Genome-wide association study for carcass traits in Hanwoo cattle using additional relatives' information of non-genotyped animals

Abstract

The aim of this study was to find significant genomic regions associated with carcass traits in Hanwoo cattle and to compare the benefit of using additional information from non-genotyped animals. Imputed whole-genome sequence data were used along with phenotypic data on 13 715 genotyped animals as well as phenotypes of 440 284 non-genotyped animals that were offspring of 454 genotyped sires. For carcass weight, 15 083 SNPs in 33 QTL regions and 313 candidate genes were identified. We found 410 SNPs in 17 QTL regions containing 122 candidate genes for back fat thickness. In total, 656 SNPs in 19 QTLs with 137 candidate genes for eye muscle area and 79 SNPs in 12 QTL regions with 77 candidate genes were identified for marbling score. The most important candidate genes included <i>ZFAT</i>, <i>TG</i>, <i>PLAG1</i>, <i>CHCHD7</i>, and <i>TOX</i> for carcass weight and eye muscle area, <i>NOG</i> for back fat thickness, and <i>EVOVL5</i> for marbling score. This study showed that the use of phenotypic records on non-genotyped progeny along with imputed whole-genome sequence data increased the power of detecting new significant genomic regions.