Mapping quantitative trait loci for longitudinal traits in line crosses.
Identifieur interne : 003D78 ( Main/Exploration ); précédent : 003D77; suivant : 003D79Mapping quantitative trait loci for longitudinal traits in line crosses.
Auteurs : Runqing Yang [République populaire de Chine] ; Quan Tian ; Shizhong XuSource :
- Genetics [ 0016-6731 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Quantitative Trait Loci.
- methods : Chromosome Mapping.
- Models, Genetic, Multifactorial Inheritance, Phenotype, Quantitative Trait, Heritable, Time Factors.
Abstract
Quantitative traits whose phenotypic values change over time are called longitudinal traits. Genetic analyses of longitudinal traits can be conducted using any of the following approaches: (1) treating the phenotypic values at different time points as repeated measurements of the same trait and analyzing the trait under the repeated measurements framework, (2) treating the phenotypes measured from different time points as different traits and analyzing the traits jointly on the basis of the theory of multivariate analysis, and (3) fitting a growth curve to the phenotypic values across time points and analyzing the fitted parameters of the growth trajectory under the theory of multivariate analysis. The third approach has been used in QTL mapping for longitudinal traits by fitting the data to a logistic growth trajectory. This approach applies only to the particular S-shaped growth process. In practice, a longitudinal trait may show a trajectory of any shape. We demonstrate that one can describe a longitudinal trait with orthogonal polynomials, which are sufficiently general for fitting any shaped curve. We develop a mixed-model methodology for QTL mapping of longitudinal traits and a maximum-likelihood method for parameter estimation and statistical tests. The expectation-maximization (EM) algorithm is applied to search for the maximum-likelihood estimates of parameters. The method is verified with simulated data and demonstrated with experimental data from a pseudobackcross family of Populus (poplar) trees.
DOI: 10.1534/genetics.105.054775
PubMed: 16751670
PubMed Central: PMC1569730
Affiliations:
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Genetic analyses of longitudinal traits can be conducted using any of the following approaches: (1) treating the phenotypic values at different time points as repeated measurements of the same trait and analyzing the trait under the repeated measurements framework, (2) treating the phenotypes measured from different time points as different traits and analyzing the traits jointly on the basis of the theory of multivariate analysis, and (3) fitting a growth curve to the phenotypic values across time points and analyzing the fitted parameters of the growth trajectory under the theory of multivariate analysis. The third approach has been used in QTL mapping for longitudinal traits by fitting the data to a logistic growth trajectory. This approach applies only to the particular S-shaped growth process. In practice, a longitudinal trait may show a trajectory of any shape. We demonstrate that one can describe a longitudinal trait with orthogonal polynomials, which are sufficiently general for fitting any shaped curve. We develop a mixed-model methodology for QTL mapping of longitudinal traits and a maximum-likelihood method for parameter estimation and statistical tests. The expectation-maximization (EM) algorithm is applied to search for the maximum-likelihood estimates of parameters. The method is verified with simulated data and demonstrated with experimental data from a pseudobackcross family of Populus (poplar) trees.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16751670</PMID><DateCompleted><Year>2006</Year><Month>11</Month><Day>13</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0016-6731</ISSN><JournalIssue CitedMedium="Print"><Volume>173</Volume><Issue>4</Issue><PubDate><Year>2006</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Genetics</Title><ISOAbbreviation>Genetics</ISOAbbreviation></Journal><ArticleTitle>Mapping quantitative trait loci for longitudinal traits in line crosses.</ArticleTitle><Pagination><MedlinePgn>2339-56</MedlinePgn></Pagination><Abstract><AbstractText>Quantitative traits whose phenotypic values change over time are called longitudinal traits. Genetic analyses of longitudinal traits can be conducted using any of the following approaches: (1) treating the phenotypic values at different time points as repeated measurements of the same trait and analyzing the trait under the repeated measurements framework, (2) treating the phenotypes measured from different time points as different traits and analyzing the traits jointly on the basis of the theory of multivariate analysis, and (3) fitting a growth curve to the phenotypic values across time points and analyzing the fitted parameters of the growth trajectory under the theory of multivariate analysis. The third approach has been used in QTL mapping for longitudinal traits by fitting the data to a logistic growth trajectory. This approach applies only to the particular S-shaped growth process. In practice, a longitudinal trait may show a trajectory of any shape. We demonstrate that one can describe a longitudinal trait with orthogonal polynomials, which are sufficiently general for fitting any shaped curve. We develop a mixed-model methodology for QTL mapping of longitudinal traits and a maximum-likelihood method for parameter estimation and statistical tests. The expectation-maximization (EM) algorithm is applied to search for the maximum-likelihood estimates of parameters. The method is verified with simulated data and demonstrated with experimental data from a pseudobackcross family of Populus (poplar) trees.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Runqing</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>School of Agriculture and Biology, Shanghai Jiaotong University, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Quan</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Shizhong</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM055321</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01-GM55321</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United 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IdType="pubmed">5149961</ArticleId></ArticleIdList></Reference><Reference><Citation>Genet Epidemiol. 2005 Jan;28(1):1-10</Citation><ArticleIdList><ArticleId IdType="pubmed">15493062</ArticleId></ArticleIdList></Reference><Reference><Citation>Behav Genet. 1996 Sep;26(5):519-25</Citation><ArticleIdList><ArticleId IdType="pubmed">8917951</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2002 Aug;161(4):1751-62</Citation><ArticleIdList><ArticleId IdType="pubmed">12196415</ArticleId></ArticleIdList></Reference><Reference><Citation>J Dairy Sci. 2001 Dec;84(12):2803-12</Citation><ArticleIdList><ArticleId IdType="pubmed">11814038</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1989 Jan;121(1):185-99</Citation><ArticleIdList><ArticleId IdType="pubmed">2563713</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1995 Jul;140(3):1111-27</Citation><ArticleIdList><ArticleId IdType="pubmed">7672582</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2001 Apr;157(4):1789-803</Citation><ArticleIdList><ArticleId IdType="pubmed">11290731</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2004 Jul 22;20(11):1808-11</Citation><ArticleIdList><ArticleId IdType="pubmed">14988108</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 1995 May;90(6):776-86</Citation><ArticleIdList><ArticleId IdType="pubmed">24172919</ArticleId></ArticleIdList></Reference><Reference><Citation>Heredity (Edinb). 1998 Mar;80 ( Pt 3):364-73</Citation><ArticleIdList><ArticleId IdType="pubmed">9569640</ArticleId></ArticleIdList></Reference><Reference><Citation>Genet Res. 2003 Feb;81(1):51-64</Citation><ArticleIdList><ArticleId IdType="pubmed">12693683</ArticleId></ArticleIdList></Reference><Reference><Citation>Heredity (Edinb). 1992 Oct;69(4):315-24</Citation><ArticleIdList><ArticleId IdType="pubmed">16718932</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2005 Nov;171(3):1365-76</Citation><ArticleIdList><ArticleId IdType="pubmed">16020786</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1990 Apr;124(4):979-93</Citation><ArticleIdList><ArticleId IdType="pubmed">2323560</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 2002 Nov;105(6-7):1043-1049</Citation><ArticleIdList><ArticleId IdType="pubmed">12582932</ArticleId></ArticleIdList></Reference><Reference><Citation>Biometrics. 1982 Sep;38(3):623-40</Citation><ArticleIdList><ArticleId IdType="pubmed">7171692</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1995 Jul;140(3):1137-47</Citation><ArticleIdList><ArticleId IdType="pubmed">7672584</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetica. 1997;101(1):47-58</Citation><ArticleIdList><ArticleId IdType="pubmed">9465409</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1994 Apr;136(4):1457-68</Citation><ArticleIdList><ArticleId IdType="pubmed">8013918</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1993 Sep;135(1):205-11</Citation><ArticleIdList><ArticleId IdType="pubmed">8224820</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1999 Jan;151(1):297-303</Citation><ArticleIdList><ArticleId IdType="pubmed">9872968</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2000 Oct;156(2):899-911</Citation><ArticleIdList><ArticleId IdType="pubmed">11014835</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1994 Nov;138(3):963-71</Citation><ArticleIdList><ArticleId IdType="pubmed">7851788</ArticleId></ArticleIdList></Reference><Reference><Citation>J Dairy Sci. 2000 May;83(5):1125-34</Citation><ArticleIdList><ArticleId IdType="pubmed">10821589</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2004 Mar;166(3):1541-51</Citation><ArticleIdList><ArticleId IdType="pubmed">15082567</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome. 2002 Feb;45(1):28-33</Citation><ArticleIdList><ArticleId IdType="pubmed">11908665</ArticleId></ArticleIdList></Reference><Reference><Citation>Genet Res. 2002 Jun;79(3):235-45</Citation><ArticleIdList><ArticleId IdType="pubmed">12220131</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1998 Nov;150(3):1257-65</Citation><ArticleIdList><ArticleId IdType="pubmed">9799277</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Hum Genet. 1974 Jul;26(4):489-503</Citation><ArticleIdList><ArticleId IdType="pubmed">4842773</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2001 Oct 11;413(6856):628-31</Citation><ArticleIdList><ArticleId IdType="pubmed">11675785</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1999 Jul;152(3):1203-16</Citation><ArticleIdList><ArticleId IdType="pubmed">10388834</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Tian, Quan" sort="Tian, Quan" uniqKey="Tian Q" first="Quan" last="Tian">Quan Tian</name><name sortKey="Xu, Shizhong" sort="Xu, Shizhong" uniqKey="Xu S" first="Shizhong" last="Xu">Shizhong Xu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Yang, Runqing" sort="Yang, Runqing" uniqKey="Yang R" first="Runqing" last="Yang">Runqing Yang</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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