Large-scale genome sequencing reveals population separation and selection signatures in major canyon yaks

Through long-term natural and artificial selection, domestic yaks (Bos grunniens) have diverged from wild ancestors and become vital to high-altitude pastoralism, providing meat, milk, fiber, and other essential resources and transportation. Especially, based on the complex and changeable environments in the canyon of the Tibetan Plateau, the canyon-type yaks show diverse phenotypic traits, including morphology, production, and adaptation. To explore the genetic basis of this breed-specific adaptation and identify key functional genes shaped by selection, we collected 225 yaks from three canyon-type yak populations and scanned genome variation information using high-throughput resequencing. We employed three approaches, nucleotide diversity (π), fixation index (Fst) and cross-population extended haplotype homozygosity (XPEHH), to detect positive selection signals in the genome. Through analyses of population structure, genetic diversity, and selection sweep signals, we identified unique Single Nucleotide Polymorphisms (SNPs) that reveal significant genomic divergence among the three yak populations, which can also serve as genetic markers for population discrimination. Furthermore, shared SNPs identified by selective sweep analysis exhibited distinctive Minor Allele Frequency (MAF) distribution patterns; these population-specific SNP markers can be directly applied to develop SNP chips for breed-specific identification. A total of 13 genes related to breed-specific adaptive traits were identified. These findings provide valuable insights into the molecular signatures of breed-specific adaptation under human management and natural selection. It also identifies key functional genes relevant to future breeding programs.