Bayesian shrinkage mapping for multiple QTL in half-sib families

Recently, an effective Bayesian shrinkage estimation method has been proposed for mapping QTL in inbred line crosses. However, with regard to outbred populations, such as half-sib populations with maternal information unavailable, it is not straightforward to utilize such a shrinkage estimation for QTL mapping. The reasons are: (1) the linkage phase of markers in the outbred population is usually unknown; and (2) only paternal genotypes can be used for inferring QTL genotypes of offspring. In this article, a novel Bayesian shrinkage method was proposed for mapping QTL under the half-sib design using a mixed model. A simulation study clearly demonstrated that the proposed method was powerful for detecting multiple QTL. In addition, we applied the proposed method to map QTL for economic traits in the Chinese dairy cattle population. Two or more novel QTL harbored in the chromosomal region were detected for each trait of interest, whereas only one QTL was found using traditional maximum likelihood analyses in our earlier studies. This further validated that our shrinkage estimation method could perform well in empirical data analyses and had practical significance in the field of linkage studies for outbred populations.