Genetic Diversity and Core Germplasm Identification in Penaeus japonicus Using Whole-Genome Resequencing

The kuruma shrimp (<i>Penaeus japonicus</i>), a globally high-value aquaculture species, faces critical challenges in sustainable development due to genetic diversity degradation and declining disease resistance. This study employed whole-genome resequencing (WGRS) to systematically assess genetic diversity, population structure, and core germplasm characteristics across 20 geographically distinct populations from Zhejiang, Fujian (China), and introduced Japanese stocks. Using 343.40 Gb of high-quality sequencing data (average depth: 12.44×), we identified 9,146,248 single nucleotide polymorphisms (SNPs), with 6.32% located in exon regions, while intergenic (56.75%) and intronic regions (30.99%) showed the highest polymorphism density. Principal component analysis (PCA) and phylogenetic tree construction revealed two major clades: Fujian (FJ) and Japan-introduced (RB) populations clustered closely due to shared artificial breeding backgrounds, whereas Zhejiang (XS) and Fujian (LS) populations displayed genetic heterogeneity driven by adaptive divergence. Core germplasm screening via the CoreHunter algorithm selected four representative individuals (FJ4-M, LS1-M, XS1-M, XS6-M), with the modified Rogers' distance (0.34) and allele coverage (0.93) confirming effective preservation of original genetic diversity. This study provides genomic insights and technical frameworks for germplasm conservation, precision breeding, and genetic improvement in <i>P. japonicus</i>.