Genetic Polymorphism of Kappa Casein Gene in Tharparkar Cattle of Pakistan

Kappa casein protein is encoded by the CSN3 gene and its polymorphism impacts the quality of milk and cheese.Genetic polymorphism of CSN3 gene in Tharparkar cattle was detected through RFLP, multiple sequence alignment and phylogenetic analysis.PCR-RFLP analysis was done by using the restriction enzyme Hinf1, animals were genotyped as AA and AB genotypes with alleles A and B with frequencies of genotype AA (0.84) and AB (0.16) while allele A (0.91) and B (0.09), respectively.The multiple sequence alignment of representative samples was done among the nucleotide sequences, and the results showed five SNPs at eight different sites, 68-T/C, 69-A/T, 308-T/C, 311-C/T, 347-A/C, 354-A/G, 408-A/G and 416-A/T in CSN3 gene of Tharparkar cattle.While comparison of nucleotide sequences of Tharparkar cattle with published sequences of Sahiwal cattle, also revealed six SNPs at eight different sites 68-T/C, 69-T/C, 308-T/C, 311-C/T, 347-A/C, 354-A/G, 408-A/G and 416-A/T.The phylogenetic analysis of partial segment of CSN3 gene in Tharparkar cattle revealed the close breed relationship among studied animals.It is concluded that Tharparkar cattle belongs to bos indicus class and mostly contains AA and AB genotypes of CSN3 gene.Besides SNPs found through sequencing have effect on protein translation, which may directly influence protein content of milk and quality of cheese.