Genomic insight into X chromosome dynamics in high altitude adaptation of trans-Himalayan yaks

This study delves into the genomic foundations of high-altitude adaptation in Indian yaks, with a specific emphasis on the X chromosome and its role in traits related to production, reproduction, and immunity. Utilizing whole-genome resequencing, we identified 319,015 high-quality X chromosomal SNPs from 30 unrelated Indian yaks and 8 Jinchuan yaks. These SNPs were analyzed through various statistical methodologies, including composite likelihood ratio (CLR) statistics, Tajima’s D, iHS, F _ST , and XP-EHH. Our findings highlight several genes associated with high-altitude adaptation, such as AIFM1, APOOL, ATRX, CHST7, DACH2, DGAT2L6, DIAPH2 , and EIF2S3B , identified through iHS, Tajima’s D, and CLR approaches. Additionally, genes including GPR119, HS6ST2, MAGED1, MOSPD1, PQBP1, SLC25A14, SLC35A2, TIMM17B , and WDR44 exhibited common selection signatures across F _ST and XP-EHH methods. Unique genes and loci specific to each yak population were uncovered on the X chromosome, which are critical for adaptability, immunity, reproduction, and production traits. Notably, our study identified selection regions containing the RLIM gene in Himachali yaks, which is crucial for Dosage Compensation on the X chromosome. This research offers new insights into X-linked selection across different yak populations, enhancing our understanding of the genomic mechanisms underlying high-altitude adaptation.