Genetic Admixture And Selection Signatures Of Yunnan Native Cattle Breeds,and Genetic Introgression Of Bos Species

As one of the major livestock species,domestic cattle have played an important role in human history since early Neolithic period and provide important resources for human beings,such as meat,milk,leather.Taurine（Bos taurus）and zebu（Bos indicus）are two types of domestic cattle,which mainly domesticated from two different auroch（Bos primigenius）populations in the Near East and the Indus Valley,respectively.During the domestication process,domestic cattle have been subject to the double influences of natural selection and artificial selection,which created differences in body shapes,heat tolerance,high altitude adaptation,and disease resistance.These differences will leave selection footprints on the genomes of cattle,called as selection signatures.Detecting selection signatures of domestic animals will help to analyze the potential genetic mechanisms that affect their phenotypes and environmental adaptation differences,and laid a significant foundation for genetic breeding of domestic animals.Additionally,the genetic introgression between domestic animals and related wild species had also played an important evolutionary role in the processes of animal domestication.Yunnan is not only a frontier zone that connects China with South Asia and Southeast Asia,but also represents an admixture zone between taurine and zebu cattle.It is recorded that there are six native cattle breeds（Wenshan cattle,Dengchuan cattle,Dianzhong cattle,Yunnan humped cattle,Zhaotong cattle and Diqing cattle）in Yunnan.Our previous study confirmed that there was genetic admixture of taurine and zebu among Yunnan cattle breeds based on mitochondrial D-loop datas.However,the mitochondrial marker can only detect maternal genetic information,and obtained results cannot reflect information of the entire genome,then,（1）what was the genetic admixture of these cattle breeds at the genome level,and whether there were special geographical distribution patterns for their mixed percentage?and（2）whether there have been selection signatures on the Yunnan cattle genome during the evolutionary process?Because there is incomplete isolation or no reproductive isolation between domestic cattle and other related Bos species（yak,gaur,Banteng and gayal）,these species can hybridize,which provides a physiological basis for the study of genetic introgression among Bos species,then,（3）whether the genetic relationships among these Bos species were consistent with their geographic origins?（4）what was the degree of genetic introgression among Bos species,and which genes were subject to selection signatures?However,little is so far known about these scientific questions.To solve the scientific problems（1）and（2）,we firstly carried out the ADMIXTURE analysis for 120 samples of Yunnan cattle breeds based on the Bovine HD chip,the results showed that the Yunnan humped cattle was zebu breed and the other five breeds showed different admixture proportion of taurine and zebu cattle,and the proportion of taurine ancestry showed a declining trend from Northeastern Yunnan to Western Yunnan,while the proportion of zebu ancestry displayed an increasing trend from Northeastern Yunnan to Western Yunnan.Secondly,we jointly used the population genetic differentiation index(F_ST),cross population extended haplotype homozygosity（XP-EHH）and cross population composite likelihood ratio（XP-CLR）methods to implement the selection signatures analysis of Yunnan humped cattle,Diqing cattle and Dengchuan cattle,respectively.We found that the selected common genes were enriched in the Wnt signaling pathway,calcium signaling pathway and amoebiasis,and these pathways were related to hot sweating and parasitic diseases,and detected some genes related to heat tolerance（e.g.PC and TTC32）and immunity（e.g.CBFA2T3,IL27RA,CDK10,PTPN2,COL4A2,LIPH and FAF1,etc.）in Yunnan humped cattle,among LIPH gene played an important role in tick resistance.A total of 90 co-selected genes were detected in Diqing cattle,which were significantly enriched in ATP binding and postreplication repair pathways,these two pathways related to energy metabolism and DNA damage repair,respectively,and found that some genes related to hypoxia tolerance（CIC）,angiogenesis（NOTCH2）,blood pressure regulation（BMPR2）,DNA damage repair（ASCC3）and defense response（GRID1）.We speculated that these pathways and genes might play important roles in high altitude adaptation of Diqing cattle.Furthermore,we detected 72 common genes in Dengchuan cattle,of which,PRKG1 gene might affect the flavor and nutritional value of milk,and ABO gene related to milk oligosaccharide content,and speculated that these two genes may be related to the dairy performance of Dengchuan cattle.Since the marker density that can be identified by the Bovine HD chip is lower than that of whole genome resequencing,which makes some selection signatures still difficult to detect in native cattle breeds.Thus,we selected separately 10 samples of Yunnan humped cattle,Dianzhong cattle and Zhaotong cattle from Yunnan native cattle breeds,among Yunnan humped cattle was regarded as the target population,and Dianzhong cattle and Zhaotong cattle were regarded as the reference population.A total of 30 samples were carried out the whole-genome resequencing and obtained 1,560 Gb raw data.After strictly quality control and filtering,the1,532 Gb clean data were included.These clean data were mapped to the reference genome and showed that the average mapping rate,the sequencing depth and the coverage were 99.40%,16.28X,and 98.03%,respectively.The Yunnan humped cattle were separated from Dianzhong cattle and Zhaotong cattle,which was clustered into an independent cluster by the principal component analysis and phylogenetic analysis.Additionally,the ADMIXTURE analysis displayed that Yunnan humped cattle was zebu breed.We utilized the F_ST,XP-EHH and XP-CLR methods to carry out the selection signatures analysis,and observed the selected common genes were significantly enriched in pathways related to energy metabolism,signal transduction,cancer and immunity,and detected some genes related to heat resistance（e.g.PARP1）and immunity（e.g.CD40,CD84,LCP1,NLRC3,PIK3IP1 and ITGA9,etc.）in Yunnan humped cattle,among the ITGA9 gene played an important role in resisting Haemonchus contortus infection.Moreover,we compared the results of selection signatures of Yunnan humped cattle based on Bovine HD chip analysis,and found that the PTPN2,COL4A2 and FAF1 were overlapping immune genes except the newly discovered above genes,showing that immune-related genes had been under strong positive selection.To address the scientific problems（3）and（4）,we implemented the PCA,ADMIXTURE,gene flow and selection signatures analyses based on the Bovine HD chip datas of 266 samples of 10 populations of taurine,zebu,yak and gaur from Yunnan,Myanmar,Tibet,Sichuan,India,Bangladesh,etc.The results showed that the genetic relationships between zebu,yak and gaur were consistent with their geographical origins;three ancestral components of the European taurine,East Asian taurine and Indian zebu were found in domestic cattle;the bidirectional genetic introgression between Diqing cattle and Zhongdian yak were detected,and Diqing cattle has approximately 2.37%Zhongdian yak ancestry,while Zhongdian yak has approximately5.04%Diqing cattle ancestry.Simultaneously,the enrichment analysis showed that the introgressed genes from Zhongdian yak to Diqing cattle were mainly enriched in immune-related pathways,such as chemokine activity,inflammatory response,lymphocyte chemotaxis,chemokine signaling pathway and leukocyte transendothelial migration,and the ENPEP,FLT1and PIK3CA gene related to the adaptation of high altitude hypoxia were detected,we speculated that the genetic introgression from Zhongdian yak into Diqing cattle would help Diqing cattle quickly adapt to the high altitude hypoxia environment;we found the genetic components of Zhongdian yak had introgressed into Tibetan cattle,and detected 30 selected genes in Tibetan cattle by selection signatures analysis,some genes were significantly enriched in immune-related chemokine signaling pathway.Interestingly,the CDC42 and SLC39A2 genes were discovered except the EPAS1 gene associated with hypoxia response,which played important roles in angiogenesis,erythropoiesis and heart function,respectively.We considered that the regulation of genes related to the above functions might have great significance for high altitude adaptation of Tibetan cattle.This result showed that genetic introgression was one of the important ways for the environmental adaptation of domestic cattle.In summary,there was the genetic admixture of taurine and zebu cattle in other Yunnan cattle breeds except for Yunnan humped cattle,and the proportion of taurine ancestry and zebu ancestry presented a different geographical distribution pattern in Yunnan.The results clarified that the genetic admixture status of Yunnan cattle breeds.Additionally,we discovered that the Yunnan humped cattle,Diqing cattle and Dengchuan cattle have been subject to selection during the domestication process,and detected some genes and pathways related to germplasm characteristics in these breeds;the different genetic components of Zhongdian yak had introgressed into Diqing cattle and Tibetan cattle,and the two breeds have obtained important genes related to high altitude adaptation,this study will lay an important theoretical foundation for improving the selection signatures on cattle genome,downstream functional genomics study and molecular breeding.