Identification of SSR Markers Correlated with Growth Traits in Swimming Crab (Portunus trituberculatus)

The swimming crab, Portunus trituberculatus, holds significant economic value in aquaculture, and marker-assisted selection (MAS) offers a powerful strategy to accelerate genetic improvement of growth-related traits. In this study, we performed an association analysis between 40 SSR markers and growth traits in 244 P. trituberculatus individuals. High genetic diversity was observed, with mean Shannon’s diversity index (SI) = 1.970, expected heterozygosity (He) = 0.773, and polymorphism information content (PIC) = 0.747. Linkage disequilibrium (LD) analysis revealed that all 485 marker pairs were in linkage equilibrium (r2 < 0.33), validating the suitability of these markers for association mapping. A total of eight SSR markers were identified as significantly associated with growth traits (p < 0.05, FDR < 0.05). Notably, marker PrMa04 was associated with six traits (FCW, CW, CL, MLC, BH, BW), suggesting pleiotropic effects. Marker TRAN20 explained the highest phenotypic variance (PVE = 17.06%) for CL. Sequence analysis revealed that PrMa01, PrMa05, and ZL06 are located near genes encoding zinc finger protein, receptor-type tyrosine-protein phosphatase, and mucin-2, respectively, which are known to be involved in growth and development. The eight candidate markers identified in the discovery population were not replicated in an independent cohort after FDR correction, suggesting that their effects may be population-specific. These findings provide valuable SSR markers and genetic insights for MAS programs in P. trituberculatus, while also highlighting the critical importance of cross-population validation before routine application.