Major loci associated with growth traits on BTA14 in Hanwoo (Korean cattle)

Abstract Text: Genome-wide single marker regression using Bovine 50K BeadChip was performed on growth traits from 1,012 Hanwoo steers in Hanwoo (Korean Cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cutoff p-value of 1E^-5. Unmapped and SNPs on sex chromosomes were also excluded. A total of 32,696 SNPs were used in this analysis. To test an association between SNP and QTL, single marker regression analysis was implemented in this study. SNP was assumed to be in LD with QTL in close proximity and the effect evaluated was additive effect (QTL allele substitution effect). The Bonferroni-corrected genome wide significant association (P<1.5×10^-6) was applied to detect significant SNPs for the GWAS. The GWAS identified one major QTL for body weight at 6, 12, 18 and 23 months ranging 23Mb to 25Mb on BTA14. The most significant SNP was Hapmap32241-BTC-054753 (24Mb, P=1.8×10^-6) for BW6, Hapmap27934-BTC-065223 (25Mb, P=1.2×10^-10) for BW12, BW18 and BW23 in Hanwoo. The most significant SNPs accounted for 8 to 10% of additive genetic variance, which is quite large proportion against total additive genetic variance. The Hapmap27934-BTC-065223 has 12.97 kg of allele substitution effect in body weight at 12 months (BW12). The results revealed that growth traits was affected by major QTL with large effect and many other SNP with small effects with the normal distribution.

Keywords: GWAS, Major loci, BTA14