Genome-Wide Association Study to Identify QTL for Carcass Traits in Korean Hanwoo Cattle

Abstract

This study aimed to identify genetic associations with carcass traits in Hanwoo cattle using a genome-wide association study. A total of 9302 phenotypes were analyzed, and all animals were genotyped using the Illumina Bovine 50K v.3 SNP chip. Heritabilities for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) were estimated as 0.42, 0.36, 0.36, and 0.47, respectively, using the GBLUP model, and 0.47, 0.37, 0.36, and 0.42, respectively, using the Bayes B model. We identified 129 common SNPs using DGEBV and 118 common SNPs using GEBV on BTA6, BTA13, and BTA14, suggesting their potential association with the traits of interest. No common SNPs were found between the GBLUP and Bayes B methods when using residuals as a response variable in GWAS. The most promising candidate genes for CWT included <i>SLIT2</i>, <i>PACRGL</i>, <i>KCNIP4</i>, <i>RP1</i>, <i>XKR4</i>, <i>LYN</i>, <i>RPS20</i>, <i>MOS</i>, <i>FAM110B</i>, <i>UBXN2B</i>, <i>CYP7A1</i>, <i>SDCBP</i>, <i>NSMAF</i>, <i>TOX</i>, <i>CA8</i>, <i>LAP3</i>, <i>FAM184B</i>, and <i>NCAPG</i>. For EMA, the genes <i>IBSP</i>, <i>LAP3</i>, <i>FAM184B</i>, <i>LCORL</i>, <i>NCAPG</i>, <i>SLC30A9</i>, and <i>BEND4</i> demonstrated significance. Similarly, <i>CYP7B1</i>, <i>ARMC1</i>, <i>PDE7A</i>, and <i>CRH</i> were associated with BF, while <i>CTSZ</i>, <i>GNAS</i>, <i>VAPB</i>, and <i>RAB22A</i> were associated with MS. This finding offers valuable insights into genomic regions and molecular mechanisms influencing Hanwoo carcass traits, aiding efficient breeding strategies.