Whole-genome Genetic Diversity And Origin Of 7 Native Cattle Breeds In Yunnan

Yunnan is located in Southwestern China,with complex geographical environment,highly variable climate and dense vegetation,which makes unique species-specific characteristics are formed in Yunnan native cattle breeds during the long-term domestication process.Wenshan cattle,Dengchuan cattle,Dianzhong cattle,Dehong humped cattle,Zhaotong cattle and Diqing cattle are 6 native cattle breeds in Yunnan which were recognized by official.Additionally,there are also some native cattle populations,such as Jiangcheng cattle.They exhibit excellent characteristics such as good adaptability,tolerance to rough feeding and disease.There are many native cattle breeds/populations in Yunnan,while their genetic evaluation has not been carried out systematically at the whole genome level.Thus,this study collected 39 samples of Yunnan native cattle breeds(Zhaotong cattle,n=5;Diqing cattle,n=10;Dehong humped cattle,n=7;Jiangcheng cattle,n=5 and Dengchuan cattle,n=12)and downloaded 12 samples of Yunnan native cattle breeds(The whole genome resequencing data of 6 Wenshan cattle and 6 Dianzhong cattle).This study reveals the unique genetic variation of the autosomes,mitochondria and Y chromosome genomes of Yunnan native cattle breeds from the whole genome level,and explores their origin,evolution and genetic diversity.In addition,Dengchuan cattle,the only dairy cattle breed in China and the only endangered cattle breed among Yunnan native cattle breeds was analyzed by selection signatures to analyze the genetic mechanism of its excellent traits such as heat resistance and good fertility.And this study provides a theoretical basis for the protection and development of Dengchuan cattle.The main findings are as follows:(1)Yunnan native cattle breeds have higher nucleotide diversity and fewer runs of homozygosity(ROH),indicating that Yunnan native cattle breeds have abundant genetic diversity.(2)Based on the data of autosomal,mitochondrial and Y chromosome genome,it is found that Yunnan native cattle breeds have a mixture of taurine and indicine pedigrees with high genetic diversity,and the indicus pedigree is dominated in Yunnan cattle breeds.Yunnan native cattle breeds showed that taurine lineage gradually decreased from northern to southern Yunnan,and the indicine lineage gradually increased from northern to southern Yunnan.No obvious phylogenetic structure was found among Yunnan native cattle breeds.The results of the whole-genome phylogenetic tree of mitochondrial DNA showed that sporadic yak introgressed into Dengchuan cattle.(3)Among the 7 Yunnan native cattle breeds,the Y3 b sub-haplotype which originated from Indian zebu is dominant(17/40,42.5%),followed by Y3a(14/40,35%),Y2b(5/40,12.5%)and Y2a(4/40,10%),indicates that Yunnan is an important channel for Indian zebu to enter southern China.(4)We used two types of statistical analysis methods,including site-frequecy spectrum(CLR and θπ)and population differentiation(Fst and XP-CLR).Several genes that carried strong selection signatures were detected in the endangered Dengchuan cattle such as lactation,meat quality,heat tolerance,immunity,reproduction,growth,coat colour,hypoxic reaction and energy metabolism.It indicates that adaptation to complex environment may not be the effect of single candidate gene,while the result of a complex gene network synergistically.In general,this study provides a theoretical basis for analyzing the genetic mechanism of Dengchuan cattle with excellent lactation and adaptability,rough feeding tolerance,good immune performance and small body size,and also laid a foundation for genetic breeding work of Dengchuan cattle in future.