Genomic landscape reveals evolutionary footprints of adaptability in Indian hill cattle

Abstract

Abstract The present study is aimed to assess the population structure of hill cattle and analyze the genomic footprints of selection and adaptation. The population structure and signatures of selection were analyzed in hill cattle in comparison to Indian milch, non-milch and exotic cattle populations, using Illumina high-density genotyping data. The present study used high-density SNP genotyping data generated on Illumina BovineHD SNP BeadChip on a total of 299 individuals representing 14 bovine populations across three groups i.e., Hill cattle (Ladakhi and Siri), Indian milch cattle (Sahiwal, Gir, Tharparkar), Indian non-milch cattle (Hariana, Hallikar, Kankrej, Ongole, and Vecheur) and exotic group (Holstein-Friesian, Jersey, Brown Swiss and Guernsey). The grouping of populations was based on utility, inheritance and characteristics related to the terrain of breeding tract. The final merged dataset included coverage on 4,68,671 common autosomal SNP markers after quality pruning using different thresholds. The population structure was assessed using principal component analysis and maximum likelihood-based TreeMix analysis while twin methods (iHS, and XP-EHH) were used to scan the whole genome for haplotype homozygosity statistics. Multiple chromosomes were observed to harbour SNPs under selective sweeps in different comparisons. TRIM44, SLC5A12, MYO1D and NAPB were important genes that showed overlap with SNP markers whose frequency was significantly different than overall hill cattle genome under selection. Various genes were found as part of selection footprints along multiple comparisons including U6, ADGRL3, RELN, DAP3, STO1, DNAJA2. A functional analysis of the genes harbouring SNPs under evolutionary pressure (as part of selection sweeps) was undertaken to gain deeper insights into the biological relevance of selection footprints. The genes as part of selection sweeps were mainly involved in important adaptation traits including cell-cell signalling, neuronal development, mitochondrial functioning, hyaluronidase functioning, ion-channel transport of solute and nutrients, and response to reactive oxygen species and other stressors. The present study provides detailed insights into the genomic landscape changes that are result of adaptation of hill cattle to agro-climatic conditions under which they are reared.