Genome-Wide Association Study Identifies Major Loci for Carcass Weight on BTA14 in Hanwoo (Korean Cattle)

Abstract

This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10ˉ⁶) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was 'BTB-01280026' (P = 4.02×10ˉ¹¹), located in the 25Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were 'Hapmap27934-BTC-065223' (P = 4.04×10ˉ¹¹) in 25.2 Mb, 'BTB-01143580' (P = 6.35×10ˉ¹¹) in 24.3 Mb, 'Hapmap30932-BTC-011225' (P = 5.92×10ˉ¹⁰) in 24.8 Mb, 'Hapmap27112-BTC-063342' (P = 5.18×10ˉ⁹) in 25.4 Mb, and 'Hapmap24414-BTC-073009' (P = 7.38×10ˉ⁸) in 25.4 Mb, all on BTA 14. One SNP ('BTB-01143580'; P = 6.35×10ˉ¹¹) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP ('BTB-01280026'; P = 4.02×10ˉ¹¹) had 16.96 kg of allele substitution effect, and the second most significant SNP ('Hapmap27934-BTC-065223'; P = 4.04×10ˉ¹¹) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.