Whole-Genome Genetic Diversity Of Three Cattle Breeds At The China-Burma Border Area

The topography of Yunnan Province in China is complex,mainly mountainous and plateau,and belongs to tropical subtropical climatic areas.Yunnan has 25 ethnic minorities in addition to Han ethnic.The special geographical environment and diverse national culture have formed a unique genetic resource of Yunnan cattle.Dehong humped cattle and Lincang humped cattle are collectively referred to as Yunnan humped cattle.Burma cattle are mainly distributed in the northeast region of Burma bordering Dehong and Lincang in Yunnan Province,and these three local cattle breeds have strong heat and disease resistance.To systematically reveal the genomic genetic diversity and origin evolutionary relationship of these three cattle breeds in the China-Burma border area,Lincang humped cattle（n=22）,Dehong humped cattle（n=13）and Burma cattle（n=20）at the China-Burma border area were collected and sequenced in this study.And the whole genome resequencing data of 61taurine cattle and indicine cattle were also collected for combined analysis.In addition,the selective pressure analysis of Lincang humped cattle at the China-Burma border area was also performed to dissect their genomic characteristics in body size,immunity,and heat tolerance.The following results were obtained in this study:（1）Based on autosomal genomic SNP analysis,it was found that Lincang humped cattle,Dehong humped cattle and Burma cattle at the China-Burma border area had higher nucleotide diversity,faster linkage disequilibrium decay rate and lower LD level,as well as fewer runs of homozygosity（ROH）,indicating that they had rich genomic genetic diversity.（2）Combined with autosomal genomic SNP,mitochondrial DNA genome and Y chromosome genomic SNP,it was found that Lincang humped cattle and Dehong humped cattle at the China-Burma border area were mainly Indian indicine pedigrees and mixed with a small amount of taurine cattle pedigrees,while Burma cattle were pure Indian indicine pedigrees.（3）Based on the Y chromosome genome SNP analysis,three cattle breeds at the China-Burma border area were found to have three Y chromosome haplotype groups:one taurine cattle haplogroups（Y2a）and two Indian indicine haplogroups（Y3a and Y3b）.Among them,the Y3b sub-haplotype was dominant,indicating that the China-Burma border area may be an important channel for Indian indicine cattle to migrate into southwest China from west to east.（4）The selective pressure analysis of Lincang humped cattle was performed for the first time using CLR,F_STand XP-EHH three selected detection methods.Some genes associated with environmental adaptations such as body size,immunity and heat tolerance were identified under strong selection in Lincang humped cattle.Among them,there were specific missense mutations in the HELB gene in thermostable indicine cattle populations such as Lincang humped cattle,indicating that this gene is related to the environmental adaptability of heat tolerance in Lincang humped cattle.These results provide a genome-wide basis for understanding the phylogenetic relationship between Lincang humped cattle,Dehong humped cattle and Burma cattle at the China-Burma border area.And they are important for the protection of genetic resources in Lincang humped cattle and Dehong humped cattle breeds.