Differentiated genome-wide methylation patterns shed light on the evolutionarily diverged adaptation in yak

Domestic yak have evolved numerous physiological adaptabilities to diversified climatic and environmental conditions following the processes of domestication and dispersal, such traits include larger hearts and lungs, stronger capacity of blood oxygen transportation, acuter sense for environment and higher metabolism as compared with other bovine species. A comparison of domestic yak with cattle breeds using integrative ‘omics’ technologies might help us understand the molecular mechanisms underlying the unique physiological and adaptive traits of yak. We profiled genome-wide DNA methylome and transcriptome landscapes for one yak and three cattle breeds. We identified tissue- (T-SMRs) and specific/breed-specific methylated regions (B-SMRs). Yak specific B-SMR genes were mainly involved in neuromodulation, immune, metabolism, endocrine system, and signal transduction. Functional genes regulated by methylation were found to be differentiated on the pathways relevant to neuromodulation for acute sense to external environmental conditions, blood pressure regulation, cardiovascular protection, high energy metabolism, larger lungs of yak, defense against high-radiation exposure and resilience to immunological stress. This comprehensive omics study provided a solid basis for understanding the epigenetic mechanisms underlying adaptive traits in yak.