A Genome-Wide Association Study of Age at First Calving and Calving Interval Trait in Hanwoo Cow (Korean Brown Cattle)

In this study, we conducted a Genome Wide Association Study (GWAS) analysis of the reproductive traits in Hanwoo cows, Age at First Calving (AFC) and Calving Interval (CI), aiming to pinpoint candidate genes and their functional relevance. A total of 24,977 Hanwoo cows from commercial farms were genotyped using Axiom Bovine 60k version 3 (Affymetrix Inc, 2006). Subsequently, individuals with genotype and phenotype data were selected from this population, resulting in 9,508 cows and 37,999 SNPs for AFC, and 6,442 cows and 38,379 SNPs for CI after Quality Control. Bonferroni correction and False Discovery Rate (FDR) correction were applied to GWAS thresholds, leading to the identification of significant SNP markers for each trait by chromosome. AFC revealed seven SNP markers on five chromosomes, and CI identified three SNP markers on three chromosomes. Sixteen candidate genes were identified from these ten significant SNP markers. Notably, TRNAC-GCA was highlighted as a gene influencing semen quality in bovines and playing a crucial role in cow reproductive traits. Additionally, Gene Ontology (GO) was identified two GO IDs, respectively, in Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) (BP: GO:0030259, GO:0005975; CC: GO:0031982, GO:0005794; MF: GO:0016758, GO:0016757), with no KEGG pathway being identified. These results contribute to advanced understanding of the genetic architecture of reproductive traits and offer valuable SNP markers for breeding programs in Hanwoo cow.