The objective of this study was to determine the allele and genotype frequencies of genetic variants in five milk protein genes and estimate the effect of these variants on milk yield in Sahiwal cattle. Genotypes of five milk protein genes (alpha s1 casein, beta casein, kappa casein, alpha lactalbumin and beta lactoglobulin) were detected using SNaPshot genotyping method. All the five milk protein genes studied exhibited polymorphism with high allele frequencies of 0.51 for alpha s1casein C, 0.93 for beta casein A2, 0.92 for kappa casein A, 0.93 for alpha lactalbumin B and 0.91 for beta lactoglobulin B. Statistically significant differences (p > 0.05) were observed in kappa casein genotypes AA (AA) and AB (AC) that is, genotype AB had more milk yield in 1 st lactation (422 kg) and 2 nd lactation (612 kg), respectively. In conclusion, the AB genotype identified in kappa casein gene is associated with higher milk production therefore incorporation of AB and BB genotypes for kappa casein may help to improve the milk yield in Sahiwal cattle population of Pakistan. To the best of our knowledge, this is the first detailed study involving frequency distribution of genetic variants and their effects on milk yield in Bos indicus Sahiwal cattle of Pakistan.

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