Genome-wide association study identifies three loci for intramuscular fat in Hanwoo (Korean cattle)

Abstract

This study identified 59 SNPs significantly (P<0.001) associated with IMF using a genome-wide SNP panel, validating three SNPs using a validation dataset. The largest numbers (9 SNPs, 15% of the total significantly associated SNPs) of SNPs significantly associated with IMF were in BTA1. Of these, five were located between BTA1:22-27. Mb and three were between BTA1:82-85. Mb. The significantly associated SNPs accounted for only 3-5% of additive genetic variance. In the validation dataset, 3 SNPs (Hapmap54608-rs29020417, ARS-BFGL-NGS-5976 and Hapmap47624-BTA-44484) that showed an association with IMF in the single-point GWAS were significantly, positively associated with percent IMF (favorable alleles). One SNP (ARS-BFGL-NGS-29493) was significantly negatively associated (unfavorable allele). This study found that, in Hanwoo cattle, three loci were associated with IMF using GWAS and a validation dataset. The 3 SNPs explain 5.4% of phenotypic variation for IMF in Hanwoo commercial steers. In conclusion, IMF had a high heritability (0.5) but was expected to be affected by many loci with small effects.