Genome-Wide Association Study in the Holstein Cattle Population Highlights Candidate Variants for Milk Production Traits

Abstract

Understanding the genetic basis of production traits in dairy cattle is important for both improving productivity and its economic significance. Although genome-wide association studie has been widely used internationally to investigate the genetic factors of milk production traits, limited genomic data are available for the Holstein cattle population. In this study, the most comprehensive genomic analysis conducted in T & uuml;rkiye to date, we aimed to identify single-nucleotide polymorphisms (SNPs) associated with milk yield (MY), fat yield (FY), protein yield (PY), and milking speed (MS) in the Holstein cattle population. Data were obtained from 79 dairy herds comprising 17 166 cows born between 2012 and 2019, as provided by the Cattle Breeders' Association of T & uuml;rkiye. Genotyping was performed using the Affymetrix Axiom Bovine 54K SNP Chip; after quality control procedures, 15 288 cows and 31 944 SNPs were included in the analysis. A total of 7 SNPs were identified as significantly associated with the studied traits. Two SNPs on BTA14 (rs109146371 and rs109350371) were significantly associated with 305MY. A significant SNP associated with PY (rs41718954) was identified on BTA14, and another SNP (rs10451141) on BTA18 showed a significant association with FY. Additionally, three SNPs significantly associated with MS were detected on BTA2, BTA11, and BTA12 (rs29009916, rs109459144, and rs42647772). Notably, the association of four SNPs (rs10451141 for FY, and rs29009916, rs109459144, and rs42647772 for MS) was identified for the first time in this study. These variants were located near genes with potential roles in mammary gland function and milk component synthesis. These variants are located near genes potentially involved in mammary gland function and milk component synthesis. Although identified in the Holstein cattle population, these findings have international relevance and applicability due to the importation of semen from various countries. Ultimately, this study contributes to the development of effective selection strategies for specific populations and provides valuable insights into the genetics of milk production traits on a global scale. (c) 2025 The Author(s). Published by Elsevier B.V. on behalf of The animal Consortium. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).