Genome-wide association study identifies significant SNPs for milk production and stature traits in Karan Fries cattle.

Crossbreeding indigenous cattle with high-yielding exotic breeds has been a key strategy in Indian dairy systems for increasing milk production. The Karan Fries (KF), a stabilised dairy cattle population derived from the Tharparkar and Holstein Friesian breeds, serves as a valuable genetic resource in India. Despite their adaptability and performance, the genomic architecture underpinning milk traits and stature in KF cattle remains largely unexplored. Therefore, a genome-wide association study (GWAS) was conducted using 777 K SNP genotyping data and estimated breeding values (EBVs) as the dependent variable for four economically important dairy traits: first lactation total milk yield (FLTMY), total fat yield (TFY), total solids-not-fat yield (TSNFY), and stature. After quality control and LD pruning, 347,621 SNPs across 355 KF animals were analysed, revealing 54 significant single-nucleotide polymorphisms (SNPs) associated with these traits, with several exhibiting pleiotropic effects. Candidate genes such as EPHA7, SCFD2, DCUN1D4, CWH43, ZMAT4, KYNU, GINS4, GPAT4, GOLGA7, and OCIAD1 were associated with milk yield and compositional traits, while CBLB, CCDC14, ALCAM, MALRD1, and MUC13 were linked to stature. Protein-protein interaction network analysis identified functionally connected gene clusters involved in lactation, fat metabolism, and structural development. These results provide preliminary insights into the genomic architecture of KF cattle and highlight candidate genes associated with milk production and stature traits. While exploratory in nature, these findings may serve as a starting point for future validation and the development of genomic selection strategies in tropical dairy cattle.