Abstract

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.

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