Identification of candidate genes associated with AHPND resistance based on genome-wide association study in Pacific white shrimp Litopenaeus vannamei

The Pacific white shrimp Litopenaeus vannamei (L. vannamei) is one of the most important mariculture species. A massive outbreak of acute hepatopancreatic necrosis disease (AHPND) resulted in a huge economic loss to the shrimp aquaculture industry. In this study, a total of 1033 individuals resistant and susceptible to AHPND were genotyped using a custom-designed SNP chip based on target sequencing technology. A total of 54,092 high-quality single-nucleotide polymorphisms (SNPs) were obtained. A genome-wide association study (GWAS) identified 122 SNPs associated with the AHPND resistance traits in shrimp, including 2 genome-wide significant SNPs and 120 chromosome-wide SNPs. These SNPs were distributed across multiple chromosomes and formed a haplotype block on chr27, revealing the polygenic nature of AHPND resistance in L. vannamei. Additionally, 76 candidate genes were identified near these SNPs. Among them, translocon-associated protein subunit alpha (TRAPα) and sphingomyelin phosphodiesterase acid-like 3 (SMPDL3) were confirmed to be associated with this trait. These findings not only offer new insights into the genetic mechanisms underlying AHPND resistance in shrimp but also provide valuable genetic markers for molecular breeding in this species.