Identification of Genome-wide Single Nucleotide Polymorphisms in Indigenous Cattle Breeds of Tamil Nadu

Abstract

Background: Indigenous cattle are well adapted to the hot tropical climate. Conservation and genetic improvement in the indigenous cattle breeds have become a necessity due to the changing climatic condition. Genome-based research in indigenous cattle for in-depth characterization of genetic variants will help in the improvement of economically important traits in these cattle breeds. Methods: Blood samples were collected for five indigenous cattle breeds of Tamil Nadu from their breeding tracts. Pooled DNA samples were sequenced using the Illumina platform. Short sequences were aligned using BWA, variant calling and annotation were done using GATK and snpEff respectively. Result: This study identified 29,366,340 variants, which include 25,944,935 SNPs and 3,421,405 indels with a variant rate of 91 bp across the genome. Around 215,820 SNPs were present in the coding region of 5,572 genes. This study will provide the framework for further genetic analysis of phenotypic variations in economically important traits in native cattle of Tamil Nadu.