Bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among Oryza sativa L. germplasms.
Association mapping can be a powerful tool for detecting quantitative trait loci (QTLs) without requiring line-crossing experiments. We previously proposed a Bayesian approach for simultaneously mapping multiple QTLs by a regression method that directly incorporates estimates of the population structure. In the present study, we extended our method to analyze ordinal and censored traits, since both types of traits are common in the evaluation of germplasm collections. Ordinal-probit and tobit models were employed to analyze ordinal and censored traits, respectively. In both models, we postulated the existence of a latent continuous variable associated with the observable data, and we used a Markov-chain Monte Carlo algorithm to sample the latent variable and determine the model parameters. We evaluated the efficiency of our approach by using simulated- and real-trait analyses of a rice germplasm collection. Simulation analyses based on real marker data showed that our models could reduce both false-positive and false-negative rates in detecting QTLs to reasonable levels. Simulation analyses based on highly polymorphic marker data, which were generated by coalescent simulations, showed that our models could be applied to genotype data based on highly polymorphic marker systems, like simple sequence repeats. For the real traits, we analyzed heading date as a censored trait and amylose content and the shape of milled rice grains as ordinal traits. We found significant markers that may be linked to previously reported QTLs. Our approach will be useful for whole-genome association mapping of ordinal and censored traits in rice germplasm collections.
Iwata
Hiroyoshi
H
Data Mining and Grid Research Team, National Agricultural Research Center, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8666, Japan. iwatah@affrc.go.jp
Ebana
Kaworu
K
Fukuoka
Shuichi
S
Jannink
Jean-Luc
JL
Hayashi
Takeshi
T
D001499:Bayes Theorem; D002874:Chromosome Mapping / Q000379:methods*; D018556:Crops, Agricultural / Q000235:genetics; D014644:Genetic Variation; D005854:Germ Cells / Q000502:physiology*; D015233:Models, Statistical; D012275:Oryza / Q000235:genetics*; D012150:Polymorphism, Restriction Fragment Length; D040641:Quantitative Trait Loci; D012372:ROC Curve