Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows

<p><strong>Background</strong></p> <p>Conducting genome-wide association studies (GWAS) for reproductive traits in Hanwoo cattle, including age at first calving (AFC), calving interval (CI), gestation length (GL), and number of artificial inseminations per conception (NAIPC), is of paramount significance. These analyses provided a thorough exploration of the genetic basis of these traits, facilitating the identification of key markers for targeted trait improvement. Breeders can optimize their selection strategies, leading to more efficient and sustainable breeding programs, by incorporating genetic insights. This impact extends beyond individual traits and contributes to the overall productivity and profitability of the Hanwoo beef cattle industry. Ultimately, GWAS is essential in ensuring the long-term genetic resilience and adaptability of Hanwoo cattle populations. The primary goal of this study was to identify significant single nucleotide polymorphisms (SNPs) or quantitative trait loci (QTLs) associated with the studied reproductive traits and subsequently map the underlying genes that hold promise for trait improvement.</p> <p><strong>Results</strong></p> <p>A genome-wide association study of reproductive traits identified 68 significant single nucleotide polymorphisms (SNPs) distributed across 29 <em>Bos taurus</em> autosomes (BTA). Among them, BTA14 exhibited the highest number of identified SNPs (25), whereas BTA6, BTA7, BTA8, BTA10, BTA13, BTA17, and BTA20 exhibited 8, 5, 5, 3, 8, 2, and 12 significant SNPs, respectively. Annotation of candidate genes within a 500 kb region surrounding the significant SNPs led to the identification of ten candidate genes relevant to age at first calving. These genes were: <em>FANCG</em>, <em>UNC13B</em>, <em>TESK1</em>, <em>TLN1</em>, and <em>CREB3</em> on BTA8; <em>FAM110B</em>, <em>UBXN2B</em>, <em>SDCBP</em>, and <em>TOX</em> on BTA14; and <em>MAP3K1</em> on BTA20. Additionally, <em>APBA3</em>, <em>TCF12</em>, and <em>ZFR2</em>, located on BTA7 and BTA10, were associated with the calving interval; <em>PAX1</em>, <em>SGCD</em>, and <em>HAND1</em>, located on BTA7 and BTA13, were linked to gestation length; and <em>RBM47</em>, <em>UBE2K</em>, and <em>GPX8</em>, located on BTA6 and BTA20, were linked to the number of artificial inseminations per conception in Hanwoo cows.</p> <p><strong>Conclusions</strong></p> <p>The findings of this study enhance our knowledge of the genetic factors that influence reproductive traits in Hanwoo cattle populations and provide a foundation for future breeding strategies focused on improving desirable traits in beef cattle. This research offers new evidence and insights into the genetic variants and genome regions associated with reproductive traits and contributes valuable information to guide future efforts in cattle breeding.</p>