Vibrio parahaemolyticus is one of the main pathogenic bacteria of Portunus trituberculatus and causes mass mortality of P. trituberculatus in aquaculture. In addition, low-salinity stimulation makes P. trituberculatus more susceptible to V. parahaemolyticus infections. In order to elucidate the molecular mechanism of resistance to V. parahaemolyticus in P. trituberculatus, comparative transcriptomic analysis of blood cells stimulated by low salinity and V. parahaemolyticus was carried out in this study. Transcriptome sequencing of low-salinity stress and pathogen infection at different time points was completed using Illumina sequencing technology. A total of 5827, 6432, 5362 and 1784 differentially expressed genes (DEGs) involved in pathways related to ion transport and immunoregulation were found under low-salinity stress at 12, 24, 48 and 72 h compared with the control at 0 h. In contrast, 4854, 4814, 5535 and 6051 DEGs, which were significantly enriched in Toll and IMD signaling pathways, were found at 12, 24, 48 and 72 h compared with the control at 0 h under V. parahaemolyticus infection. Among them, 952 DEGs were shared in the two treatment groups, which were mainly involved in apoptosis and Hippo signaling pathway. Cluster analysis screened 103 genes that were differentially expressed in two factors that were negatively correlated, including immunoglobulin, leukocyte receptor cluster family, scavenger receptor, macroglobulin and other innate-immune-related genes. These results provide data support for the analysis of the mechanisms of immunity to V. parahaemolyticus under low-salinity stress in P. trituberculatus and help to elucidate the molecular mechanisms by which environmental factors affect immunity.

The swimming crab (Portunus trituberculatus) is a commercially important marine aquaculture species. After multiple generations of selective breeding, the third improved variety in China, “Huangxuan No 2” (HX2), was successfully developed in 2018. Compared to the original wild populations, HX2 exhibits enhanced resistance to low salinity stress and growth RATE. However, the genomic characteristics underlying these selected traits remain largely unexplored. To investigate the genetic variation associated with artificial selection, we genotyped 90 individuals from the HX2 strain and two wild populations (C and D) using a high-density SNP array. A total of 43,314 single nucleotide polymorphisms (SNPs) were identified, which were evenly distributed across the genome in 1 Mb windows. Genetic diversity analysis showed that HX2 and wild populations were similar but overall low in diversity levels. Population structure analysis and fixation index (Fst) values revealed low-to-moderate genetic differentiation between HX2 and the wild populations, whereas no differentiation was observed between the two wild populations. Using the wild populations as a reference, we identified 24 genomic regions under potential selection in HX2 based on the Fst between populations and the nucleotide diversity ratio (π-ratio), encompassing 425 candidate genes. Enrichment analysis indicated that these genes are primarily involved in pathways related to immune response, infection, signal transduction, and metabolism. Notably, genes associated with stress tolerance (e.g., GPX3, HMGCS1, Duox), immunity (e.g., LAMB1, HSPG2), and growth (e.g., Cht5) were identified. These findings provide valuable insights into the genomic signatures of artificial selection and offer fundamental resources for further genetic improvement of P. 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.