Dissecting the molecular mechanism of shrimp resistance to AHPND in Litopenaeus (Penaeus) vannamei via multi-year...

Acute hepatopancreatic necrosis disease (AHPND) has continuously caused substantial losses to the shrimp industry. Elucidating the molecular mechanisms underlying disease resistance is the basis for breeding disease-resistant shrimp strains to mitigate the impact of this disease. Disease resistance of shrimp is a quantitative trait, which is highly influenced by genetic background, environmental factors, and their interactions. Therefore, gene identification based on different populations might yield distinct candidate genes. This study aimed to identify stable candidate genes associated with AHPND resistance in Litopenaeus (Penaeus) vannamei by conducting a multi-year comparative transcriptomic analysis to provide more data to clarify the genetic background of shrimp resistance. A total of 389 differentially expressed genes (DEGs) between resistant and susceptible families of shrimp were identified through comparative transcriptomic analysis. KEGG enrichment analysis revealed that DEGs were significantly enriched in exosome biogenesis, pancreatic secretion, and immunity or stress-related signaling pathways, including PI3K-Akt and PPAR pathways. Most DEGs in the above enriched pathways were upregulated in susceptible families of shrimp. The shrimp in the susceptible families exhibited a chronically pre-activated immune-metabolic state, characterized by elevated basal immune activation, dysregulation of the IGFBP-IGF axis, increased protein catabolism, and enhanced gluconeogenesis. Key candidate genes, including alkaline phosphatase-like (LvAP), oplophorus-luciferin non-catalytic subunit-like (LvOLNC), and cilia- and flagella-associated protein 298-like gene (LvCFAP298) were consistently differentially expressed between resistant and susceptible families across multiple years. Further RNA interference experiments confirmed that LvOLNC and LvCFAP298 play important roles in shrimp defense against Vibrio infection. Except for the candidate genes related to shrimp resistance to AHPND, SNPs associated with AHPND resistance were also identified based on the transcriptomic data. This study not only provides more information for understanding the genetic basis underlying disease resistance of shrimp, but also provides important genetic markers for breeding of disease resistant shrimp.