Short communication: new alleles of the bovine kappa-casein gene revealed by resequencing and haplotype inference analysis.

We tested the hypothesis that extensive undiscovered genetic diversity exists in important functional genes from domestic and wild cattle species (Bos spp.). We resequenced 483 bp of a key exon (exon IV) from the kappa (kappa)-casein gene (CSN3) for a panel of samples of domestic cattle from 8 countries and a close relative species, the gayal (Bos frontalis). Six single nucleotide polymorphisms were identified. Haplotype inference revealed 12 haplotypes, of which 8 were newly discovered. Among these 8 new haplotypes, 5 differed by one nonsynonymous mutation and 3 differed by one silent mutation from previously well-characterized CSN3 alleles. From those, one was shared by the gayal and Zebu, was different from CSN3*B at position Ile136Thr, and showed a close phylogenetic relationship with the banteng, gaur, and yak. The other 7 new haplotypes were detected in our panel of worldwide local cattle breeds but were absent from previously reported commercial breeds. These results support the hypothesis that genetic diversity at the coding region of CSN3 has been underestimated. This study also highlights how important it is to resequence functionally important genes in worldwide local cattle breeds, many of which are threatened by extinction or replacement by commercial breeds.