Whole-genome resequencing suggests adaptive role of copy number variation regions in Indian cattle

Copy Number Variations (CNVs) are structural variations in the genome, ranging from 50 base pairs to megabase pairs, and they contribute significantly to genetic diversity. In this study, whole-genome resequencing was carried out at ~ 10× depth on 21 samples from three indicine cattle breeds adapted to tropical (Sahiwal and Kangayam) and temperate (Ladakhi) ecosystems to evaluate CNVs/CNVRs (Copy Number Variation Regions), their diversity, and functionality. A total of 8,166 autosomal CNVRs were identified and a six-fold higher density of deletion events was detected compared to duplications in each of the breeds. Admixture and Principal Component Analysis using CNVRs grouped Ladakhi cattle into one cluster and Kangayam and Sahiwal into another cluster. Ladakhi exhibited a significant enrichment of CNVRs associated genes for example, LDHB, HIGD1C, TAS2R16 and TAS2R38 which are involved in the olfactory transduction pathway responsible for high altitude adaptation. In contrast, genes linked to thermal adaptation, like HSF2BP, KIT, and CSDE1 as well as the response to ionizing radiation pathway were observed to be associated with CNVRs in Kangayam and Sahiwal. Overall CNVRs in this study were significantly enriched for adaptation to high and low altitude than for production-related traits.