Unraveling candidate genes related to heat tolerance and immune response traits in some native sheep using whole genome sequencing data

Abstract

BackgroundIn the sheep breeding industry, heat stress caused by the general increase in global temperature has become a significant issue, having both direct and indirect effects on animal health and productivity. The identification of effective pathways for responding to heat stress and immune responses, as well as the discovery of related genes, can improve the production and sustainability of genetic diversity in this area. In this study, we used nucleotide diversity (θπ) and FST statistical measurements to analyze the genomic data of the native Iranian sheep in order to find potential genes related to heat adaptation and immune response. We also compared the whole genome sequencing data of 29 indigenous Iranian sheep (the Afshari, Ghezel, Makuei, Moghani, Shal, Zel, Karakul, Grey-Shiraz, Baluchi, and Kermani breeds) with a number of other sheep breeds from Asia (n = 28), Europe (n = 28), and Africa (n = 25) to evaluate the genetic structure of the Iranian sheep population. The resultsThe results from the sheep population genetic analysis showed a clear separation between different populations that corresponds well with their geographic origins. Iranian sheep were further divided into a southern and a northern group, which coincided with the most prominent climatic division in Iran. Our search to identify potential genomic regions under selection showed several candidate genes involved in (1) response to heat stress (SIK2, FER, ATP1A1, CDK5RAP3, and TLR4), (2) immune response in hot and dry environments (CD109, CR2, EOMES, and MARCHF1), (3) response to drought stress and adaptation to desert areas (ZFP1, PLCB1, and PDGFD), and also (4) response to heat stress by controlling digestive metabolism (HTR4, TRHDE, and ALDH1A3). ConclusionsThe findings of this study may aid in our understanding of the molecular processes by which tiny ruminants adapt to hot, dry environments. In addition to the results of earlier studies, our findings also revealed a number of novel candidate genes related to heat adaptation. These genes will be valuable for future studies to choose livestock breeds that live in desert regions.