Genetic characterization and identification of single nucleotide polymorphisms of ATP1A1 gene in Indian humped cattle

Abstract

Climate change in India is likely to aggravate the heat stress in dairy animals due to rise in temperature coupled with increased precipitation. In animals heat stress affects the alteration of plasma Potassium (K (+)) and Sodium Na (+) ions. ATP1A1 gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na+ and K+ ions across the plasma membrane. The present study is aimed to investigate the polymorphisms in the entire coding region of ATP1A1 gene in Bos indicus (Deoni) cattle by PCR- Single-Strand Conformation Polymorphism (PCR- SSCP) and direct sequencing of variants. Sequence analysis showed 16 SNPs, of which 5 SNPs were in the coding region and the remaining 11 SNPs were detected in the non-coding region of ATP1A1 gene. All the observed variations in the coding regions of ATP1A1 gene were silent mutations. The genotypic, allelic frequencies, c<sup>2</sup> test for Hardy-Weinberg equilibrium and Shannon’s information index were calculated using POPGENE-32. The study revealed a high degree of genetic variability in ATP1A1 gene in the Deoni cattle population which indicated the utility of this gene for further studies for identification of markers associated with heat tolerance in Indian humped cattle for using in marker assisted selection for heat tolerance.