Large-scale, multibreed, multitrait analyses of quantitative trait loci experiments: the case of porcine X chromosome.

A QTL analysis of multibreed experiments (i.e., crossed populations involving more than two founder breeds) offers clear advantages over classical two-breed crosses, among them increased power and a more comprehensive coverage of the total genetic variability in the species. An alternative to designed multibreed crosses is to reanalyze jointly several experiments involving different breeds. We report a multibreed, multitrait QTL analysis of SSCX that involves five different crosses, six breeds, and almost 3,000 genotyped individuals using a truly multibreed strategy to allow for any number of founder breed origins. Traits analyzed were growth, fat thickness, carcass length, and shoulder and ham weights. Generally, the joint analysis resulted in more significant QTL than the single-experiment analyses. We show that the QTL for fatness, which is highly significant (nominal P < 10(-43)), is of Asiatic origin (Meishan). The next most significant QTL (nominal P < 10(-15)) affected ham weight and seems to be segregating only between Large White and the rest of the breeds. A multitrait, multi-QTL analysis suggests that these are two distinct loci. Additionally, a locus segregating only between Iberian and Landrace affects live weight. The advantages of joint, multibreed analyses clearly outweigh their potential risks.