Work

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

Year: 2026

Type: preprint

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.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.09.10.750604