Genome-wide evaluation for quantitative trait loci under the variance component model

ISSN： 0016-6707

Source： Genetica, Vol.138, Iss.9-10, 2010-10, pp. : 1099-1109

Disclaimer: Any content in publications that violate the sovereignty, the constitution or regulations of the PRC is not accepted or approved by CNPIEC.

Previous Menu Next

Abstract

The identity-by-descent (IBD) based variance component analysis is an important method for mapping quantitative trait loci (QTL) in outbred populations. The interval-mapping approach and various modified versions of it may have limited use in evaluating the genetic variances of the entire genome because they require evaluation of multiple models and model selection. In this study, we developed a multiple variance component model for genome-wide evaluation using both the maximum likelihood (ML) method and the MCMC implemented Bayesian method. We placed one QTL in every few cM on the entire genome and estimated the QTL variances and positions simultaneously in a single model. Genomic regions that have no QTL usually showed no evidence of QTL while regions with large QTL always showed strong evidence of QTL. While the Bayesian method produced the optimal result, the ML method is computationally more efficient than the Bayesian method. Simulation experiments were conducted to demonstrate the efficacy of the new methods.