Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables.
Identifieur interne : 000026 ( PubMed/Corpus ); précédent : 000025; suivant : 000027Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables.
Auteurs : Lindsay V. Clark ; Andrea Drauch SchreierSource :
- Molecular ecology resources [ 1755-0998 ] ; 2016.
Abstract
A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here, we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite data set from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.6.
DOI: 10.1111/1755-0998.12639
PubMed: 27868358
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Gregory Drive, Urbana, IL, 61801, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Schreier, Andrea Drauch" sort="Schreier, Andrea Drauch" uniqKey="Schreier A" first="Andrea Drauch" last="Schreier">Andrea Drauch Schreier</name><affiliation><nlm:affiliation>Department of Animal Science, University of California - Davis, Davis, CA, 95616, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27868358</idno><idno type="pmid">27868358</idno><idno type="doi">10.1111/1755-0998.12639</idno><idno type="wicri:Area/PubMed/Corpus">000026</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000026</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables.</title><author><name sortKey="Clark, Lindsay V" sort="Clark, Lindsay V" uniqKey="Clark L" first="Lindsay V" last="Clark">Lindsay V. Clark</name><affiliation><nlm:affiliation>Department of Crop Sciences, University of Illinois, Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL, 61801, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Schreier, Andrea Drauch" sort="Schreier, Andrea Drauch" uniqKey="Schreier A" first="Andrea Drauch" last="Schreier">Andrea Drauch Schreier</name><affiliation><nlm:affiliation>Department of Animal Science, University of California - Davis, Davis, CA, 95616, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Molecular ecology resources</title><idno type="eISSN">1755-0998</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here, we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite data set from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.6.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">27868358</PMID><DateCreated><Year>2016</Year><Month>11</Month><Day>21</Day></DateCreated><DateRevised><Year>2017</Year><Month>01</Month><Day>05</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1755-0998</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2016</Year><Month>Nov</Month><Day>21</Day></PubDate></JournalIssue><Title>Molecular ecology resources</Title><ISOAbbreviation>Mol Ecol Resour</ISOAbbreviation></Journal><ArticleTitle>Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1111/1755-0998.12639</ELocationID><Abstract><AbstractText NlmCategory="UNASSIGNED">A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here, we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite data set from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.6.</AbstractText><CopyrightInformation>© 2016 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Clark</LastName><ForeName>Lindsay V</ForeName><Initials>LV</Initials><AffiliationInfo><Affiliation>Department of Crop Sciences, University of Illinois, Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL, 61801, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schreier</LastName><ForeName>Andrea Drauch</ForeName><Initials>AD</Initials><AffiliationInfo><Affiliation>Department of Animal Science, University of California - Davis, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>11</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol Resour</MedlineTA><NlmUniqueID>101465604</NlmUniqueID><ISSNLinking>1755-098X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">R package</Keyword><Keyword MajorTopicYN="N">polyploidy</Keyword><Keyword MajorTopicYN="N">simple sequence repeat</Keyword><Keyword MajorTopicYN="N">sturgeon</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>11</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>11</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>11</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>11</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>11</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>11</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27868358</ArticleId><ArticleId IdType="doi">10.1111/1755-0998.12639</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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