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

Abstract

[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, cGMP-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.

Abstract

摘要：【目的】 基于全基因组重测序研究分析广西地方猪种与西方商业猪种的遗传结构, 挖掘出广西地方猪种的 选择基因, 为我国地方猪种质资源的保存和利用打下基础。 【方法】对广西地方猪种 (巴马香猪、东山猪和陆川猪) 和西 方商业猪种 (杜洛克猪、长白猪和大白猪) 共60头猪个体进行基因组重测序分析, 经质控后分别进行猪种亲缘关系、主 成分层次、连锁不平衡衰减、群体遗传结构、系统发育进化树及群体遗传分化指数 (F _st) 等分析。 【结果】西方商业猪种 与广西地方猪种间的群体遗传关系较远, 西方商业猪种群体聚集在一起, 而广西地方猪种群体较分散;构建的系统发 育进化树显示, 6个猪种聚类成3个分支, 其中, 东山猪单独聚为一支, 巴马香猪和陆川猪聚为一支, 而杜洛克猪、大白 猪和长白猪聚类在另一分支上。广西地方猪种组均被选择的位点共有641个受选择区域, 最终定位注释到108个基 因, 其中 Cenpp基因的受选择区域高达25个。这些基因显著注释到自然杀伤细胞分化正向调控、翻译抑制因子活性、 mRNA调控元件结合、肽激素加工、正调控细胞迁移参与新生血管生成、电压门控离子通道活性及离子跨膜转运调控 等GO功能条目;KEGG信号通路富集分析发现显著富集于内吞作用、cGMP-PKG信号、胆汁分泌、肌醇磷酸盐代谢和 磷脂酰肌醇信号系统等通路上。 【结论】广西地方猪种与西方商业猪种间存在明显差异, 但广西地方猪种内部存在较 高的近交现象, 部分猪种可能受到西方商业猪种的影响, 而导致其血统不纯。广西地方猪种共有641个受选择信号区 域, 定位注释到的108个基因主要参与离子跨膜转运、磷脂酰肌醇信号系统、正调控细胞迁移及新生血管生成等通路, 其中 Mrps27基因可能与广西地方猪种独特的生长发育有关。