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

SIMPLE SUMMARY: Genome-wide association study (GWAS) is a widely used approach to identify genetic variants and genomic regions associated with phenotypes. However, there are limited studies on GWAS that have focused on carcass traits in Korean Hanwoo using large sample sizes and employing residual or genomic estimated breeding value (GEBV) as response variables. Given these circumstances, our study aimed to reexamine GWAS in Hanwoo using a substantial population sample. We performed a simple single-marker regression analysis, utilizing the deregressed genomic estimated breeding value (DGEBV), GEBV, and residual values as response variables in genomic best linear unbiased prediction (GBLUP) and Bayes B methods. Our primary focus was on identifying common single nucleotide polymorphisms (SNPs) using both approaches, as this approach has been rarely reported. Therefore, the objective of this study was to uncover the genetic regions strongly associated with carcass traits in Hanwoo using a large cattle population. We identified 129 common SNPs using DGEBV and 118 common SNPs using GEBV, located on chromosomes 6, 13, and 14, demonstrating their significant associations with the studied carcass traits. The identification of these regions, along with the discovery of potential candidate genes, will contribute to a deeper understanding of the genetic and biological mechanisms underlying carcass traits in the Hanwoo population. 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 SLIT2, PACRGL, KCNIP4, RP1, XKR4, LYN, RPS20, MOS, FAM110B, UBXN2B, CYP7A1, SDCBP, NSMAF, TOX, CA8, LAP3, FAM184B, and NCAPG. For EMA, the genes IBSP, LAP3, FAM184B, LCORL, NCAPG, SLC30A9, and BEND4 demonstrated significance. Similarly, CYP7B1, ARMC1, PDE7A, and CRH were associated with BF, while CTSZ, GNAS, VAPB, and RAB22A were associated with MS. This finding offers valuable insights into genomic regions and molecular mechanisms influencing Hanwoo carcass traits, aiding efficient breeding strategies.