Qin Ming, Li Chuanhao, Li Zhixin, Chen Wei, Zeng Yongqing
Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai' an City, China.
Front Genet. 2020 Jan 22;10:1351. doi: 10.3389/fgene.2019.01351. eCollection 2019.
Shandong indigenous pig breeds are an invaluable source of data on genetics in Chinese pigs. However, information on the genetic basis of these breeds remains limited. In this study, we used specific-locus amplified fragment sequencing to conduct whole-genome screening to investigate genetic diversity in Shandong indigenous breeds and Western pig breeds. The results showed that Duroc pigs (DD) had clear genetic relationships with Dapulian pigs (DPL; Fst = 0.4386) and Laiwu pigs (LW; Fst = 0.5134), and DPL and LW were relatively close genetically (Fst = 0.2334). In general, Shandong indigenous breeds showed greater genetic variety than the Western breeds. Both neighbor-joining trees and principal components analyses were able to differentiate the breeds, but population structure analyses indicated that the Western breeds genetically influenced the Shandong indigenous breeds to some extent. A total of 162 differentially selected regions (DSRs) with 841 genes and 157 DSRs with 707 genes were identified in DPL and LW, respectively. Gene annotation of the selected regions identified a series of genes regulating immunity and fat deposition. Our data confirm the rationality and accuracy of the current classification of pig breeds in Shandong province. Our results point to candidate genes in Shandong indigenous pig breeds and further promote the importance of follow-up research on functional verification.
山东本地猪品种是中国猪遗传数据的宝贵来源。然而，关于这些品种遗传基础的信息仍然有限。在本研究中，我们使用特定位点扩增片段测序进行全基因组筛选，以调查山东本地品种和西方猪品种的遗传多样性。结果表明，杜洛克猪（DD）与大蒲莲猪（DPL；Fst = 0.4386）和莱芜猪（LW；Fst = 0.5134）有明确的遗传关系，并且DPL和LW在遗传上相对接近（Fst = 0.2334）。总体而言，山东本地品种比西方品种表现出更大的遗传多样性。邻接树分析和主成分分析都能够区分这些品种，但群体结构分析表明西方品种在一定程度上对山东本地品种有遗传影响。在DPL和LW中分别鉴定出总共162个具有841个基因的差异选择区域（DSR）和157个具有707个基因的DSR。所选区域的基因注释鉴定出一系列调节免疫和脂肪沉积的基因。我们的数据证实了山东省目前猪品种分类的合理性和准确性。我们的结果指出了山东本地猪品种中的候选基因，并进一步凸显了后续功能验证研究的重要性。
