Genome-Wide Association Study of Spawning Traits and Candidate Gene Mining in Portunus trituberculatus

Portunus trituberculatus is a commercially crucial marine aquaculture crab species in China, renowned for its high economic value. Spawning performance is one of the most important target traits in selective breeding programs for this species; however, the genetic architecture underlying this trait remains largely uncharacterized. In the present study, 160 artificially cultivated broodstock individuals were subjected to genomic analysis, with high-throughput liquid chip arrays employed for individual SNP genotyping. By combining these data with phenotypic records of spawning traits, the heritability of the target trait was estimated to be 0.065. A genome-wide association study (GWAS) using a mixed linear model detected nine SNP loci suggestively associated with spawning performance, with an average proportion of phenotypic variance explained (PVE) of 1.96%. One-way ANOVA of these suggestive loci revealed significant differences in phenotypic values among genotype groups, supporting the marker–trait associations; however, because this analysis used the same cohort as the GWAS, it should be considered exploratory rather than independent validation. These suggestive loci were distributed across 8 chromosomes including chromosome 24, 26, 30, 31, 32, 33, 36, and 48. The genetic effect analysis revealed that among the 9 suggestive loci, 8 exhibited additive genetic effects and the remaining 1 locus showed dominant effects. Based on the physical position information of these associated SNPs, 38 positional candidate genes were identified in adjacent genomic regions; 15 of these genes had clear annotation information, including three genes previously documented as reproduction-related: MOXD1, NFAT5, and DDX11. These results delineate the preliminary genetic basis of spawning traits in P. trituberculatus and provide important molecular markers and promising candidate genes for breeding improved varieties with high fecundity.