Whole-genome sequencing of Ganzi horse reveals the genetic diversity and provides unique insights into its plateau adaptation

Ganzi horse is distributed in the Ganzi Tibetan Autonomous Prefecture. As we all know, this region on the southeast of the Tibetan Plateau is characterized by low oxygen levels, low atmospheric pressure, and intense ultraviolet light. The extreme environment causes the genomic variation of plateau animals for environmental adaptation. At present, the genetic diversity and the genetic basis of high-altitude adaptation of Ganzi horses remain unclear. Here, an extensive genetic analysis was conducted utilizing whole-genome sequencing data from 145 individual horses. The analysis of autosomal genetic diversity confirmed that Ganzi horses had experienced low intensity artificial selection and had high genetic diversity. Examination of mitochondrial DNA information from whole-genome sequencing data revealed multiple maternal origins for Ganzi horses. Further, four different selective scanning methods were used to identify positive selected genomic regions and genes associated with high-altitude adaptation. We identified genes associated with altitude adaptation at selection windows in Ganzi horses, such as EPAS1, ABTB2, RHOQ, and TMEM247. Notably, EPAS1 and OR52A1J gene exhibited high select signal values, different nucleotide diversities, and haplotype patterns, and missense mutations in EPAS1 (A > T) and OR52A1J (C > T) were found to be more frequent in high-altitude horses. Moreover, our research illuminated significant gene flow between Ganzi and Chaidamu horses, which may be related to the formation of Ganzi horses. In general, these findings not only enhance our understanding of this unique native breed but also further our understanding of Ganzi horse's high-altitude adaptation.