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.

Background: The oriental river prawn (Macrobrachium nipponense) is an economically important aquaculture species in China. Methods: In this study, the genetic diversity and population structure of 12 populations were investigated using ten microsatellite markers. Among them, the Xiaolong Mountain (XLS) population is a cultured stock, while the Songjiachang Reservoir (SJC) population originates from the Yangtze River as an outgroup. Results: A total of 213 alleles were detected across 342 individuals, with an average of 21.3 alleles per locus. The observed heterozygosity (Ho) ranged from 0.362 to 0.902 (mean = 0.724), and the expected heterozygosity (He) ranged from 0.581 to 0.925 (mean = 0.805). Shannon’s diversity index (I) ranged from 1.224 to 2.810 (mean = 2.130). The polymorphism information content (PIC) varied from 0.532 to 0.920 (mean = 0.787), indicating high informativeness of the markers. Population structure analysis revealed a weak genetic subdivision with a subtle clustering signal (K = 2), but evaluation of LnP(K) indicated that K = 1 could not be confidently rejected. Pairwise Fst values ranged from 0.008 to 0.058, with high gene flow (Nm = 4.060–31.000), denoting low-to-moderate genetic differentiation. AMOVA showed that 98% of genetic variation resided within populations, with only 2% among populations (overall Fst = 0.020, p < 0.01). Nei’s genetic distances ranged from 0.094 to 0.277. Conclusions: Overall, the 12 populations of M. nipponense exhibited high genetic diversity, low-to-moderate genetic differentiation, and a weak population structure with most variation residing within populations. These findings provide valuable molecular markers for selective breeding and offer theoretical guidance for the conservation and sustainable utilization of M. nipponense germplasm resources, although the inferred population structure should be interpreted with caution given the weak differentiation signal.