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

Abstract

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.

Keywords: Mi pig; SINE; genetic diversity; population structure; retrotransposon insertion polymorphisms.

Figure 1

Photos of Mi pigs. (A) Photo of Mi pig taken by Zhang (48) in 1956; (B) photo of Mi pig taken by Cao (2) in 1982; (C) photo of Mi pig in 1991 (48); (D) photo of Mi pig in 2023. Reproduced with permission.

Figure 2

Representative electropherogram of SINE-RIPs in the Mi pig population. M: DL2000 DNA marker; 1–24: 24 individuals; the right side shows the names of the SINE-RIPs loci.

Figure 3

UPGMA tree for cluster analysis with Mi pigs and the other six germplasm individuals based on Nei’s genetic distance and analysis of population structure in Mi pigs based on UPGMA tree. The number of individuals included in each family, as well as the ID of male breed indicated by the black signs.

Figure 4

Heatmap of fixation index (Fst) among Mi pig families and six breeds of pigs. LD, Landrace; LW, Large White; DRC, Duroc; EHL, Erhualian; HDL, Hongdenglong; M, Mi; H, Huai (Red indicated higher Fst values, while green indicate lower Fst values).

Figure 5

(A) Calculation of the true K of the YHSBLP following procedure outlined and graphical representation with K2-4 by STRUCTURE software. (B) PCA plot of Mi pig pedigree vs. other six breeds of pigs. LD, Landrace; LW, Large White; DRC, Duroc; EHL, Erhualian pig; HDL, Hongdenglong pig; M, Mi pig; H, Huai pig.