Genome-wide association study and genetic differentiation analysis reveal the genetic basis of Vibrio harveyi resistance in blackspotted croaker (Protonibea diacanthus)

Abstract

Vibrio harveyi is a primary causative agent of vibriosis, leading to catastrophic economic losses in the blackspotted croaker (Protonibea diacanthus) aquaculture. However, the genetic architecture underlying its resistance remains poorly understood. In this study, we conducted the first integrated genome-wide association study (GWAS) and genetic differentiation analysis (F_ST) to investigate the genetic basis of V. harveyi resistance. A total of 450 juveniles were challenged, and 300 individuals (comprising 150 resistant and 150 susceptible) were selected for whole-genome resequencing. Genomic heritability (h^2) was estimated at 0.374+/-0.29 for survival time (ST) and 0.237+/-0.185 for survival status (SS), indicating moderate genetic control. Notably, an exceptionally high genetic correlation (r_g = 0.999) was observed between ST and SS, while resistance traits were genetically independent of growth performance (r_g < 0.03). Through the convergence of GWAS and selection sweep signals, a major-effect QTL was identified on chromosome 4. Candidate gene prioritization identified high-confidence targets involved in post-transcriptional regulation and mRNA stability, specifically elavl4 (harboring a top-tier exon variant), rorb, cbpc6, and epn4. Functional enrichment analysis further revealed that resistance is significantly associated with "rRNA processing", "mRNA surveillance pathway", and "nucleocytoplasmic transport", suggesting that efficient RNA metabolic control is a critical determinant of host survival. These findings provide novel insights into the non-canonical immune mechanisms of P. diacanthus and offer robust molecular markers for marker-assisted selection and genomic selection, facilitating the development of disease-resistant strains in the sciaenid industry.