Population genetic structure and selection signature analysis reveal the genetic basis of rapid growth trait in Portunus trituberculatus “Huangxuan No. 1”

The swimming crab Portunus trituberculatus is widely distributed along the coast of China and represents an economically important marine aquaculture species. The breeding line “Huangxuan No. 1”(HX) has undergone 17 generations of selective breeding to enhance growth performance, yielding significant improvements. However, genomic markers associated with artificial selection in this species remain largely unexplored. In this study, four populations, including Haizhou Bay (HZ), Laizhou Bay (LZ), Dandong (D) and the domesticated population (HX), were genotyped using a liquid-phase SNP array, yielding 43,314 high-quality SNPs that were evenly distributed across the P. trituberculatus genome. Population genetic analyses indicated low levels of genetic diversity across the four populations, with moderate genetic differentiation between the selected HX population and the wild populations. Based on fixation index ( Fst ) and nucleotide diversity (π-ratio) analyses, 242 and 214 candidate genes were identified in the HX population. Enrichment analysis indicated that these genes were mainly involved in pathways related to energy metabolism, signal transduction, and immune response, which are closely associated with selected traits. Among them, TPI1 (triosephosphate isomerase 1) and QKI (RNA-binding proteins) were identified as key growth-related genes, playing important roles in energy supply and skeletal muscle development. RNA interference (RNAi) knockdown of these genes resulted in a significant reduction in expression levels, both peaking at 24 h with knockdown efficiencies of 75.5% and 71%, respectively. After RNAi treatment for 3, 6, and 11 days, the body weight gain rate was significantly lower than that of the control group at day 11. Overall, this study provides valuable insights into the genetic basis of key traits in P. trituberculatus and offers useful guidance for germplasm conservation and further genetic improvement.