The use of genetic markers to improve milk and udder health traits in dairy cattle are rapidly growing worldwide. This study was designed to evaluate genetic associations of markers from a SNP-Chip including 20 SNPs in eight candidate genes, namely JAK2, TRAPPC9, DGAT1, LAG3, STAT5A, STAT5B, CD4 and PTK2, with milk production and mastitis resistance traits in four dairy cattle breeds. The study included 420 lactating dairy cows (Holstein Friesian and indigenous Achai, Red Sindhi, and Sahiwal) that were genotyped using the Chinese Cow’s SNPs Chip-1 (CCSC-1). Out of the 20 SNPs evaluated, 13 SNPs were significantly associated with milk and/or udder health traits. Also, genetic associations varied across breeds, with certain SNPs being significantly associated with one or multiple breeds. In Holstein Friesian the CC genotype (SNP 7 on TRAPPC9 gene) increased 305 milk yield and reduced the incidence of clinical mastitis. Also in Red Sindhi, the CC genotype (SNP 14 on DGAT1 gene) increased 305 milk yield, protein (%), and lactose (%), and reduced the level of somatic cell score. Candidate genes such as JAK2 in Achai, JAK2 and LAG3 in Holstein Friesian, and CD4 in Sahiwal were significantly associated with the presence of Staphylococcus aureus isolated from raw milk. These results infer that genetic markers located on candidate genes present in CCSC-1 could be potentially used in genetic selection to improve milk production and mastitis resistance in dairy cattle breeds of Pakistan.

To Cite This Article: Kamal M, Martinez-Boggio G, Rafiq N, Yu Y, Peñagaricano F and Usman T, 2025. Genetic association of candidate genes with milk and mastitis resistance traits using SNP-Chip array in Holstein Friesian and Pakistani indigenous dairy cattle breeds. Pak Vet J. http://dx.doi.org/10.29261/pakvetj/2025.119