Genome-wide association study for Vibrio parahaemolyticus resistance in the swimming crab Portunus trituberculatus

The swimming crab ( Portunus trituberculatus ), a species of significant economic value in China, has recently experienced substantial losses due to Acute Hepatopancreatic Necrosis Disease (AHPND), caused by the pathogen Vibrio parahaemolyticus . In this study, 298 P. trituberculatus specimens were experimentally challenged with a virulent V. parahaemolyticus strain. Whole-genome resequencing (WGS) detected 3955,382 high-quality single nucleotide polymorphisms (SNPs), which were analyzed to estimate the heritability of AHPND resistance and identify associated loci through genome-wide association study (GWAS). The heritability of AHPND resistance was estimated to be 0.10, indicating low heritability. GWAS identified five suggestively significant SNPs, collectively explaining 2.75 %-2.99 % of the phenotypic variance. Combining the GWAS candidate genes with the DEGs led to the identification of three immunity-related genes: IAP, Sf3a3, and evm.TU.Chr23.301, which are implicated in AHPND resistance. These results demonstrate the polygenic architecture of AHPND resistance in P. trituberculatus , providing insights into the molecular mechanisms of disease resistance and informing future genetic breeding strategies. • Found low heritability of AHPND resistance. • Identified five SNP loci and annotated 12 candidate genes for AHPND resistance. • The AHPND resistance trait in P. trituberculatus might be controlled by multigenes.