Genomic diversity and selection signatures in Asian Zebu Cattle: insights into adaptation and genetic erosion
Year: 2025
Type: article
Abstract: 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 60K 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 (FST) 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 (FST) 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.
Source: Scientific Reports
Authors: Tafara Kundai Mavunga, Johann Sölkner, Gábor Mészáros, Rudolf Pichler, Saravanan Ramasamy, Vandana Manomohan, S. Rajesh Kumar, Kamran Abbas, Tanveer Hussain, Masroor Ellahi Babar, L. G. S. Lokugalappatti, Ei Thandar, Menghak Phem, Sothyra Tum, Mohammad Musharraf Uddin Bhuiyan, Myagmarsuren Purevdorj, Mario Barbato, Kathiravan Periasamy
Institutions: International Atomic Energy Agency, BOKU University, Tamil Nadu Veterinary and Animal Sciences University, Virtual University of Pakistan, University of Veterinary and Animal Sciences, University of Peradeniya, Livestock Breeding and Veterinary Department, Ministry of Agriculture Forestry and Fisheries, Bangladesh Agricultural University, Research Institute of Animal Husbandry, University of Messina, Indian Council of Agricultural Research, National Research Centre on Mithun
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $2,690
OpenAlex ID: W4414602530