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

作者：Tafara Kundai Mavunga, Johann Sölkner, Gábor Mészáros, Rudolf Pichler, Saravanan Ramasamy, Vandana Manomohan, Satish 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 · 发表于：Scientific Reports · 年份：2025 · DOI：10.1038/s41598-025-14744-z · 被引用次数：8 · 研究领域：Genetic and phenotypic traits in livestock、Livestock Farming and Management、Genetic Mapping and Diversity in Plants and Animals

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 (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 respon...