# Genetic Diversity and Population Structure of Hainan Indigenous Pig Breeds Revealed by Microsatellite and mtDNA D-Loop Analysis

## TL;DR

This study reveals the genetic diversity and population structure of Hainan indigenous pigs using microsatellite and mtDNA analysis to guide their conservation and breeding.

## Contribution

The study provides new insights into the genetic uniqueness of Duntou and Wuzhishan pigs and highlights the need for conservation of Lingao pigs.

## Key findings

- Duntou and Wuzhishan pigs exhibit the highest genetic diversity and unique genetic information.
- Lingao pigs show no genetic variation and require focused conservation efforts.
- Hainan pigs form a distinct subclade closely related to Luchuan pigs, indicating their evolutionary significance.

## Abstract

Local pig breeds in Hainan are unique to China’s tropical region, but their distinct genetic characteristics have not been fully clarified, potentially affecting their protection and proper use. This study aimed to determine the genetic traits and differences among seven local pig breeds in Hainan. We used two common biological research methods to analyze the genes of 147 pigs. The results show that these local pigs have rich genetic diversity, but the genetic characteristics of different breeds are quite different—among them, Duntou and Wuzhishan pigs have the most unique genetic information, while Lingao pigs require more effort to maintain their genetic diversity. This study can help relevant departments formulate more scientific protection plans for Hainan local pigs, thereby ensuring that these unique pig breeds are not lost, while also providing a basis for breeding pigs with better characteristics in the future, which is of great significance to the protection of agricultural biodiversity and the development of local animal husbandry.

This study investigated the genetic diversity and population structure of five Hainan indigenous pig breeds (147 individuals from 7 populations representing 5 breeds: 3 Duntou pig subpopulations (DT-DZ, DT-SJ, and DT-SG) and four additional breeds (Wuzhishan, Wenchang, Lingao, and Tunchang)) to address germplasm conservation needs driven by exotic crossbreeding, African swine fever, and inadequate genetic evaluation. After strict quality screening, we used 147 qualified samples for microsatellite genotyping and 104 samples for mtDNA D-loop sequencing. The analyses integrated 17 FAO-recommended microsatellite markers and mtDNA D-loop sequencing. In total, 15 out of 17 loci exhibited high polymorphism (PIC > 0.6), with Wuzhishan pigs exhibiting the highest genetic diversity (He = 0.666, I = 1.279). Pairwise Fst values indicated significant genetic differentiation among all populations (p < 0.05), and AMOVA attributed 87.32% of the genetic variation to within-population differences. Three complementary clustering methods (UPGMA, PCoA, and STRUCTURE with the optimal K value of 2 identified via the ΔK algorithm) divided the populations into two clades, clearly separating the Duntou subpopulations from other breeds. mtDNA D-loop sequencing of 104 individuals yielded a 1175 bp fragment, identifying 12 haplotypes and a high haplotype diversity (Hd = 0.688) low nucleotide diversity (π = 0.00193) pattern; Lingao pigs showed no genetic variation, while Duntou and Wuzhishan pigs had the highest Hd. NJ phylogenetic analysis indicated that Hainan pigs form an independent subclade within Chinese indigenous pigs, closely related to Luchuan pigs. These findings confirm the high overall genetic diversity and distinct population-level divergence in Hainan pigs, with Duntou pigs representing a unique lineage. This work provides a scientific basis for targeted conservation strategies, including prioritizing the conservation of Duntou and Wuzhishan pigs and restoring genetic variation in Lingao pigs.