Mapping multiple Quantitative Trait Loci by Bayesian classification.
We developed a classification approach to multiple quantitative trait loci (QTL) mapping built upon a Bayesian framework that incorporates the important prior information that most genotypic markers are not cotransmitted with a QTL or their QTL effects are negligible. The genetic effect of each marker is modeled using a three-component mixture prior with a class for markers having negligible effects and separate classes for markers having positive or negative effects on the trait. The posterior probability of a marker's classification provides a natural statistic for evaluating credibility of identified QTL. This approach performs well, especially with a large number of markers but a relatively small sample size. A heat map to visualize the results is proposed so as to allow investigators to be more or less conservative when identifying QTL. We validated the method using a well-characterized data set for barley heading values from the North American Barley Genome Mapping Project. Application of the method to a new data set revealed sex-specific QTL underlying differences in glucose-6-phosphate dehydrogenase enzyme activity between two Drosophila species. A simulation study demonstrated the power of this approach across levels of trait heritability and when marker data were sparse.
Zhang
Min
M
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.
Montooth
Kristi L
KL
Wells
Martin T
MT
Clark
Andrew G
AG
Zhang
Dabao
D
D000818:Animals; D001499:Bayes Theorem; D002874:Chromosome Mapping; D004330:Drosophila; D005819:Genetic Markers; D005954:Glucosephosphate Dehydrogenase / Q000235:genetics; D001467:Hordeum / Q000235:genetics; D016014:Linear Models; D008957:Models, Genetic; D015233:Models, Statistical; D015999:Multivariate Analysis; D040641:Quantitative Trait Loci; D013045:Species Specificity; D013223:Statistics as Topic / Q000379:methods; D013997:Time Factors
D005819:Genetic Markers; D005954:Glucosephosphate Dehydrogenase