Identification of the Causative Variations of the Bovine Carcass Weight QTL (CW-1) on Chromosome 14 by Targeted Re-sequencing

We previously performed bovine quantitative trait locus (QTL) mapping for growth and carcass traits using Japanese Black paternal half-sib families. In these studies, a carcass weight QTL, CW-1 on bovine chromosome 14 (BTA 14), was detected in several families and narrowed down to a 1.1-Mb region by identical-by-descent and linkage disequilibrium (LD) mapping. Recent development of genomic tools such as BovineSNP50 BeadChips made possible to perform genome-wide association study (GWAS) in bovine. The GWAS using 1156 Japanese Black steers identified three loci associated with carcass weight. The most significant SNP (p=1.03E-12) resided on BTA 14, but it was located at 1-Mb centromeric from the previously identified CW-1 region. Therefore we reexamined the regions by LD mapping and revised the CW-1 region at 24.5-25.5 Mb on the UMD3.1 assembly. To identify the causative variation, targeted re-sequencing was performed using three Q/q heterozygous sires, three Q-homozygous sires and a q-homozygous steer. Among obtained candidate variations, one non-synonymous SNP and 8 variations (7 SNPs and 1 VNTR) within highly conserved elements (PhastCons score >0.9) were examined for an association with carcass weight. The most significant association was obtained for the variations in the PLAG1-CHCHD7 intergenic region that were recently identified as regulatory QTNs influencing bovine stature [Karim et al. (2011) Nature Genetics]. The Q haplotype of Japanese Black had a mosaic structure of the Q and q haplotypes of the F1 (Holstein x Jersey) sires [Karim et al.], which could genetically identify the causative variations.