Identification of genes associated with resistance trait to VP_AHPND in Pacific white shrimp (Litopenaeus vannamei) using Bulk Segregation Analysis (BSA)

Vibrio parahaemolyticus harboring the PirA/PirB toxin (VP_AHPND) is regarded as one of the main pathogens that caused Acute hepatopancreatic necrosis disease (AHPND) in the Pacific white shrimp Litopenaeus vannamei (L. vannamei). Breeding new varieties resistant to VP_AHPND is considered to be the most effective way to reduce the economic losses in shrimp aquaculture. Identification of genes and SNP markers associated with resistance trait could accelerate the breeding efficiency by application of marker assisted selection and genomic selection. In the present study, a Bulk Segregation Analysis coupled to whole genome sequencing method was employed to identify SNPs and genes associated with resistance trait to VP_AHPND in L. vannamei. The DNA of susceptible and resistant individuals was pooled separately. ED (Euclidean distance) and the chi-square test were applied to calculate the allele frequency and genotype frequency differences between susceptible and resistant individuals. A total of 2238 SNPs and 97 genes were identified to be associated with resistance trait to VP_AHPND. KEGG enrichment analysis showed that these genes were significantly enriched in PPAR signaling pathway, PI3K-Akt signaling pathway, NLR pathway and O-Antigen nucleotide sugar biosynthesis pathway. The acyl-CoA delta-9 desaturase gene, 14–3–3 epsilon-like gene, retrovirus-related Pol polyprotein gene, enzymatic polyprotein gene in these pathways were considered as candidate genes associated with resistance trait to VP_AHPND of shrimp. This study demonstrated that BSA based on whole genome re-sequencing was a cost-effective method for identifying disease resistant genes in aquaculture animals. These data will not only provide useful information for understanding the genetic basis of shrimp resistance trait to VP_AHPND, but also offer a source of SNPs for marker-assisted selection and genomic selection in shrimp breeding.