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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Joint linkage and association mapping of complex traits in shrub willow (<italic>Salix purpurea</italic> L.)</title><author><name sortKey="Carlson, Craig H" sort="Carlson, Craig H" uniqKey="Carlson C" first="Craig H" last="Carlson">Craig H. Carlson</name><affiliation><nlm:aff id="AF0001"><institution>Horticulture Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Gouker, Fred E" sort="Gouker, Fred E" uniqKey="Gouker F" first="Fred E" last="Gouker">Fred E. Gouker</name><affiliation><nlm:aff id="AF0001"><institution>Horticulture Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Crowell, Chase R" sort="Crowell, Chase R" uniqKey="Crowell C" first="Chase R" last="Crowell">Chase R. Crowell</name><affiliation><nlm:aff id="AF0002"><institution>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Evans, Luke" sort="Evans, Luke" uniqKey="Evans L" first="Luke" last="Evans">Luke Evans</name><affiliation><nlm:aff id="AF0003"><institution>Institute for Behavioral Genetics and Department of Ecology and Evolutionary Biology, University of Colorado</institution>, Boulder, CO,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation><nlm:aff id="AF0004"><institution>Department of Biology, West Virginia University</institution>, Morgantown, WV,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Smart, Christine D" sort="Smart, Christine D" uniqKey="Smart C" first="Christine D" last="Smart">Christine D. Smart</name><affiliation><nlm:aff id="AF0002"><institution>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Smart, Lawrence B" sort="Smart, Lawrence B" uniqKey="Smart L" first="Lawrence B" last="Smart">Lawrence B. Smart</name><affiliation><nlm:aff id="AF0001"><institution>Horticulture Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31008500</idno><idno type="pmc">6821232</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821232</idno><idno type="RBID">PMC:6821232</idno><idno type="doi">10.1093/aob/mcz047</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000426</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000426</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Joint linkage and association mapping of complex traits in shrub willow (<italic>Salix purpurea</italic> L.)</title><author><name sortKey="Carlson, Craig H" sort="Carlson, Craig H" uniqKey="Carlson C" first="Craig H" last="Carlson">Craig H. Carlson</name><affiliation><nlm:aff id="AF0001"><institution>Horticulture Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Gouker, Fred E" sort="Gouker, Fred E" uniqKey="Gouker F" first="Fred E" last="Gouker">Fred E. Gouker</name><affiliation><nlm:aff id="AF0001"><institution>Horticulture Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Crowell, Chase R" sort="Crowell, Chase R" uniqKey="Crowell C" first="Chase R" last="Crowell">Chase R. Crowell</name><affiliation><nlm:aff id="AF0002"><institution>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Evans, Luke" sort="Evans, Luke" uniqKey="Evans L" first="Luke" last="Evans">Luke Evans</name><affiliation><nlm:aff id="AF0003"><institution>Institute for Behavioral Genetics and Department of Ecology and Evolutionary Biology, University of Colorado</institution>, Boulder, CO,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation><nlm:aff id="AF0004"><institution>Department of Biology, West Virginia University</institution>, Morgantown, WV,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Smart, Christine D" sort="Smart, Christine D" uniqKey="Smart C" first="Christine D" last="Smart">Christine D. Smart</name><affiliation><nlm:aff id="AF0002"><institution>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author><author><name sortKey="Smart, Lawrence B" sort="Smart, Lawrence B" uniqKey="Smart L" first="Lawrence B" last="Smart">Lawrence B. Smart</name><affiliation><nlm:aff id="AF0001"><institution>Horticulture Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></nlm:aff></affiliation></author></analytic><series><title level="j">Annals of Botany</title><idno type="ISSN">0305-7364</idno><idno type="eISSN">1095-8290</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><sec id="s0100"><title>Background and Aims</title><p>Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (<italic>Salix</italic> spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in <italic>S. purpurea</italic>.</p></sec><sec id="s0101"><title>Methods</title><p>A panel of North American naturalized <italic>S. purpurea</italic> accessions and full-sib F<sub>2</sub><italic>S. purpurea</italic> population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F<sub>2</sub>, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits.</p></sec><sec id="s0102"><title>Key Results</title><p>Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F<sub>2</sub>, many large-effect QTL were identified, as well as QTL hotspots.</p></sec><sec id="s0103"><title>Conclusions</title><p>This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in <italic>Salix</italic>, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.</p></sec></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Ann Bot</journal-id><journal-id journal-id-type="iso-abbrev">Ann. Bot</journal-id><journal-id journal-id-type="publisher-id">annbot</journal-id><journal-title-group><journal-title>Annals of Botany</journal-title></journal-title-group><issn pub-type="ppub">0305-7364</issn><issn pub-type="epub">1095-8290</issn><publisher><publisher-name>Oxford University Press</publisher-name><publisher-loc>UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31008500</article-id><article-id pub-id-type="pmc">6821232</article-id><article-id pub-id-type="doi">10.1093/aob/mcz047</article-id><article-id pub-id-type="publisher-id">mcz047</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Articles</subject></subj-group></article-categories><title-group><article-title>Joint linkage and association mapping of complex traits in shrub willow (<italic>Salix purpurea</italic> L.)</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Carlson</surname><given-names>Craig H</given-names></name><xref ref-type="aff" rid="AF0001">1</xref><xref ref-type="author-notes" rid="fn-001"></xref></contrib><contrib contrib-type="author"><name><surname>Gouker</surname><given-names>Fred E</given-names></name><xref ref-type="aff" rid="AF0001">1</xref><xref ref-type="author-notes" rid="fn-001"></xref></contrib><contrib contrib-type="author"><name><surname>Crowell</surname><given-names>Chase R</given-names></name><xref ref-type="aff" rid="AF0002">2</xref></contrib><contrib contrib-type="author"><name><surname>Evans</surname><given-names>Luke</given-names></name><xref ref-type="aff" rid="AF0003">3</xref></contrib><contrib contrib-type="author"><name><surname>DiFazio</surname><given-names>Stephen P</given-names></name><xref ref-type="aff" rid="AF0004">4</xref></contrib><contrib contrib-type="author"><name><surname>Smart</surname><given-names>Christine D</given-names></name><xref ref-type="aff" rid="AF0002">2</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0002-7812-7736</contrib-id><name><surname>Smart</surname><given-names>Lawrence B</given-names></name><xref ref-type="aff" rid="AF0001">1</xref><xref ref-type="corresp" rid="c1"></xref><pmc-comment>lbs33@cornell.edu </pmc-comment>
</contrib></contrib-group><aff id="AF0001"><label>1</label><institution>Horticulture Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></aff><aff id="AF0002"><label>2</label><institution>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University</institution>, Cornell AgriTech, Geneva, NY,<country country="US">USA</country></aff><aff id="AF0003"><label>3</label><institution>Institute for Behavioral Genetics and Department of Ecology and Evolutionary Biology, University of Colorado</institution>, Boulder, CO,<country country="US">USA</country></aff><aff id="AF0004"><label>4</label><institution>Department of Biology, West Virginia University</institution>, Morgantown, WV,<country country="US">USA</country></aff><author-notes><corresp id="c1">For correspondence. E-mail <email>lbs33@cornell.edu</email></corresp><fn id="fn-001"><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="ppub"><month>10</month><year>2019</year></pub-date><pub-date pub-type="epub" iso-8601-date="2019-04-22"><day>22</day><month>4</month><year>2019</year></pub-date><pub-date pub-type="pmc-release"><day>29</day><month>10</month><year>2020</year></pub-date><pmc-comment> PMC Release delay is 12 months and
0 days and was based on the
<volume>124</volume><issue>4</issue><issue-title>Special Issue on Developing sustainable bioenergy crops for future climates</issue-title><fpage>701</fpage><lpage>715</lpage><history><date date-type="received"><day>27</day><month>8</month><year>2018</year></date><date date-type="rev-request"><day>24</day><month>1</month><year>2019</year></date><date date-type="accepted"><day>08</day><month>3</month><year>2019</year></date></history><permissions><copyright-statement>© The Author(s) 2019. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</copyright-statement><copyright-year>2019</copyright-year><license license-type="publisher-standard" xlink:href="https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"><license-p>This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (<ext-link ext-link-type="uri" xlink:href="https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model">https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model</ext-link>)</license-p></license></permissions><self-uri xlink:href="mcz047.pdf"></self-uri><abstract><title>Abstract</title><sec id="s0100"><title>Background and Aims</title><p>Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (<italic>Salix</italic> spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in <italic>S. purpurea</italic>.</p></sec><sec id="s0101"><title>Methods</title><p>A panel of North American naturalized <italic>S. purpurea</italic> accessions and full-sib F<sub>2</sub><italic>S. purpurea</italic> population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F<sub>2</sub>, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits.</p></sec><sec id="s0102"><title>Key Results</title><p>Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F<sub>2</sub>, many large-effect QTL were identified, as well as QTL hotspots.</p></sec><sec id="s0103"><title>Conclusions</title><p>This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in <italic>Salix</italic>, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.</p></sec></abstract><kwd-group><kwd>Biomass</kwd><kwd>bioenergy</kwd><kwd>breeding</kwd><kwd>phenology</kwd><kwd>GWAS</kwd><kwd>QTL</kwd><kwd>wood composition</kwd><kwd>yield</kwd></kwd-group><funding-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">U.S. Department of Energy Office of Science</named-content></funding-source></award-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">Office of Biological and Environmental Research</named-content></funding-source><award-id>DE-SC0008375</award-id></award-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">U.S. Department of Agriculture National Institute of Food and Agriculture</named-content></funding-source></award-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">Agriculture and Food Research</named-content></funding-source><award-id>2012-68005-19703</award-id></award-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">National Science Foundation</named-content><named-content content-type="funder-identifier">10.13039/501100008982</named-content></funding-source><award-id>DEB-1542486</award-id></award-group></funding-group><counts><page-count count="15"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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