Population genomics of the eastern cottonwood (Populus deltoides).
Identifieur interne : 001249 ( Main/Exploration ); précédent : 001248; suivant : 001250Population genomics of the eastern cottonwood (Populus deltoides).
Auteurs : Annette M. Fahrenkrog ; Leandro G. Neves ; Márcio F R. Resende ; Christopher Dervinis ; Ruth Davenport ; W Brad Barbazuk ; Matias KirstSource :
- Ecology and evolution [ 2045-7758 ] ; 2017.
Abstract
Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (FST = 0.022-0.106), high genetic diversity (θW = 0.00100, π = 0.00170), a large effective population size (Ne ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (XTX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.
DOI: 10.1002/ece3.3466
PubMed: 29187979
PubMed Central: PMC5696417
Affiliations:
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Fahrenkrog</name><affiliation><nlm:affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">School of Forest Resources and Conservation University of Florida Gainesville FL USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.</wicri:noCountry></affiliation></author><author><name sortKey="Neves, Leandro G" sort="Neves, Leandro G" uniqKey="Neves L" first="Leandro G" last="Neves">Leandro G. Neves</name><affiliation><nlm:affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">School of Forest Resources and Conservation University of Florida Gainesville FL USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Present address: RAPiD Genomics LLC756 2nd Avenue Gainesville FL 32601 USA.</nlm:affiliation><wicri:noCountry code="no comma">Present address: RAPiD Genomics LLC756 2nd Avenue Gainesville FL 32601 USA.</wicri:noCountry></affiliation></author><author><name sortKey="Resende, Marcio F R" sort="Resende, Marcio F R" uniqKey="Resende M" first="Márcio F R" last="Resende">Márcio F R. Resende</name><affiliation><nlm:affiliation>Horticultural Sciences Department University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">Horticultural Sciences Department University of Florida Gainesville FL USA.</wicri:noCountry></affiliation></author><author><name sortKey="Dervinis, Christopher" sort="Dervinis, Christopher" uniqKey="Dervinis C" first="Christopher" last="Dervinis">Christopher Dervinis</name><affiliation><nlm:affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">School of Forest Resources and Conservation University of Florida Gainesville FL USA.</wicri:noCountry></affiliation></author><author><name sortKey="Davenport, Ruth" sort="Davenport, Ruth" uniqKey="Davenport R" first="Ruth" last="Davenport">Ruth Davenport</name><affiliation><nlm:affiliation>Biology Department University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">Biology Department University of Florida Gainesville FL USA.</wicri:noCountry></affiliation></author><author><name sortKey="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W Brad" last="Barbazuk">W Brad Barbazuk</name><affiliation><nlm:affiliation>Biology Department University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">Biology Department University of Florida Gainesville FL USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>University of Florida Genetics Institute University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">University of Florida Genetics Institute University of Florida Gainesville FL USA.</wicri:noCountry></affiliation></author><author><name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name><affiliation><nlm:affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">School of Forest Resources and Conservation University of Florida Gainesville FL USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>University of Florida Genetics Institute University of Florida Gainesville FL USA.</nlm:affiliation><wicri:noCountry code="no comma">University of Florida Genetics Institute University of Florida Gainesville FL USA.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Ecology and evolution</title><idno type="ISSN">2045-7758</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (<i>Populus deltoides</i>). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural <i>P. deltoides</i> population showed low levels of subpopulation differentiation (<i>F</i><sub>ST</sub> = 0.022-0.106), high genetic diversity (θ<sub>W</sub> = 0.00100, π = 0.00170), a large effective population size (<i>N</i><sub>e</sub> ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's <i>D</i>), subpopulation differentiation (<i>X</i><sup><i>T</i></sup><i>X</i>), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, <i>Populus trichocarpa</i>, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in <i>P. deltoides</i> throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">29187979</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2045-7758</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><Issue>22</Issue><PubDate><Year>2017</Year><Month>11</Month></PubDate></JournalIssue><Title>Ecology and evolution</Title><ISOAbbreviation>Ecol Evol</ISOAbbreviation></Journal><ArticleTitle>Population genomics of the eastern cottonwood (<i>Populus deltoides</i>).</ArticleTitle><Pagination><MedlinePgn>9426-9440</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/ece3.3466</ELocationID><Abstract><AbstractText>Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (<i>Populus deltoides</i>). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural <i>P. deltoides</i> population showed low levels of subpopulation differentiation (<i>F</i><sub>ST</sub> = 0.022-0.106), high genetic diversity (θ<sub>W</sub> = 0.00100, π = 0.00170), a large effective population size (<i>N</i><sub>e</sub> ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's <i>D</i>), subpopulation differentiation (<i>X</i><sup><i>T</i></sup><i>X</i>), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, <i>Populus trichocarpa</i>, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in <i>P. deltoides</i> throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fahrenkrog</LastName><ForeName>Annette M</ForeName><Initials>AM</Initials><Identifier Source="ORCID">0000-0002-7553-6382</Identifier><AffiliationInfo><Affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Neves</LastName><ForeName>Leandro G</ForeName><Initials>LG</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Plant Molecular and Cellular Biology Graduate Program University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Present address: RAPiD Genomics LLC756 2nd Avenue Gainesville FL 32601 USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Resende</LastName><ForeName>Márcio F R</ForeName><Initials>MFR</Initials><Suffix>Jr</Suffix><AffiliationInfo><Affiliation>Horticultural Sciences Department University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dervinis</LastName><ForeName>Christopher</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Davenport</LastName><ForeName>Ruth</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Biology Department University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barbazuk</LastName><ForeName>W Brad</ForeName><Initials>WB</Initials><AffiliationInfo><Affiliation>Biology Department University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>University of Florida Genetics Institute University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kirst</LastName><ForeName>Matias</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>School of Forest Resources and Conservation University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>University of Florida Genetics Institute University of Florida Gainesville FL USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>10</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Ecol Evol</MedlineTA><NlmUniqueID>101566408</NlmUniqueID><ISSNLinking>2045-7758</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus deltoides</Keyword><Keyword MajorTopicYN="Y">eastern cottonwood</Keyword><Keyword MajorTopicYN="Y">exome capture</Keyword><Keyword MajorTopicYN="Y">genetic diversity</Keyword><Keyword MajorTopicYN="Y">local adaptation</Keyword><Keyword MajorTopicYN="Y">population structure</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>01</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>08</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>08</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>12</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>12</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>12</Month><Day>1</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29187979</ArticleId><ArticleId IdType="doi">10.1002/ece3.3466</ArticleId><ArticleId IdType="pii">ECE33466</ArticleId><ArticleId IdType="pmc">PMC5696417</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Genetics. 2000 Jun;155(2):945-59</Citation><ArticleIdList><ArticleId 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IdType="pubmed">8375663</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W Brad" last="Barbazuk">W Brad Barbazuk</name><name sortKey="Davenport, Ruth" sort="Davenport, Ruth" uniqKey="Davenport R" first="Ruth" last="Davenport">Ruth Davenport</name><name sortKey="Dervinis, Christopher" sort="Dervinis, Christopher" uniqKey="Dervinis C" first="Christopher" last="Dervinis">Christopher Dervinis</name><name sortKey="Fahrenkrog, Annette M" sort="Fahrenkrog, Annette M" uniqKey="Fahrenkrog A" first="Annette M" last="Fahrenkrog">Annette M. Fahrenkrog</name><name sortKey="Kirst, Matias" sort="Kirst, Matias" uniqKey="Kirst M" first="Matias" last="Kirst">Matias Kirst</name><name sortKey="Neves, Leandro G" sort="Neves, Leandro G" uniqKey="Neves L" first="Leandro G" last="Neves">Leandro G. Neves</name><name sortKey="Resende, Marcio F R" sort="Resende, Marcio F R" uniqKey="Resende M" first="Márcio F R" last="Resende">Márcio F R. Resende</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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