Integrating genome-wide association study and functional analysis identify PvPdcd6 and PvDnajc22 as two key regulators of Vibrio parahaemolyticus resistance in Penaeus vannamei

Vibrio parahaemolyticus is a major threat to Penaeus vannamei aquaculture industry. Uncovering V. parahaemolyticus resistance gene and utilizing them to breed disease-resistant shrimp varieties represent an effective strategy to resolve this issue. In this study, we performed a genome wide association study (GWAS) on an F₂ shrimp population (n = 200) utilizing specific locus amplified fragment sequencing (SLAF-seq) to identify V. parahaemolyticus resistance genes. A total of 207,767 high-quality SNPs were detected, 12 of which were significantly associated with resistance to V. parahaemolyticus. Within 100 kb regions flanking of these significant SNPs, 20 candidate genes were identified. By integrating the GWAS results with prior transcriptomic data, PvPdcd6, PvDnajc22, and PvGlyctk were selected for further functional research. The results indicated that silencing PvPdcd6 and PvDnajc22, but not PvGlyctk significantly increased mortality of shrimp, Vibrio load and pathological damage in hemolymph, hepatopancreas and intestines following V. parahaemolyticus challenge. Further analysis demonstrated that inhibition of PvPdcd6 downregulated the expression of genes involved in the NF-κB pathway, antimicrobial peptides (AMPs), and autophagy, suggesting that PvPdcd6 contributed to host defense by activating autophagy and upregulating NF-κB signaling pathway, thereby promoting AMPs expression. Moreover, SNP association analysis identified four SNPs in PvPdcd6 and two in PvDnajc22 notably linked to V. parahaemolyticus resistance. Collectively, this study enhances our comprehension of the mechanisms underlying V. parahaemolyticus tolerance and lays a theoretical foundation for marker-assisted breeding of disease-resistant varieties.