Genome-wide association mapping of scuticociliatosis resistance in a vaccinated population of olive flounder (Paralichthys olivaceus)

Abstract

Scuticociliatosis, a parasitic disease caused by the scuticociliate Miamiensis avidus (M. avidus), poses a grave threat to the olive flounder industry owing to its high morbidity and mortality rates. Vaccination is a safe and effective approach commonly practiced in farms to control key diseases, thus replacing conventional therapeutic measures with many limitations. Concurrently, selective breeding for enhanced disease resistance is underway in olive flounder breeding programs contingent on challenge tests involving unvaccinated fish. However, vaccination status may affect genetic predisposition to infection. This study pioneered the investigation of the genetic diversity underlying scuticociliatosis resistance in vaccinated olive flounders. A cohort of 720 fish received vaccination with formalin-killed M. avidus, followed by an intraperitoneal challenge test with live M. avidus. Genotyping of 474 vaccinated fish from 130 families was performed using a custom high-density 70 k single-nucleotide polymorphism (SNP) array, revealing a polygenic architecture with substantial genetic variation in scuticociliatosis resistance, with an estimated heritability of approximately 0.10 in the vaccinated population. A Genome-Wide Association Study identified 16 suggestively (1 × 10⁻⁴) associated SNP variants distributed over chromosomes 1, 7, 11, 12, and 13 and no genome-wide significant SNP. The top 17 candidate genes linked with identified SNPs were enriched with vital biological processes, essential for combating parasitic infections. These findings provide insights into the polygenic architecture of scuticociliatosis resistance in olive flounders. While the identified genetic markers explain limited phenotypic variance of 0.49 %, this study lays the groundwork for further genomic selection approaches, contributing to more effective disease management and sustainable aquaculture of olive flounders.