Beyond Genome Wide Association Tests in the Livestock Industry: Genetic Architecture of Growth and Carcass Weight in Hanwoo

Abstract

Genome-wide association study was performed on data from 1,012 Hanwoo steers derived from 118 sire using Bovine 50K BeadChip 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 1-15. Unmapped and SNPs on sex chromosomes were also excluded. A total of 32,696 SNPs were included in the 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 number of significant SNP at a threshold of P<0.001 was ranged 4 to 47 for body weight at different growth stage and carcass weight. The false positive rate (FDR) was much higher in body weight at different stage (50 % to 88%) than in carcass weight (8% to 66%) in Hanwoo. For body weight at different age, significant SNP were spread out across chromosome but some of significant SNP (ARS-BFGL-NGS-101465 on BTA8 and ARS-BFGL-NGS-87371 on BTA21) was shown highly significant effects. As for the distribution of size of SNP effects, most of significant SNP for body weight at different age have small effects (2 to 5% of additive genetic variance) against total additive genetic variance. However, in carcass weight (CWT), one highly significant chromosome region was mapped to 25Mb of Btau4.0 on BTA14. Most significant SNP (BTB-01280026) explains large additive genetic variance (around 11% of additive genetic variance) and 8.1kg of phenotypic effect in Hanwoo. In conclusion, for the genetic architecture of complex traits (body weight at different age and carcass weight) in Hanwoo, body weight at different age were affected by many loci with small effects across genome but carcass weight will be controlled by one large QTL and many other loci with small effect in Hanwoo.