Towards the Identification of Gene Candidates for Maternal Effects on Weaning Weight in Six Beef Cattle Breeds

Detection of quantitative trait loci was carried out for maternal effect on weaning weight in French Charolais, Limousin, Blonde d’Aquitaine, Partenaise, Aubrac and Salers breeds using a Bayesian Variable Selection method.

A total of 2,540 animals were genotyped (87%) or imputed (13%) for 706,791 SNPs located on the Illumina BovineHD BeadChip®. These samples included 795 Charolais, 601 Limousin, 387 Blonde d’Aquitaine, 299 Aubrac, 263 Parthenais and 198 Salers animals, that were mainly well proven bulls. SNPs were mapped onto the UMD 3.1 bovine whole-genome sequence assembly.

In total 706 QTLs were identified across the six breeds, number ranging from 56 QTLs in Limousin to 275 QTLs in Charolais cattle. Only 30% of those QTLs were detected at least in 2 breeds and never in more than 4 out of the 6 breeds analyzed. Most of the main QTLs were breed specific. For instance, among the 26 largest QTLs found in Charolais (Bayes factor above 400), only 8 QTLs were detected in another breed; including 3 detected in three different breeds. Only one major QTL in Charolais breed was evidenced as a major QTL in another breed (Salers) and contains IGF-I as a very likely causative candidate gene. In total, 50 QTLs regions were fine mapped with 14 harbouring only a single candidate gene, 10 with only 2 genes and 8 with only 3 candidate genes.