Genetic Diversity and Population Structure of the Chinese Three-Keeled Pond Turtle (Mauremys reevesii)

To investigate the genetic diversity and structure of farmed Chinese three-keeled pond turtles (<i>Mauremys reevesii</i>), we performed whole-genome resequencing on 238 individuals from eight farms across six Chinese regions. Genetic diversity indices (nucleotide diversity π, inbreeding coefficient <i>F_HOM</i>, polymorphism information content PIC, observed heterozygosity <i>Ho</i>), principal component analysis (PCA), phylogenetic reconstruction, and population structure analysis were integrated. The results revealed that the Guangdong Maoming (MM) and Anhui Wuwei (WW) populations exhibited the highest genetic diversity (MM: PIC = 0.149, <i>Ho</i> = 0.299; WW: PIC = 0.144, <i>Ho</i> = 0.287), while the Guangdong Huizhou (HZ) and Hunan Changhan (CH) populations showed the lowest diversity due to elevated inbreeding coefficients (HZ: <i>F_HOM</i> = 0.043; CH: <i>F_HOM</i> = 0.041). Low genetic differentiation (<i>F_st</i> = 0.00043-0.04758) indicated limited population divergence. However, PCA and phylogenetic analysis demonstrated that MM and Guangxi Pingxiang (PX) populations formed distinct genetic clusters, suggesting that management differences might contribute to their genetic uniqueness. Admixture analysis identified <i>K</i> = 2 (based on the lowest cross-validation error) as the optimal ancestral cluster number, with MM and PX populations displaying admixed genetic backgrounds while others showed homogeneous compositions. Conservation priorities should focus on preserving MM and PX's unique genetic resources, introducing genetic material to high-inbreeding populations, and establishing interregional breeding networks. This study provides genomic insights for germplasm conservation and sustainable utilisation of <i>M. reevesii</i>.