Single nucleotide polymorphism in cytochrome B oxidase gene among indigenous cattle breeds of Tamil Nadu

Abstract

The present study was carried out to validate the single nucleotide polymorphism (SNP) in mitochondrial gene- cytochrome b oxidase at 14,716 bp (C to T transition) position obtained from whole genome sequence data of indigenous cattle breeds at Department of Animal Genetics and Breeding, Madras Veterinary College, Tamil Nadu. A total of 288 animals, viz. Alambadi (16), Bargur (99), Kangayam (54), Pulikulam (58) and Umblachery (61) were genotyped. The wild type allele C was observed to be fixed in all the breeds except Kangayam cattle. The gene frequency of C and T alleles and genotype frequencies of CC, CT and TT were estimated in Kangayam breed of cattle and chi-square test revealed the population in Hardy- Weinberg disequilibrium at CYTB locus. Phylogenetic analysis showed that the indigenous cattle breeds were present under the same genetic ancestry of Bos indicus reference genome, while the Bos taurus reference genome diverged separately. From this study, the possibilities of selective sweep or population expansion after a recent bottleneck among the indigenous cattle breeds of Tamil Nadu could be concluded.

Keywords

• Cytochrome b oxidase, Mitochondrial DNA, Indigenous breed, SNP