Genome-Wide Association Study of Insertions and Deletions Identified Novel Loci Associated with Milk Production Traits in Dairy Cattle

Genome-wide association study (GWAS) have identified a large number of SNPs associated with milk production traits in dairy cattle. Behind SNPs, INDELs are the second most abundant genetic polymorphisms in the genome, which may exhibit an independent association with complex traits in humans and other species. However, there are no reports on GWASs of INDELs for milk production traits in dairy cattle. In this study, using imputed sequence data, we performed INDEL-based and SNP-based GWASs for milk production traits in a Holstein cattle population. We identified 58 unique significant INDELs for one or multiple traits. The majority of these INDELs are in considerable LD with nearby significant SNPs. However, through conditional association analysis, we identified nine INDELs which showed independent associations. Genomic annotations of these INDELs indicated some novel associated genes, i.e., TRNAG-CCC, EPPK1, PPM1K, PTDSS1, and mir-10163, which were not reported in previous SNP-based GWASs. Our findings suggest that INDEL-based GWASs could be valuable complement to SNP-based GWASs for milk production traits.