Genome-wide assessment of genetic diversity and population structure in Gayal (Bos frontalis) using whole-genome resequencing

Abstract The Gayal is a rare, semi-domesticated bovine species of considerable ecological and genetic importance, yet its long-term persistence is threatened by small population size and sustained in breeding. To characterize its genomic diversity and evolutionary relationships, we performed whole-genome resequencing of 30 Gayal individuals and jointly analyzed these data with 69 publicly available genomes representing 18 domestic and wild bovine populations. High-quality variants were identified through a unified SNP-calling pipeline, and population genomic analyses were conducted to evaluate genetic diversity, population structure, inbreeding, and signatures of selection. Genetic diversity estimates, including nucleotide diversity, heterozygosity, and ROH-based inbreeding coefficients, consistently indicated markedly reduced genomic variation in Gayal compared with other cattle populations. Linkage disequilibrium decay patterns further supported the presence of historical inbreeding. Principal component analysis (PCA), phylogenetic reconstruction, and ADMIXTURE analysis revealed that Gayal forms a distinct genetic cluster, showing a closer relationship to wild bovines than to local Yunnan cattle. Genome-wide selection scans detected multiple strong selective sweeps, and candidate genes associated with immunity ( TRIM77 , RASGRP1 , API5 ), meat quality ( CLDN18 , NAALAD2 , DZIP1L , RAB3C ), and reproduction ( PDE4D ). These findings provide new genomic evidence for the independent evolutionary origin of Gayal and highlight the urgent need for conservation strategies to prevent further genetic erosion. The candidate genes and genomic regions identified here provide a foundation for functional validation of the biological traits unique to Gayal and may inform future conservation breeding, germplasm management, and sustainable genetic improvement.