Population structure and genetic diversity of Mi pigs based on SINE-RIPs

Xiaoyan Wang^1,2*Chenyu Zhou¹Yao Zheng¹Miao Yu¹Jia He¹Cai Chen¹Suwei Qiao¹Ali Shoaib Moawad^1,3Guoxing Tian⁴Bixia Li^5*CHENGYI SONG^1*

• ¹College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, China
• ²International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou, China
• ³Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Kafr el-Sheikh, Egypt
• ⁴Jintan Mi pig breeding farm, Changzhou, China
• ⁵Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China

Mi pigs, a Chinese native breed found in Jintan and Yangzhong in Jiangsu Province, were recorded as having only a few hundred members in the latest national livestock and poultry genetic resources survey. To explore their conservation and breeding prospects, 18 SINE Retrotransposon Insertion Polymorphisms (SINE-RIPs) were analyzed using PCR to assess the population structure and genetic diversity of Mi pigs. These pigs were grouped into eight families based on a UPGMA phylogenetic tree. The genetic distances between the Mi pig populations and commercial breeds ranged from 0.3712 to 0.7609, indicating significant divergence. Conversely, they showed a closer genetic relationship with other local Jiangsu breeds, with distances varying from 0.0943 to 0.6122, a finding supported by the UPGMA tree. The populations displayed a substantial degree of outbreeding, with Fis values from -0.4744 (M5) to -0.0847 (M8) and Fst values from 0.0534 (M3, M8) to 0.2265 (M2, M7), highlighting their genetic diversity which is crucial for the conservation of Mi pigs. Despite this diversity, the population sizes were uneven, with M5, M7, and M8 having 6, 5, and 7 individuals respectively. These findings lay a theoretical foundation for the ongoing conservation and breeding efforts for Mi pigs.