Deciphering climate resilience in Indian cattle breeds by selection signature analyses

Abstract

Abstract The signature of selection is a crucial concept in evolutionary biology that refers to the pattern of genetic variation that arises in a population as a result of natural selection. In the context of climate adaptation, the signature of selection can reveal the genetic basis of adaptive traits that enable organisms to survive and thrive in changing environmental conditions. Breeds cultivated in diverse agroecological zones exhibit genetic "footprints" within their genomes that mirror the influence of climate-induced selective pressures, subsequently impacting phenotypic variance. We examined genotypic data from eight different cattle groups (Gir, Hariana, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, and Tharparkar) that are adapted to diverse regional climates in India. It is assumed that the genomes of animals residing in these regions have been altered through selection for various climatic adaptations. In this study, we utilized bovine 50k chip data and four genome scan techniques to assess the genetic regions of positive selection for high temperature adaptation in eight distinct cattle populations. We have also investigated the population stratification i.e. PCA, genome-wide investigation of genetic diversity, inbreeding, effective population size in our target dataset. To identify selection signature regions in this work, we used four intra-population statistics: Tajima's D, CLR, iHS, and ROH. We identified potential regions for selection that is likely to be caused by climate. We have identified many adaption genes as several potential selection signature areas. These include genes like HSPB2, HSPB3, HSP20, HSP90AB1, HSF4, HSPA1B, CLPB, GAP43, MITF, and MCHR1 that have been previously identified in the cattle population that lives in high- and low-temperature regions.