Genomic diversity and selection signatures in Asian Zebu Cattle: insights into adaptation and genetic erosion

Indigenous cattle breeds in Asia are highly adapted to their local environments providing essential commodities such as meat, milk and draught power while also playing a key role in traditional ceremonies, and sports. Despite ongoing efforts to characterize and conserve these breeds, the increasing trend of indiscriminate crossbreeding of Zebu cattle with high-yielding taurine breeds, threatens their genetic diversity. This study investigates the population structure, inbreeding levels, effective population size, gene flow and identification of selection footprints of Asian Zebu (Bos indicus) cattle. Using an Axiom 60 K SNP chip, we analyzed genotypes from 1303 cattle across 36 populations in nine countries, including seven taurine outgroups and 29 Zebu populations from Bangladesh, Cambodia, India, Myanmar, Pakistan, and Sri Lanka. Zebu populations demonstrated moderate genetic diversity, with heterozygosity levels averaging 0.356, inbreeding coefficients ranging from 0.026 to 0.074 and genetic differentiation (F_ST) varied between 0.01 and 0.11. Breed clusters aligned closely with their geographic locations except for Achai (Pakistan) and Baru Harak (Sri Lanka) breeds that appeared in both Zebu and taurine clusters indicating evidence of taurine admixture. Genomic analyses identified regions under selection using extended haplotype homozygosity (EHH) and fixation index (F_ST) methods. Candidate genes associated with key biological functions related to environmental responsiveness, including heat tolerance (HSP90AA1), immunity (RIPK3), metabolism and fertility (REC8, CLIC4, TSSK4), were identified, reflecting adaptive traits critical for Zebu survival and utility across diverse environments. These findings provide valuable insights for conservation and management strategies aimed at preserving the unique genetic diversity of Asian Bos indicus breeds.