Polymorphisms of the kappa casein (CSN3) gene and inference of its variants in water buffalo (Bubalus bubalis)

Kappa casein plays a crucial role in the formation of stable casein micelles and has a key influence on milk-clotting properties. However, current understanding of buffalo CSN3 gene polymorphisms is not sufficient. In this study, the polymorphisms in the complete coding sequence (CDS) of the buffalo CSN3 were detected using PCR product direct sequencing. The CDS of CSN3 for river and swamp buffalo was the same in length, which contained an open reading frame of 573 nucleotides encoding a peptide containing 190 amino acid residues. A total of eight single nucleotide polymorphisms (SNPs) was identified in two types of buffalo. Among them, c.86C>T, c.252G>C, c.445G>A, c.467C>T and c.516A>C were non-synonymous, which leads to p.Pro8Leu, p.Lys63Asn, p.Val128Ile, p.Thr135Ile and p.Glu151Asp substitutions in buffalo kappa casein ([Formula: see text]-CN), respectively. The substitution of p.Thr135Ile may exert a vital effect on the function of buffalo [Formula: see text]-CN. Eleven haplotypes were defined based on the SNPs found in buffalo, and accordingly, seven protein variants and four synonymous variants of buffalo [Formula: see text]-CN were inferred, called variants A, B, B [Formula: see text] , C, C [Formula: see text] , C [Formula: see text] , D, E, F, F [Formula: see text] and G. The variants observed in water buffalo did not exist in the Bos genus. In addition, 14 amino acid differential sites of [Formula: see text]-CN between buffalo and the Bos genus were identified, of which 3 were located at glycosylation sites (80S, 96T, 141S) and 4 at phosphorylation sites (19S, 80S, 96T, 141S). It is speculated that they may lead to differences in the physicochemical properties of [Formula: see text]-CN between buffalo and the Bos genus. This study will lay a foundation for exploring the association between the variation in the CSN3 gene and the lactation traits of buffalo.