Multiallelic epistatic model for an out-bred cross and mapping algorithm of interactive quantitative trait loci.
Identifieur interne : 002D84 ( Main/Exploration ); précédent : 002D83; suivant : 002D85Multiallelic epistatic model for an out-bred cross and mapping algorithm of interactive quantitative trait loci.
Auteurs : Chunfa Tong [États-Unis] ; Bo Zhang ; Zhong Wang ; Meng Xu ; Xiaoming Pang ; Jingna Si ; Minren Huang ; Rongling WuSource :
- BMC plant biology [ 1471-2229 ] ; 2011.
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Abstract
BACKGROUND
Genetic mapping has proven to be powerful for studying the genetic architecture of complex traits by characterizing a network of the underlying interacting quantitative trait loci (QTLs). Current statistical models for genetic mapping were mostly founded on the biallelic epistasis of QTLs, incapable of analyzing multiallelic QTLs and their interactions that are widespread in an outcrossing population.
RESULTS
Here we have formulated a general framework to model and define the epistasis between multiallelic QTLs. Based on this framework, we have derived a statistical algorithm for the estimation and test of multiallelic epistasis between different QTLs in a full-sib family of outcrossing species. We used this algorithm to genomewide scan for the distribution of multiallelic epistasis for a rooting ability trait in an outbred cross derived from two heterozygous poplar trees. The results from simulation studies indicate that the positions and effects of multiallelic QTLs can well be estimated with a modest sample and heritability.
CONCLUSIONS
The model and algorithm developed provide a useful tool for better characterizing the genetic control of complex traits in a heterozygous family derived from outcrossing species, such as forest trees, and thus fill a gap that occurs in genetic mapping of this group of important but underrepresented species.
DOI: 10.1186/1471-2229-11-148
PubMed: 22039993
PubMed Central: PMC3377927
Affiliations:
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Zhong" sort="Wang, Zhong" uniqKey="Wang Z" first="Zhong" last="Wang">Zhong Wang</name></author><author><name sortKey="Xu, Meng" sort="Xu, Meng" uniqKey="Xu M" first="Meng" last="Xu">Meng Xu</name></author><author><name sortKey="Pang, Xiaoming" sort="Pang, Xiaoming" uniqKey="Pang X" first="Xiaoming" last="Pang">Xiaoming Pang</name></author><author><name sortKey="Si, Jingna" sort="Si, Jingna" uniqKey="Si J" first="Jingna" last="Si">Jingna Si</name></author><author><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name></author><author><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:22039993</idno><idno type="pmid">22039993</idno><idno type="doi">10.1186/1471-2229-11-148</idno><idno type="pmc">PMC3377927</idno><idno 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type="state">Pennsylvanie</region><settlement type="city">University Park (Pennsylvanie)</settlement></placeName><orgName type="university">Université d'État de Pennsylvanie</orgName></affiliation></author><author><name sortKey="Zhang, Bo" sort="Zhang, Bo" uniqKey="Zhang B" first="Bo" last="Zhang">Bo Zhang</name></author><author><name sortKey="Wang, Zhong" sort="Wang, Zhong" uniqKey="Wang Z" first="Zhong" last="Wang">Zhong Wang</name></author><author><name sortKey="Xu, Meng" sort="Xu, Meng" uniqKey="Xu M" first="Meng" last="Xu">Meng Xu</name></author><author><name sortKey="Pang, Xiaoming" sort="Pang, Xiaoming" uniqKey="Pang X" first="Xiaoming" last="Pang">Xiaoming Pang</name></author><author><name sortKey="Si, Jingna" sort="Si, Jingna" uniqKey="Si J" first="Jingna" last="Si">Jingna Si</name></author><author><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name></author><author><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Crosses, Genetic (MeSH)</term><term>Epistasis, Genetic (MeSH)</term><term>Models, Genetic (MeSH)</term><term>Monte Carlo Method (MeSH)</term><term>Populus (genetics)</term><term>Quantitative Trait Loci (MeSH)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes (MeSH)</term><term>Croisements génétiques (MeSH)</term><term>Locus de caractère quantitatif (MeSH)</term><term>Logiciel (MeSH)</term><term>Modèles génétiques (MeSH)</term><term>Méthode de Monte Carlo (MeSH)</term><term>Populus (génétique)</term><term>Épistasie (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Crosses, Genetic</term><term>Epistasis, Genetic</term><term>Models, Genetic</term><term>Monte Carlo Method</term><term>Quantitative Trait Loci</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Croisements génétiques</term><term>Locus de caractère quantitatif</term><term>Logiciel</term><term>Modèles génétiques</term><term>Méthode de Monte Carlo</term><term>Épistasie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Genetic mapping has proven to be powerful for studying the genetic architecture of complex traits by characterizing a network of the underlying interacting quantitative trait loci (QTLs). Current statistical models for genetic mapping were mostly founded on the biallelic epistasis of QTLs, incapable of analyzing multiallelic QTLs and their interactions that are widespread in an outcrossing population.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Here we have formulated a general framework to model and define the epistasis between multiallelic QTLs. Based on this framework, we have derived a statistical algorithm for the estimation and test of multiallelic epistasis between different QTLs in a full-sib family of outcrossing species. We used this algorithm to genomewide scan for the distribution of multiallelic epistasis for a rooting ability trait in an outbred cross derived from two heterozygous poplar trees. The results from simulation studies indicate that the positions and effects of multiallelic QTLs can well be estimated with a modest sample and heritability.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The model and algorithm developed provide a useful tool for better characterizing the genetic control of complex traits in a heterozygous family derived from outcrossing species, such as forest trees, and thus fill a gap that occurs in genetic mapping of this group of important but underrepresented species.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22039993</PMID><DateCompleted><Year>2012</Year><Month>04</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><PubDate><Year>2011</Year><Month>Oct</Month><Day>31</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Multiallelic epistatic model for an out-bred cross and mapping algorithm of interactive quantitative trait loci.</ArticleTitle><Pagination><MedlinePgn>148</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-11-148</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Genetic mapping has proven to be powerful for studying the genetic architecture of complex traits by characterizing a network of the underlying interacting quantitative trait loci (QTLs). 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The results from simulation studies indicate that the positions and effects of multiallelic QTLs can well be estimated with a modest sample and heritability.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The model and algorithm developed provide a useful tool for better characterizing the genetic control of complex traits in a heterozygous family derived from outcrossing species, such as forest trees, and thus fill a gap that occurs in genetic mapping of this group of important but underrepresented species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Chunfa</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Bo</ForeName><Initials>B</Initials></Author><Author 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IdType="doi">10.1186/1471-2229-11-148</ArticleId><ArticleId IdType="pmc">PMC3377927</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Bioinform Biol Insights. 2010 Feb 04;4:1-8</Citation><ArticleIdList><ArticleId IdType="pubmed">20213011</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1989 Jan;121(1):185-99</Citation><ArticleIdList><ArticleId IdType="pubmed">2563713</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genet. 2004 Jul 26;5:20</Citation><ArticleIdList><ArticleId IdType="pubmed">15274749</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2003 Oct;165(2):901-13</Citation><ArticleIdList><ArticleId IdType="pubmed">14573497</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2003 Oct;165(2):867-83</Citation><ArticleIdList><ArticleId IdType="pubmed">14573494</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1995 Feb;139(2):963-73</Citation><ArticleIdList><ArticleId IdType="pubmed">7713445</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Popul Biol. 2002 May;61(3):349-63</Citation><ArticleIdList><ArticleId IdType="pubmed">12027621</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2002 Mar;160(3):1243-61</Citation><ArticleIdList><ArticleId IdType="pubmed">11901137</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1994 Apr;136(4):1457-68</Citation><ArticleIdList><ArticleId IdType="pubmed">8013918</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1990 Jul;125(3):645-54</Citation><ArticleIdList><ArticleId IdType="pubmed">1974227</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1994 Nov;138(3):963-71</Citation><ArticleIdList><ArticleId IdType="pubmed">7851788</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Jul 15;27(14):2006-8</Citation><ArticleIdList><ArticleId IdType="pubmed">21586519</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2003 Mar;163(3):1169-75</Citation><ArticleIdList><ArticleId IdType="pubmed">12663553</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1994 Aug;137(4):1121-37</Citation><ArticleIdList><ArticleId IdType="pubmed">7982566</ArticleId></ArticleIdList></Reference><Reference><Citation>J Stat Plan Inference. 2009 Mar 1;139(3):978-989</Citation><ArticleIdList><ArticleId IdType="pubmed">20160841</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>University Park (Pennsylvanie)</li></settlement><orgName><li>Université d'État de Pennsylvanie</li></orgName></list><tree><noCountry><name sortKey="Huang, Minren" sort="Huang, Minren" uniqKey="Huang M" first="Minren" last="Huang">Minren Huang</name><name sortKey="Pang, Xiaoming" sort="Pang, Xiaoming" uniqKey="Pang X" first="Xiaoming" last="Pang">Xiaoming Pang</name><name sortKey="Si, Jingna" sort="Si, Jingna" uniqKey="Si J" first="Jingna" last="Si">Jingna Si</name><name sortKey="Wang, Zhong" sort="Wang, Zhong" uniqKey="Wang Z" first="Zhong" last="Wang">Zhong Wang</name><name sortKey="Wu, Rongling" sort="Wu, Rongling" uniqKey="Wu R" first="Rongling" last="Wu">Rongling Wu</name><name sortKey="Xu, Meng" sort="Xu, Meng" uniqKey="Xu M" first="Meng" last="Xu">Meng Xu</name><name sortKey="Zhang, Bo" sort="Zhang, Bo" uniqKey="Zhang B" first="Bo" last="Zhang">Bo Zhang</name></noCountry><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Tong, Chunfa" sort="Tong, Chunfa" uniqKey="Tong C" first="Chunfa" last="Tong">Chunfa Tong</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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