Genetic polymorphism in the HSP90AA1 gene revealed in indigenous cattle adapted to tropical coastal climate

Heat stress proteins are important factors in protecting the cells of animals and humans against environmental stress, leading to cellular homeostasis. Zebu cattle are well known for the prevalence of novel mutations responsible for heat tolerance. Hence, the study was carried out to identify single nucleotide polymorphisms in the heat shock protein gene (HSP90AA1) in Shweta Kapila, Sahiwal, Gir and Malnad Gidda cattle breeds adapted to hot and humid coastal climate. Blood samples were collected and genomic DNA amplified for HSP90AA1 gene using designed oligonucleotide primers and sequenced. Rectal temperature and respiration rate both were observed elevated during the hot period compared to the cold period. Sequence data of all the amplified regions of HSP90 gene was analyzed using EditSeq and SeqMan of LASERGENE software. The analysis of custom sequencing data unveiled the presence of ten novel Single Nucleotide Polymorphisms SNPs) located at g.G4733C, g.C4765A and g.A4848G in 3′ UTR; g.C1012T and g.A1209G in exon 3; g.C1300T in intron 3; g.C2245T and g.T2266G in exon 5; and g.T3814A and g.G4212T in exon 10. The identified SNPs were genotyped by PCR-RFLP (AciI and HpyCH4III enzymes) and Tetra-primer ARMS-PCR. Genotypic and allelic frequencies for the regions ranged between 0.094 and 0.760, and 0.2645 to 0.7355, respectively. This was the novel report of genetic variations in the HSP90AA1 gene in selected indigenous cattle breeds of India adapted to hot and humid coastal climates. Further studies with large sample sizes are needed to genotype the loci for their significant effect on thermotolerance ability in cattle.