Population Genomics Of Chaidamu Cattle

The Chaidamu cattle is produced in the Tsaidam Basin of Qinghai Province.Chaidamu cattle mainly live in the Tsaidam Basin with an altitude of 2800~3000m,they have the advantages of resistance to extensive management,and could adapt to hypoxia and harsh ecological environment.In the past 20 years,the number of Chaidamu cattle have been declining because of poor production conditions and low degree of seed production.Therefore,further research on the genome-wide scale of Chaidamu cattle has become particularly important.In this study,we constructed a genome-wide genetic variation map of Chaidamu cattle and compared them with lowaltitude cattle breeds to understand diversity and population genetic structure of Chaidamu cattle,and to explain the high altitude adaptation mechanism.In our study,high-throughput whole-genome sequencing of 9 Chaidamu cattle generated a total of 173 G raw data.Quality control of the raw data and alignment with the reference genome of UMD3.1 showed an average depth of 11.09× and an average coverage of 99.26%.We also analyzed previously published whole-genome sequence data from individuals of representative breeds,and detected a total of 11.21 million SNPs.And then,we can got the genetic variation,population structure and population genetic of different breeds.Further population genetic analysis showed that the Qaidam cattle were clearly distinguished from the other seven low-altitude cattle groups,and have the smallest Fst valve with Qinchuan cattle.In addition,21 strong positional candidates genes for high altitude adaptation was highlighted: EGR1,FGA,PLEK,BPIFB2,NLRC4,CSPP1,MAGEL2,NDN,ACSF2 and so on.Our population genomics data reveal the genetic diversity and high altitude adaptation mechanism of Chaidamu cattle,which not only reinforce the understanding of the genetic basis of different cattle breeds,but also provide valuable resources for future molecular breeding research.