Genome-wide Assessment of Genetic Diversity and Population Structure in Gayal (Bos frontalis) Using Whole-Genome Resequencing

The Gayal is a rare and semi-domesticated bovine species with important ecological and genetic value but threatened by small population size and long-term inbreeding. To comprehensively assess its genomic diversity and evolutionary status, we performed whole-genome resequencing of 30 Gayal and analyzed them together with 69 publicly available genomes from 18 domestic and wild cattle breeds. 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 identified candidate genes offer valuable insights into the unique biological traits of the species and support its potential application in future genetic improvement and germplasm utilization.