Identification of quantitative trait loci affecting economic traits based on divergently selected genomic regions between beef and dairy cattle

In our previous study, we examined divergently selected regions between Japanese Black cattle and Holstein cattle based on a 50k single nucleotide polymorphism (SNP) panel and a Sliding Window Allele Difference method resulting in the identification of 11 genomic regions. The aim of the present study was to investigate the association between these genomic regions and economic traits, including seven carcass and five milk production traits. For this purpose, representative SNP markers were selected from the 11 genomic regions and used to estimate the effects on the traits in Japanese Black cattle (N=488) and Holstein cattle (N=194). Association analyses revealed that five SNPs showed a significant effect on the carcass traits in Japanese Black cattle and other five SNP showed a significant association with milk production traits in Holstein cattle (P<0.05). These results indicated that divergently selected regions identified using a Sliding Window Allele Difference method contain the quantitative trait loci (QTL) for economic traits. Furthermore, most of the QTL identified in this study were consistent with the previously reported QTL. Further investigations of these regions may lead to the identification of the genes and polymorphisms responsible for the economic traits.