopsis thaliana transcription factor APETALA2 (AP2) has numerous functions, including roles in seed development, stem cell maintenance, and specification of floral organ identity. To understand the relationship between these different roles, we mapped direct targets of AP2 on a genome-wide scale in two tissue types. We find that AP2 binds to thousands of loci in the developing flower, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two microRNA genes that influence AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We compare the genome-wide direct target repertoire of AP2 with that of SCHLAFMUTZE, a closely related transcription factor that also represses the transition to flowering. We detect clear similarities and important differences in the direct target repertoires that are also tissue specific. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions as both a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE15 and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1.

@article{wahl_fantastic_2010,
	title = {The {FANTASTIC} {FOUR} proteins influence shoot meristem size in {Arabidopsis} thaliana},
	volume = {10},
	issn = {1471-2229},
	doi = {10/dt2kjb},
	abstract = {BACKGROUND: Throughout their lives plants produce new organs from groups of pluripotent cells called meristems, located at the tips of the shoot and the root. The size of the shoot meristem is tightly controlled by a feedback loop, which involves the homeodomain transcription factor WUSCHEL (WUS) and the CLAVATA (CLV) proteins. This regulatory circuit is further fine-tuned by morphogenic signals such as hormones and sugars.
RESULTS: Here we show that a family of four plant-specific proteins, encoded by the FANTASTIC FOUR (FAF) genes, has the potential to regulate shoot meristem size in Arabidopsis thaliana. FAF2 and FAF4 are expressed in the centre of the shoot meristem, overlapping with the site of WUS expression. Consistent with a regulatory interaction between the FAF gene family and WUS, our experiments indicate that the FAFs can repress WUS, which ultimately leads to an arrest of meristem activity in FAF overexpressing lines. The finding that meristematic expression of FAF2 and FAF4 is under negative control by CLV3 further supports the hypothesis that the FAFs are modulators of the genetic circuit that regulates the meristem.
CONCLUSION: This study reports the initial characterization of the Arabidopsis thaliana FAF gene family. Our data indicate that the FAF genes form a plant specific gene family, the members of which have the potential to regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop.},
	language = {eng},
	journal = {BMC plant biology},
	author = {Wahl, Vanessa and Brand, Luise H. and Guo, Ya-Long and Schmid, Markus},
	month = dec,
	year = {2010},
	pmid = {21176196},
	pmcid = {PMC3023791},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Glucuronidase, Homeodomain Proteins, In Situ Hybridization, Meristem, Microscopy, Electron, Scanning, Oligonucleotide Array Sequence Analysis, Plant Shoots, Plant Vascular Bundle, Repressor Proteins},
	pages = {285},
}

BACKGROUND: Throughout their lives plants produce new organs from groups of pluripotent cells called meristems, located at the tips of the shoot and the root. The size of the shoot meristem is tightly controlled by a feedback loop, which involves the homeodomain transcription factor WUSCHEL (WUS) and the CLAVATA (CLV) proteins. This regulatory circuit is further fine-tuned by morphogenic signals such as hormones and sugars. RESULTS: Here we show that a family of four plant-specific proteins, encoded by the FANTASTIC FOUR (FAF) genes, has the potential to regulate shoot meristem size in Arabidopsis thaliana. FAF2 and FAF4 are expressed in the centre of the shoot meristem, overlapping with the site of WUS expression. Consistent with a regulatory interaction between the FAF gene family and WUS, our experiments indicate that the FAFs can repress WUS, which ultimately leads to an arrest of meristem activity in FAF overexpressing lines. The finding that meristematic expression of FAF2 and FAF4 is under negative control by CLV3 further supports the hypothesis that the FAFs are modulators of the genetic circuit that regulates the meristem. CONCLUSION: This study reports the initial characterization of the Arabidopsis thaliana FAF gene family. Our data indicate that the FAF genes form a plant specific gene family, the members of which have the potential to regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop.

@article{wu_role_2010,
	title = {A role for {ABCB19}-mediated polar auxin transport in seedling photomorphogenesis mediated by cryptochrome 1 and phytochrome {B}: {ABCB19} and the photocontrol of hypocotyl growth},
	volume = {62},
	issn = {09607412},
	shorttitle = {A role for {ABCB19}-mediated polar auxin transport in seedling photomorphogenesis mediated by cryptochrome 1 and phytochrome {B}},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2010.04137.x},
	doi = {10/cp6ptv},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Wu, Guosheng and Cameron, John N. and Ljung, Karin and Spalding, Edgar P.},
	month = jan,
	year = {2010},
	pages = {179--191},
}

@article{hall_using_2010,
	title = {Using association mapping to dissect the genetic basis of complex traits in plants},
	volume = {9},
	issn = {2041-2649, 2041-2657},
	url = {https://academic.oup.com/bfg/article-lookup/doi/10.1093/bfgp/elp048},
	doi = {10/dmfv6q},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Briefings in Functional Genomics},
	author = {Hall, D. and Tegstrom, C. and Ingvarsson, P. K.},
	month = mar,
	year = {2010},
	pages = {157--165},
}

@article{de_carvalho_admixture_2010,
	title = {Admixture facilitates adaptation from standing variation in the {European} aspen ( \textit{{Populus} tremula} {L}.), a widespread forest tree},
	volume = {19},
	issn = {09621083, 1365294X},
	url = {http://doi.wiley.com/10.1111/j.1365-294X.2010.04595.x},
	doi = {10/c3zz45},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Molecular Ecology},
	author = {De Carvalho, Dulcineia and Ingvarsson, Pär K. and Joseph, Jeffrey and Suter, Leonie and Sedivy, Claudio and Macaya-Sanz, David and Cottrell, Joan and Heinze, Berthold and Schanzer, Ivan and Lexer, Christian},
	month = apr,
	year = {2010},
	pages = {1638--1650},
}

@article{eklund_homologues_2010,
	title = {Homologues of the \textit{{Arabidopsis} thaliana {SHI}/{STY}/{LRP1}} genes control auxin biosynthesis and affect growth and development in the moss \textit{{Physcomitrella} patens}},
	volume = {137},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/137/8/1275/44242/Homologues-of-the-Arabidopsis-thaliana-SHI-STY},
	doi = {10/fgs5s3},
	abstract = {The plant hormone auxin plays fundamental roles in vascular plants. Although exogenous auxin also stimulates developmental transitions and growth in non-vascular plants, the effects of manipulating endogenous auxin levels have thus far not been reported. Here, we have altered the levels and sites of auxin production and accumulation in the moss Physcomitrella patens by changing the expression level of homologues of the Arabidopsis SHI/STY family proteins, which are positive regulators of auxin biosynthesis genes. Constitutive expression of PpSHI1 resulted in elevated auxin levels, increased and ectopic expression of the auxin response reporter GmGH3pro:GUS, and in an increased caulonema/chloronema ratio, an effect also induced by exogenous auxin application. In addition, we observed premature ageing and necrosis in cells ectopically expressing PpSHI1. Knockout of either of the two PpSHI genes resulted in reduced auxin levels and auxin biosynthesis rates in leafy shoots, reduced internode elongation, delayed ageing, a decreased caulonema/chloronema ratio and an increased number of axillary hairs, which constitute potential auxin biosynthesis sites. Some of the identified auxin functions appear to be analogous in vascular and non-vascular plants. Furthermore, the spatiotemporal expression of the PpSHI genes and GmGH3pro:GUS strongly overlap, suggesting that local auxin biosynthesis is important for the regulation of auxin peak formation in non-vascular plants.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Eklund, D. Magnus and Thelander, Mattias and Landberg, Katarina and Ståldal, Veronika and Nilsson, Anders and Johansson, Monika and Valsecchi, Isabel and Pederson, Eric R. A. and Kowalczyk, Mariusz and Ljung, Karin and Ronne, Hans and Sundberg, Eva},
	month = apr,
	year = {2010},
	pages = {1275--1284},
}

The plant hormone auxin plays fundamental roles in vascular plants. Although exogenous auxin also stimulates developmental transitions and growth in non-vascular plants, the effects of manipulating endogenous auxin levels have thus far not been reported. Here, we have altered the levels and sites of auxin production and accumulation in the moss Physcomitrella patens by changing the expression level of homologues of the Arabidopsis SHI/STY family proteins, which are positive regulators of auxin biosynthesis genes. Constitutive expression of PpSHI1 resulted in elevated auxin levels, increased and ectopic expression of the auxin response reporter GmGH3pro:GUS, and in an increased caulonema/chloronema ratio, an effect also induced by exogenous auxin application. In addition, we observed premature ageing and necrosis in cells ectopically expressing PpSHI1. Knockout of either of the two PpSHI genes resulted in reduced auxin levels and auxin biosynthesis rates in leafy shoots, reduced internode elongation, delayed ageing, a decreased caulonema/chloronema ratio and an increased number of axillary hairs, which constitute potential auxin biosynthesis sites. Some of the identified auxin functions appear to be analogous in vascular and non-vascular plants. Furthermore, the spatiotemporal expression of the PpSHI genes and GmGH3pro:GUS strongly overlap, suggesting that local auxin biosynthesis is important for the regulation of auxin peak formation in non-vascular plants.

@article{fei_novel_2010,
	title = {A {Novel} {Negative} {Fe}-{Deficiency}-{Responsive} {Element} and a {TGGCA}-{Type}-{Like} {FeRE} {Control} the {Expression} of \textit{{FTR1}} in \textit{{Chlamydomonas} reinhardtii}},
	volume = {2010},
	issn = {1110-7243, 1110-7251},
	url = {http://www.hindawi.com/journals/bmri/2010/790247/},
	doi = {10.1155/2010/790247},
	abstract = {We have reported three Fe-deficiency-responsive elements (FEREs),
              FOX1, ATX1,
              and
              FEA1
              , all of which are positive regulatory elements in response to iron deficiency in
              Chlamydomonas reinhardtii
              . Here we describe
              FTR1
              , another iron regulated gene and mutational analysis of its promoter. Our results reveal that the FeREs of
              FTR1
              distinguish itself from other iron response elements by containing both
              negative
              and
              positive
              regulatory regions. In
              FTR1
              , the
              
                −
              
              291/
              
                −
              
              236 region from the transcriptional start site is necessary and sufficient for Fe-deficiency-inducible expression. This region contains two positive FeREs with a TGGCA-like core sequence: the FtrFeRE1 (A
              TGCA
              GGCT) at
              
                −
              
              287/
              
                −
              
              279 and the FtrFeRE2 (AAGCGAT
              TGCCA
              GAGCGC) at
              
                −
              
              253/
              
                −
              
              236. Furthermore, we identified a novel FERE, FtrFeRE3 (AGTAACTGTTAAGCC) localized at
              
                −
              
              319/
              
                −
              
              292, which negatively influences the expression of
              FTR1
              .},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Biomedicine and Biotechnology},
	author = {Fei, Xiaowen and Eriksson, Mats and Li, Yajun and Deng, Xiaodong},
	year = {2010},
	pages = {1--9},
}

We have reported three Fe-deficiency-responsive elements (FEREs), FOX1, ATX1, and FEA1 , all of which are positive regulatory elements in response to iron deficiency in Chlamydomonas reinhardtii . Here we describe FTR1 , another iron regulated gene and mutational analysis of its promoter. Our results reveal that the FeREs of FTR1 distinguish itself from other iron response elements by containing both negative and positive regulatory regions. In FTR1 , the − 291/ − 236 region from the transcriptional start site is necessary and sufficient for Fe-deficiency-inducible expression. This region contains two positive FeREs with a TGGCA-like core sequence: the FtrFeRE1 (A TGCA GGCT) at − 287/ − 279 and the FtrFeRE2 (AAGCGAT TGCCA GAGCGC) at − 253/ − 236. Furthermore, we identified a novel FERE, FtrFeRE3 (AGTAACTGTTAAGCC) localized at − 319/ − 292, which negatively influences the expression of FTR1 .

@article{hoffman_changes_2010,
	title = {Changes in diurnal patterns within the {Populus} transcriptome and metabolome in response to photoperiod variation},
	volume = {33},
	issn = {1365-3040},
	doi = {10/d2xk8m},
	abstract = {Changes in seasonal photoperiod provides an important environmental signal that affects the timing of winter dormancy in perennial, deciduous, temperate tree species, such as hybrid aspen (Populus tremula x Populus tremuloides). In this species, growth cessation, cold acclimation and dormancy are induced in the autumn by the detection of day-length shortening that occurs at a given critical day length. Important components in the detection of such day-length changes are photoreceptors and the circadian clock, and many plant responses at both the gene regulation and metabolite levels are expected to be diurnal. To directly examine this expectation and study components in these events, here we report transcriptomic and metabolomic responses to a change in photoperiod from long to short days in hybrid aspen. We found about 16\% of genes represented on the arrays to be diurnally regulated, as assessed by our pre-defined criteria. Furthermore, several of these genes were involved in circadian-associated processes, including photosynthesis and primary and secondary metabolism. Metabolites affected by the change in photoperiod were mostly involved in carbon metabolism. Taken together, we have thus established a molecular catalog of events that precede a response to winter.},
	language = {eng},
	number = {8},
	journal = {Plant, Cell \& Environment},
	author = {Hoffman, Daniel E. and Jonsson, Pär and Bylesjö, Max and Trygg, Johan and Antti, Henrik and Eriksson, Maria E. and Moritz, Thomas},
	month = aug,
	year = {2010},
	pmid = {20302601},
	keywords = {Carbohydrate Metabolism, Circadian Rhythm, DNA, Complementary, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Metabolome, Oligonucleotide Array Sequence Analysis, Photoperiod, Populus, Seasons},
	pages = {1298--1313},
}

Changes in seasonal photoperiod provides an important environmental signal that affects the timing of winter dormancy in perennial, deciduous, temperate tree species, such as hybrid aspen (Populus tremula x Populus tremuloides). In this species, growth cessation, cold acclimation and dormancy are induced in the autumn by the detection of day-length shortening that occurs at a given critical day length. Important components in the detection of such day-length changes are photoreceptors and the circadian clock, and many plant responses at both the gene regulation and metabolite levels are expected to be diurnal. To directly examine this expectation and study components in these events, here we report transcriptomic and metabolomic responses to a change in photoperiod from long to short days in hybrid aspen. We found about 16% of genes represented on the arrays to be diurnally regulated, as assessed by our pre-defined criteria. Furthermore, several of these genes were involved in circadian-associated processes, including photosynthesis and primary and secondary metabolism. Metabolites affected by the change in photoperiod were mostly involved in carbon metabolism. Taken together, we have thus established a molecular catalog of events that precede a response to winter.

@article{spegel_metabolomic_2010,
	title = {Metabolomic analysis of a human oral glucose tolerance test reveals fatty acids as reliable indicators of regulated metabolism},
	volume = {6},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-009-0177-z},
	doi = {10/frw67z},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Metabolomics},
	author = {Spégel, Peter and Danielsson, Anders P. H. and Bacos, Karl and Nagorny, Cecilia L. F. and Moritz, Thomas and Mulder, Hindrik and Filipsson, Karin},
	month = mar,
	year = {2010},
	pages = {56--66},
}

@article{kozarewa_alteration_2010,
	title = {Alteration of {PHYA} expression change circadian rhythms and timing of bud set in {Populus}},
	volume = {73},
	issn = {0167-4412, 1573-5028},
	url = {http://link.springer.com/10.1007/s11103-010-9619-2},
	doi = {10/dp553q},
	language = {en},
	number = {1-2},
	urldate = {2021-06-08},
	journal = {Plant Molecular Biology},
	author = {Kozarewa, Iwanka and Ibáñez, Cristian and Johansson, Mikael and Ögren, Erling and Mozley, David and Nylander, Eva and Chono, Makiko and Moritz, Thomas and Eriksson, Maria E.},
	month = may,
	year = {2010},
	pages = {143--156},
}

@article{albrectsen_endophytic_2010,
	title = {Endophytic fungi in {European} aspen ({Populus} tremula) leaves—diversity, detection, and a suggested correlation with herbivory resistance},
	volume = {41},
	issn = {1560-2745, 1878-9129},
	url = {http://link.springer.com/10.1007/s13225-009-0011-y},
	doi = {10/cg5zgd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Fungal Diversity},
	author = {Albrectsen, Benedicte R. and Björkén, Lars and Varad, Akkamahadevi and Hagner, Åsa and Wedin, Mats and Karlsson, Jan and Jansson, Stefan},
	month = mar,
	year = {2010},
	pages = {17--28},
}

@article{bashandy_interplay_2010,
	title = {Interplay between the {NADP}-{Linked} {Thioredoxin} and {Glutathione} {Systems} in \textit{{Arabidopsis}} {Auxin} {Signaling}},
	volume = {22},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/22/2/376/6095921},
	doi = {10/cmkrm9},
	abstract = {Abstract
            Intracellular redox status is a critical parameter determining plant development in response to biotic and abiotic stress. Thioredoxin (TRX) and glutathione are key regulators of redox homeostasis, and the TRX and glutathione pathways are essential for postembryonic meristematic activities. Here, we show by associating TRX reductases (ntra ntrb) and glutathione biosynthesis (cad2) mutations that these two thiol reduction pathways interfere with developmental processes through modulation of auxin signaling. The triple ntra ntrb cad2 mutant develops normally at the rosette stage, undergoes the floral transition, but produces almost naked stems, reminiscent of the phenotype of several mutants affected in auxin transport or biosynthesis. In addition, the ntra ntrb cad2 mutant shows a loss of apical dominance, vasculature defects, and reduced secondary root production, several phenotypes tightly regulated by auxin. We further show that auxin transport capacities and auxin levels are perturbed in the mutant, suggesting that the NTR-glutathione pathways alter both auxin transport and metabolism. Analysis of ntr and glutathione biosynthesis mutants suggests that glutathione homeostasis plays a major role in auxin transport as both NTR and glutathione pathways are involved in auxin homeostasis.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Bashandy, Talaat and Guilleminot, Jocelyne and Vernoux, Teva and Caparros-Ruiz, David and Ljung, Karin and Meyer, Yves and Reichheld, Jean-Philippe},
	month = mar,
	year = {2010},
	pages = {376--391},
}

Abstract Intracellular redox status is a critical parameter determining plant development in response to biotic and abiotic stress. Thioredoxin (TRX) and glutathione are key regulators of redox homeostasis, and the TRX and glutathione pathways are essential for postembryonic meristematic activities. Here, we show by associating TRX reductases (ntra ntrb) and glutathione biosynthesis (cad2) mutations that these two thiol reduction pathways interfere with developmental processes through modulation of auxin signaling. The triple ntra ntrb cad2 mutant develops normally at the rosette stage, undergoes the floral transition, but produces almost naked stems, reminiscent of the phenotype of several mutants affected in auxin transport or biosynthesis. In addition, the ntra ntrb cad2 mutant shows a loss of apical dominance, vasculature defects, and reduced secondary root production, several phenotypes tightly regulated by auxin. We further show that auxin transport capacities and auxin levels are perturbed in the mutant, suggesting that the NTR-glutathione pathways alter both auxin transport and metabolism. Analysis of ntr and glutathione biosynthesis mutants suggests that glutathione homeostasis plays a major role in auxin transport as both NTR and glutathione pathways are involved in auxin homeostasis.

@article{bobbink_global_2010,
	title = {Global assessment of nitrogen deposition effects on terrestrial plant diversity: a synthesis},
	volume = {20},
	issn = {1051-0761},
	shorttitle = {Global assessment of nitrogen deposition effects on terrestrial plant diversity},
	url = {http://doi.wiley.com/10.1890/08-1140.1},
	doi = {10/cmgxt6},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Ecological Applications},
	author = {Bobbink, R. and Hicks, K. and Galloway, J. and Spranger, T. and Alkemade, R. and Ashmore, M. and Bustamante, M. and Cinderby, S. and Davidson, E. and Dentener, F. and Emmett, B. and Erisman, J-W. and Fenn, M. and Gilliam, F. and Nordin, A. and Pardo, L. and De Vries, W.},
	month = jan,
	year = {2010},
	pages = {30--59},
}

@article{ingvarsson_natural_2010,
	title = {Natural {Selection} on {Synonymous} and {Nonsynonymous} {Mutations} {Shapes} {Patterns} of {Polymorphism} in {Populus} tremula},
	volume = {27},
	issn = {0737-4038, 1537-1719},
	url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msp255},
	doi = {10/c9qbgq},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Molecular Biology and Evolution},
	author = {Ingvarsson, P. K.},
	month = mar,
	year = {2010},
	pages = {650--660},
}

@article{boutte_endocytosis_2010,
	title = {Endocytosis restricts {Arabidopsis} {KNOLLE} syntaxin to the cell division plane during late cytokinesis},
	volume = {29},
	issn = {0261-4189, 1460-2075},
	url = {http://emboj.embopress.org/cgi/doi/10.1038/emboj.2009.363},
	doi = {10/cz4qbf},
	number = {3},
	urldate = {2021-06-08},
	journal = {The EMBO Journal},
	author = {Boutté, Yohann and Frescatada-Rosa, Márcia and Men, Shuzhen and Chow, Cheung-Ming and Ebine, Kazuo and Gustavsson, Anna and Johansson, Lenore and Ueda, Takashi and Moore, Ian and Jürgens, Gerd and Grebe, Markus},
	month = feb,
	year = {2010},
	pages = {546--558},
}

@article{ishida_no_2010,
	title = {No evidence that nitrogen enrichment affect fungal communities of {Vaccinium} roots in two contrasting boreal forest types},
	volume = {42},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071709003988},
	doi = {10/d26fvw},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Soil Biology and Biochemistry},
	author = {Ishida, Takahide A. and Nordin, Annika},
	month = feb,
	year = {2010},
	pages = {234--243},
}

@article{hall_thioredoxin_2010,
	title = {Thioredoxin targets of the plant chloroplast lumen and their implications for plastid function},
	volume = {10},
	issn = {16159853},
	url = {http://doi.wiley.com/10.1002/pmic.200900654},
	doi = {10/c53qmw},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PROTEOMICS},
	author = {Hall, Michael and Mata-Cabana, Alejandro and Åkerlund, Hans-Erik and Florencio, Francisco J. and Schröder, Wolfgang P. and Lindahl, Marika and Kieselbach, Thomas},
	month = mar,
	year = {2010},
	pages = {987--1001},
}

@article{nilsson_proteomics_2010,
	title = {Proteomics of {Plasma} {Membranes} from {Poplar} {Trees} {Reveals} {Tissue} {Distribution} of {Transporters}, {Receptors}, and {Proteins} in {Cell} {Wall} {Formation}},
	volume = {9},
	issn = {15359476},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1535947620338068},
	doi = {10/bvk46j},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Molecular \& Cellular Proteomics},
	author = {Nilsson, Robert and Bernfur, Katja and Gustavsson, Niklas and Bygdell, Joakim and Wingsle, Gunnar and Larsson, Christer},
	month = feb,
	year = {2010},
	pages = {368--387},
}

@article{naramoto_adp-ribosylation_2010,
	title = {{ADP}-ribosylation factor machinery mediates endocytosis in plant cells},
	volume = {107},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1016260107},
	doi = {10/cwst7p},
	language = {en},
	number = {50},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Naramoto, S. and Kleine-Vehn, J. and Robert, S. and Fujimoto, M. and Dainobu, T. and Paciorek, T. and Ueda, T. and Nakano, A. and Van Montagu, M. C. E. and Fukuda, H. and Friml, J.},
	month = dec,
	year = {2010},
	pages = {21890--21895},
}

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

@article{wang_marker-based_2010,
	title = {Marker-based parentage analysis facilitates low input ‘breeding without breeding’ strategies for forest trees},
	volume = {6},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-009-0243-8},
	doi = {10/dcs3vc},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Wang, Xiao-Ru and Torimaru, Takeshi and Lindgren, Dag and Fries, Anders},
	month = feb,
	year = {2010},
	pages = {227--235},
}

@article{matte_risopatron_vascular_2010,
	title = {The vascular cambium: molecular control of cellular structure},
	volume = {247},
	issn = {0033-183X, 1615-6102},
	shorttitle = {The vascular cambium},
	url = {http://link.springer.com/10.1007/s00709-010-0211-z},
	doi = {10/b367ts},
	language = {en},
	number = {3-4},
	urldate = {2021-06-08},
	journal = {Protoplasma},
	author = {Matte Risopatron, Juan Pablo and Sun, Yuqiang and Jones, Brian Joseph},
	month = dec,
	year = {2010},
	pages = {145--161},
}

@article{thysell_metabolomic_2010,
	title = {Metabolomic {Characterization} of {Human} {Prostate} {Cancer} {Bone} {Metastases} {Reveals} {Increased} {Levels} of {Cholesterol}},
	volume = {5},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0014175},
	doi = {10/d69xb9},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Thysell, Elin and Surowiec, Izabella and Hörnberg, Emma and Crnalic, Sead and Widmark, Anders and Johansson, Annika I. and Stattin, Pär and Bergh, Anders and Moritz, Thomas and Antti, Henrik and Wikström, Pernilla},
	editor = {Creighton, Chad},
	month = dec,
	year = {2010},
	pages = {e14175},
}

@article{saona_environmental_2010,
	title = {Environmental stresses mediate endophyte-grass interactions in a boreal archipelago},
	volume = {98},
	issn = {00220477, 13652745},
	url = {http://doi.wiley.com/10.1111/j.1365-2745.2009.01613.x},
	doi = {10/cbcwrq},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Ecology},
	author = {Saona, Nora M. and Albrectsen, Benedicte Riber and Ericson, Lars and Bazely, Dawn R.},
	month = mar,
	year = {2010},
	pages = {470--479},
}

@article{zadnikova_role_2010,
	title = {Role of {PIN}-mediated auxin efflux in apical hook development of \textit{{Arabidopsis} thaliana}},
	volume = {137},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/137/4/607/44209/Role-of-PIN-mediated-auxin-efflux-in-apical-hook},
	doi = {10/cs9rb3},
	abstract = {The apical hook of dark-grown Arabidopsis seedlings is a simple structure that develops soon after germination to protect the meristem tissues during emergence through the soil and that opens upon exposure to light. Differential growth at the apical hook proceeds in three sequential steps that are regulated by multiple hormones, principally auxin and ethylene. We show that the progress of the apical hook through these developmental phases depends on the dynamic, asymmetric distribution of auxin, which is regulated by auxin efflux carriers of the PIN family. Several PIN proteins exhibited specific, partially overlapping spatial and temporal expression patterns, and their subcellular localization suggested auxin fluxes during hook development. Genetic manipulation of individual PIN activities interfered with different stages of hook development, implying that specific combinations of PIN genes are required for progress of the apical hook through the developmental phases. Furthermore, ethylene might modulate apical hook development by prolonging the formation phase and strongly suppressing the maintenance phase. This ethylene effect is in part mediated by regulation of PIN-dependent auxin efflux and auxin signaling.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Žádníková, Petra and Petrášek, Jan and Marhavý, Peter and Raz, Vered and Vandenbussche, Filip and Ding, Zhaojun and Schwarzerová, Kateřina and Morita, Miyo T. and Tasaka, Masao and Hejátko, Jan and Van Der Straeten, Dominique and Friml, Jiří and Benková, Eva},
	month = feb,
	year = {2010},
	pages = {607--617},
}

The apical hook of dark-grown Arabidopsis seedlings is a simple structure that develops soon after germination to protect the meristem tissues during emergence through the soil and that opens upon exposure to light. Differential growth at the apical hook proceeds in three sequential steps that are regulated by multiple hormones, principally auxin and ethylene. We show that the progress of the apical hook through these developmental phases depends on the dynamic, asymmetric distribution of auxin, which is regulated by auxin efflux carriers of the PIN family. Several PIN proteins exhibited specific, partially overlapping spatial and temporal expression patterns, and their subcellular localization suggested auxin fluxes during hook development. Genetic manipulation of individual PIN activities interfered with different stages of hook development, implying that specific combinations of PIN genes are required for progress of the apical hook through the developmental phases. Furthermore, ethylene might modulate apical hook development by prolonging the formation phase and strongly suppressing the maintenance phase. This ethylene effect is in part mediated by regulation of PIN-dependent auxin efflux and auxin signaling.

@article{karlman_juvenile_2010,
	title = {Juvenile growth of provenances and open pollinated families of four {Russian} larch species ({Larix} {Mill}.) in {Swedish} field tests},
	volume = {60},
	doi = {10/gjcmpz},
	abstract = {Four Russian larch species; (Larix sukaczewii Dyl.,L. sibirica Ledeb., L. gmelinii Rupr. and L. cajanderi Mayr.) were tested in combined provenance-progeny tests on three sites in Sweden. 29 provenances, two seedorchards and four seed stands-material were assessed for juvenile height growth and survival after five growing seasons in the field. Genetic parameters were also determined on the family level. The results show that provenances of L. sukaczewii originating from western Russia have the highest survival. Compared to the closely related L. sibirica, L. sukaczewii show better adaptation, a pattern that has also been observed in Finland and Iceland. Provenances of L. gmelinii from the Russian Far East demonstrate best juvenile height growth on all three sites. L. cajanderi from northern interior Siberia failed on all three sites. Both climatic and geographical variables showed strong correlation with survival and height. At this early evaluation it seems like provenances of L. sukaczewii can be transferred northward with satisfactory survival whereas southern transfer or transfer from strongly continental areas in Russia to the semi maritime climate in Sweden results in poor growth. CVA values suggested relatively high genetic variation in height for L. sukaczewii and L. sibirica. The heritabilities for height growth and survival were at this early evaluation generally low (h2 {\textless} 0.10) and often non-significant.},
	journal = {Silvae Genetica},
	author = {Karlman, Lars and Fries, Anders and Martinsson, O. and Westin, Johan},
	month = aug,
	year = {2010},
	pages = {165},
}

Four Russian larch species; (Larix sukaczewii Dyl.,L. sibirica Ledeb., L. gmelinii Rupr. and L. cajanderi Mayr.) were tested in combined provenance-progeny tests on three sites in Sweden. 29 provenances, two seedorchards and four seed stands-material were assessed for juvenile height growth and survival after five growing seasons in the field. Genetic parameters were also determined on the family level. The results show that provenances of L. sukaczewii originating from western Russia have the highest survival. Compared to the closely related L. sibirica, L. sukaczewii show better adaptation, a pattern that has also been observed in Finland and Iceland. Provenances of L. gmelinii from the Russian Far East demonstrate best juvenile height growth on all three sites. L. cajanderi from northern interior Siberia failed on all three sites. Both climatic and geographical variables showed strong correlation with survival and height. At this early evaluation it seems like provenances of L. sukaczewii can be transferred northward with satisfactory survival whereas southern transfer or transfer from strongly continental areas in Russia to the semi maritime climate in Sweden results in poor growth. CVA values suggested relatively high genetic variation in height for L. sukaczewii and L. sibirica. The heritabilities for height growth and survival were at this early evaluation generally low (h2 \textless 0.10) and often non-significant.

@article{sundberg_tools_2010,
	title = {Tools and perspectives for molecular breeding of forest tree feedstock},
	volume = {150},
	issn = {01681656},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168165610006851},
	doi = {10/cn6c9m},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Biotechnology},
	author = {Sundberg, B.},
	month = nov,
	year = {2010},
	pages = {114--114},
}

@article{sanchez_effect_2010,
	title = {Effect of selection method on genetic correlation and gain in a two-trait selection scheme},
	volume = {74},
	doi = {10/f2467c},
	abstract = {Adverse genetic correlations between wood volume and quality traits are one of the main constraints in advancing radiata pine and other pine breeding programs. To overcome or deal with adverse genetic correlation in radiata pine and other conifer breeding programs, a Monte Carlo simulation study for the adversely correlated traits DBH and wood density was conducted using allele-based models. Two allelic models were generated for the study: a mixed-loci model using independent and pleiotropic loci (i.e. each locus affecting more than one trait) for adversely correlated traits and an all-antagonistic-pleiotropic-loci model. Selection was conducted for three scenarios: the first was based on a single trait, the second on index selection for two adversely correlated traits (DBH and wood density) with equal or, third, unequal economic weights. Results indicated that: 1. Adverse genetic correlation tends to increase under pleiotropic models with selection. 2. Genetic gains for adversely correlated traits (such as DBH and wood density) could be made for many generations with selective breeding if there are independent loci for individual traits. 3. New alleles (from infusion or mutation) with less antagonistic effect are required for further genetic gain in the two adversely correlated traits simultaneously if all independent alleles are fixed (i.e. without allelic variation) and pleiotropic loci with antagonistic effects are not fixed. 4. For short-term genetic gain in adversely correlated traits, selection based on two traits simultaneously is more effective than selection based on a single trait. Developing economic weights through breeding objectives is a sound approach for short-term breeding programs. Economic weights will influence genetic gain for individual traits and genetic correla tion between traits. 5. For long-term genetic gain, dissecting the genetic basis of traits using a large association population is recommended. When the genetic mechanisms controlling adversely correlated traits are better understood, an allele model could be developed to study optimal strategies under different gene actions.},
	journal = {Australian Forestry},
	author = {Sanchez, Leopoldo and Wu, Harry},
	month = dec,
	year = {2010},
	pages = {36--42},
}

Adverse genetic correlations between wood volume and quality traits are one of the main constraints in advancing radiata pine and other pine breeding programs. To overcome or deal with adverse genetic correlation in radiata pine and other conifer breeding programs, a Monte Carlo simulation study for the adversely correlated traits DBH and wood density was conducted using allele-based models. Two allelic models were generated for the study: a mixed-loci model using independent and pleiotropic loci (i.e. each locus affecting more than one trait) for adversely correlated traits and an all-antagonistic-pleiotropic-loci model. Selection was conducted for three scenarios: the first was based on a single trait, the second on index selection for two adversely correlated traits (DBH and wood density) with equal or, third, unequal economic weights. Results indicated that: 1. Adverse genetic correlation tends to increase under pleiotropic models with selection. 2. Genetic gains for adversely correlated traits (such as DBH and wood density) could be made for many generations with selective breeding if there are independent loci for individual traits. 3. New alleles (from infusion or mutation) with less antagonistic effect are required for further genetic gain in the two adversely correlated traits simultaneously if all independent alleles are fixed (i.e. without allelic variation) and pleiotropic loci with antagonistic effects are not fixed. 4. For short-term genetic gain in adversely correlated traits, selection based on two traits simultaneously is more effective than selection based on a single trait. Developing economic weights through breeding objectives is a sound approach for short-term breeding programs. Economic weights will influence genetic gain for individual traits and genetic correla tion between traits. 5. For long-term genetic gain, dissecting the genetic basis of traits using a large association population is recommended. When the genetic mechanisms controlling adversely correlated traits are better understood, an allele model could be developed to study optimal strategies under different gene actions.

@article{kjellsen_proteomics_2010,
	title = {Proteomics of extreme freezing tolerance in {Siberian} spruce ({Picea} obovata)},
	volume = {73},
	issn = {18743919},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391909003923},
	doi = {10/dpfnkz},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Journal of Proteomics},
	author = {Kjellsen, Trygve D. and Shiryaeva, Liudmila and Schröder, Wolfgang P. and Strimbeck, G. Richard},
	month = mar,
	year = {2010},
	pages = {965--975},
}