Novel single nucleotide polymorphisms in the heat shock protein 70.1 gene in South African Nguni crossbred cattle

Abstract

High environmental temperatures are one of the main causes of reduced productivity and reproduction in livestock. In an endeavour to counteract the effects of high temperature, a special class of proteins known as heat shock proteins function to alleviate heat stress in the cells. In this study, two regions (3′- and 5′-UTR) of the heat shock protein 70.1 (HSP70.1) gene were studied in Nguni crossbred cattle. Subsequently, the population genetic structure was elucidated. The 5′-UTR contained the most polymorphisms with 46 and 67 SNPs, while the 3′-UTR contained 7 and 16 SNPs in the Umzimkulu and Port Shepstone populations, respectively. The T64G polymorphism had the greatest frequency of all returned SNPs in the 3′-UTR; it was fixed for the Umzimkulu population (allele frequency = 1.00) and was nearing fixation in the Port Shepstone population (allele frequency = 0.979). In the 5′-UTR, the cytosine insertion at position 1110 was fixed for both populations. These polymorphisms are presumed to play a major role in the high thermotolerance exhibited in Nguni crossbred cattle. Partitioning of genetic variation displayed that the majority of the variation (96%) was within populations, whereas only 4% of the variation was due to population genetic differentiation. A total of 22 haplotypes defined the 5′-UTR while the 3′-UTR contained 4. In conclusion, this study demonstrated that Nguni crossbred cattle in the KwaZulu-Natal province of South Africa are clustered into two genetic groups based on the HSP70.1 gene. The findings of this research will provide future directions on the identification of important SNPs within the HSP70.1 gene in South African indigenous cattle because this is one of the first of such studies.