Preliminary Study On Genetic Introgression Among Representative Indigenous Pig Breeds In China Based On Whole-Genome Sequencing Data

Pigs provide humans high-quality animal protein and a large amount of fat energy,and are also considered as an ideal animal model for human medical research.China is rich in pig breeding resources and has a long history of domesticating pigs for nearly 9000 years.Due to its vast territory and wide climatic differences,domestic indigenous pigs in China have gradually formed lines with different characteristics and excellent traits.Previously,studies have shown that some Chinese indigenous pigs(such as Min pigs)have been genetically introgressed from European pigs,and that Chinese indigenous pig lineages(such as Meishan pigs)have also been introduced into Western European pigs.However,there are few studies on genetic exchange between Chinese local pig breeds.In this study,a preliminary study was conducted on the genetic exchange between Chinese local pig breeds.The next generation sequencing data of 115 pigs from 19 pig breeds in Europe and China plus one java Warty pig were obtained.These data were used to analyze the population genetic structure and gene introgression among pig breeds in southern,northern,southwestern(including Tibetan)and eastern China.The following results were obtained:1.The results of phylogenetic NJ tree,PCA,and Admixture analysis showed that: 1)Chinese local pig breeds have a relatively distant evolutionary relationship with European pig breeds,and the Min pig,Hetao pig,Gansu Tibetan pig,and Laiwu pig admixtured with European pig lineages;2)Among the local pig breeds in China,the genetic relationship between South China pig and East China pig is the farthest,while the genetic relationship between Southwest(including Tibetan)pig breeds and East China and North China pig breeds is relatively close.2.Genetic introgression analysis showed that: 1)there was a strong gene flow between northern Chinese pig breeds and European pig breeds,confirming the reported high level of genetic introgression in northern Chinese domestic pigs;2)There is widespread gene exchange among local breeds of pigs in China,such as South China pigs,East China pigs,and some southwest pigs(Neijiang,Sichuan,and Yunnan).Laiwu pigs,East China pigs,and Southwest pigs also have gene exchange.3.The topology weighting method was used to further identify the genomic loci that were genetically introgressed from South China pigs(Bamaxiang pig,Luchuan pig,and Wuzhishan pig)to East China pig breeds(Erhualian pig and Jinhua pig).In the high introgression candidate regions,we have identified candidate genes related to bone morphogenesis,exercise behavior,digestion and absorption,metabolism,and immune related functions.Through subsequent validation and analysis,we identified two potential candidate genes(SNTG1、CHST3)that affect spinal and skeletal development,which may have an important impact on body shape development and formation of East China pig breeds.In this study,we used genome wide data from pig breeds in southern,northern,and eastern China to reveal the population genetic structure of European and Chinese local pig breeds through population genetics methods.Meanwhile,we detected bidirectional introgression signals between southern and eastern China pig breeds,and identified candidate genes related to functional characteristics such as metabolism,behavior,and bone growth,revealing that gene introgression may increase the genetic diversity of Chinese domestic pigs,which may be beneficial to the formation of excellent traits and the cultivation of excellent strains of domestic pigs.In summary,this study provides molecular biological evidence for a comprehensive understanding of the population genetic structure and gene introgression in different Chinese local pig breeds,and provides a scientific theoretical basis for the cultivation and conservation improvement of local pig strains in China.