Identifying genetic variants underlying phenotypic variation in plants without complete genomes.
Identifieur interne : 000037 ( PubMed/Corpus ); précédent : 000036; suivant : 000038Identifying genetic variants underlying phenotypic variation in plants without complete genomes.
Auteurs : Yoav Voichek ; Detlef WeigelSource :
- Nature genetics [ 1546-1718 ] ; 2020.
Abstract
Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the type of genetic variants detected in GWAS to include major deletions, insertions and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we reanalyzed 2,000 traits in Arabidopsis thaliana, tomato and maize populations. Associations identified with k-mers recapitulate those found with SNPs, but with stronger statistical support. Importantly, we discovered new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allows the detection of a wider range of genetic variants responsible for phenotypic variation.
DOI: 10.1038/s41588-020-0612-7
PubMed: 32284578
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identifying genetic variants underlying phenotypic variation in plants without complete genomes.</title><author><name sortKey="Voichek, Yoav" sort="Voichek, Yoav" uniqKey="Voichek Y" first="Yoav" last="Voichek">Yoav Voichek</name><affiliation><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Weigel, Detlef" sort="Weigel, Detlef" uniqKey="Weigel D" first="Detlef" last="Weigel">Detlef Weigel</name><affiliation><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. weigel@weigelworld.org.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32284578</idno><idno type="pmid">32284578</idno><idno type="doi">10.1038/s41588-020-0612-7</idno><idno type="wicri:Area/PubMed/Corpus">000037</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000037</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Identifying genetic variants underlying phenotypic variation in plants without complete genomes.</title><author><name sortKey="Voichek, Yoav" sort="Voichek, Yoav" uniqKey="Voichek Y" first="Yoav" last="Voichek">Yoav Voichek</name><affiliation><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Weigel, Detlef" sort="Weigel, Detlef" uniqKey="Weigel D" first="Detlef" last="Weigel">Detlef Weigel</name><affiliation><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. weigel@weigelworld.org.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Nature genetics</title><idno type="eISSN">1546-1718</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the type of genetic variants detected in GWAS to include major deletions, insertions and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we reanalyzed 2,000 traits in Arabidopsis thaliana, tomato and maize populations. Associations identified with k-mers recapitulate those found with SNPs, but with stronger statistical support. Importantly, we discovered new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allows the detection of a wider range of genetic variants responsible for phenotypic variation.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32284578</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1546-1718</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Apr</Month><Day>13</Day></PubDate></JournalIssue><Title>Nature genetics</Title><ISOAbbreviation>Nat. Genet.</ISOAbbreviation></Journal><ArticleTitle>Identifying genetic variants underlying phenotypic variation in plants without complete genomes.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41588-020-0612-7</ELocationID><Abstract><AbstractText>Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the type of genetic variants detected in GWAS to include major deletions, insertions and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we reanalyzed 2,000 traits in Arabidopsis thaliana, tomato and maize populations. Associations identified with k-mers recapitulate those found with SNPs, but with stronger statistical support. Importantly, we discovered new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allows the detection of a wider range of genetic variants responsible for phenotypic variation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Voichek</LastName><ForeName>Yoav</ForeName><Initials>Y</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8460-7018</Identifier><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Weigel</LastName><ForeName>Detlef</ForeName><Initials>D</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2114-7963</Identifier><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. weigel@weigelworld.org.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>AdG IMMUNEMENSIS</GrantID><Agency>EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Nat Genet</MedlineTA><NlmUniqueID>9216904</NlmUniqueID><ISSNLinking>1061-4036</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>10</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32284578</ArticleId><ArticleId IdType="doi">10.1038/s41588-020-0612-7</ArticleId><ArticleId IdType="pii">10.1038/s41588-020-0612-7</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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