Genetic diversity and selection signals analysis of Guangxi local pig breeds based on whole-genome resequencing

【Objective】Genetic structure of Guangxi local pig breeds and western commercial pig breeds was analyzed based on whole-genome resequencing and selection signals of Guangxi local pig breeds were detected, to lay foundation for the preservation and utilization of local pig germplasm resources in China.【Method】Genome resequencing was conducted on a total of 60 individual pigs from three Guangxi local pig breeds(Bama Xiang pig, Dongshan pig and Luchuan pig) and three western commercial pig breeds(Duroc pig, Landrace pig and Large White pig). After quality control, the genetic relationship, principal component level, linkage imbalance attenuation, population genetic structure, phylogenetic tree and population genetic differentiation index(F_st) were analyzed.【Result】The population genetic relationship between western commercial pig breeds and Guangxi local pig breeds was far. Western commercial pig breeds grouped together, while Guangxi local pig breeds were scattered.The constructed phylogenetic tree showed that the six pig species clustered into three categories. Dongshan pigs were grouped into one category, Bama Xiang pigs and Luchuan pigs were grouped into one category, and the three western commercial pig breeds, Duroc pig, Large white pig and Landrace pig, were grouped into one category. There were 641 selected regions that all Guangxi local pig breed groups were selected. Gene mapping was performed, and 108 genes were finally annotated, among which Cenpp gene selected regions reached 25. These genes significantly annotated GO functional terms such as positive regulation of natural killer cell differentiation, translation repressor activity, mRNA regulatory element binding, peptide hormone processing, positive regulation of cell migration involved in sprouting angiogenesis, voltage-gated ion channel activity and regulation of ion transmembrane transport. KEGG signaling pathway enrichment analysis found that significant enrichment pathways include dendocytosis, c GMP-PKG signal, bile secretion, inositol phosphate metabolism and phosphatidyl inositol signaling system.【Conclusion】There are obvious differences between Guangxi local pig breeds and western commercial pig breeds.However, there is a relatively frequent inbreeding phenomenon in Guangxi local pig breeds, and some pig breeds may be affected by western commercial pig breeds, which leads to impure bloodlines. There are 641 selected signal regions in Guangxi local pig breeds. The 108 mapped and annotated genes are mainly involved in ion transmembrane transport, phosphatidyl inositol signaling system, positive regulation of cell migration and sprouting angiogenesis. Gene Mrps27 may be related to the unique growth and development of Guangxi local pig breeds.