Genomic clues of association between clinical mastitis and SNPs identified by ddRAD sequencing in Murrah buffaloes

The total milk production of India is 209.96 MT out of which 45% is contributed by the indigenous buffalo and due to their high producing virtue, the prevalence of mastitis is 5-20%. Despite the increasing level of technological advancement, mastitis is still an issue of concern for dairy industry in India as well as across the world. Therefore, the present study aimed to identify the SNPs and associate them with the incidence of clinical mastitis in Murrah buffalo using the ddRAD sequencing approach taking mastitis incidence data of 96 Murrah buffaloes. A total of 246 million quality controlled reads were obtained with an average alignment rate of 99.01% and at a read depth of 10, quality controlled SNPs obtained were 18,056. The logistic regression model was used and a total of seven SNPs were found significantly associated (p < 0.001) with mastitis incidence and seven genes were identified viz., NCBP1, FOXN3, TPK1, XYLT2, CPXM2, HERC1, and OPCML. The majority of them were having tumor suppressing action, related to immunogenetics or glycolytic and energy production. Conclusively, the SNPs identified in this study may be useful for future studies on mastitis incidence in Murrah buffalo and the SNP associations can be further validated.