Genetic diversity and adaptation to Mongolian Plateau environment of three Inner Mongolia indigenous cattle breeds

Genetic diversity of native cattle breeds is a crucial resource in livestock industry, reflecting their excellent traits and the adaptability to specific environments. This study investigates the population structure, genetic diversity, and selection footprints of three indigenous cattle breeds (Mongolian, Sunite and Sanhe) in the Inner Mongolia region, aiming to explore the genetic basis underlying their environmental adaptation. Here, we collected 277 whole-genome resequencing data from 12 different cattle breeds, including 137 newly sequenced samples from three Inner Mongolia cattle breeds and integrated with 140 public data. Population structure and genetic diversity analyses showed that Mongolian and Sunite cattle have relatively independent genetic backgrounds, whereas Sanhe cattle are genetically closer to European commercial cattle breeds. Moreover, selection signatures and functional enrichment analyses revealed that several selected genes associated with exercise stress (e.g., SNAP25 , CHRNA4 , CACNA1A , CACNA2D1 , SGCD , ANKRD1 ), cold stress (e.g., CIRBP , EIF2AK4 , VANGL2 , CACNG4 , CNCNA1C , IRX3 ), hypoxia stress (e.g., ALKBH5 , PLOD2 , PECAM1 , VEGFC , MB , EGR1 , DPP4 , FZD5 ), and physiological stress (e.g., GNAT1 , MEIS1 , GRIK2 , ATP8A2 , GPX7 , RORA ) in these three cattle breeds. Through integrating of the CattleGTEx resource, we found that these selected genes are specifically highly expressed in the heart, pituitary, hypothalamus, lung, liver, adipose, and muscle tissues, indicating their significant roles in cardiovascular function, thermoregulation, skeletal muscle development, and energy metabolism. This also suggests the unique plateau adaptability of the native cattle breeds in the Mongolian region in terms of adapting to long-distance nomadism, cold, moderate hypoxia, and seasonal food shortages. Our findings provide valuable resources for preserving the unique genetic diversity and elucidating the genetic basis of environmental adaptability of Inner Mongolia indigenous cattle breeds.