A comprehensive genome-wide association study and genomic prediction in olive flounder for assessing disease resistance to Enteromyxum leei.

Abstract

Enteromyxosis, or emaciation disease, caused by myxosporean parasites of the Enteromyxum genus, results in significant economic losses in aquaculture, particularly affecting adult flounders. Although the pathogen has been identified, effective treatments for Enteromyxum infections remain limited. In this study, a genome-wide association study (GWAS) and genomic prediction (GP) were conducted to evaluate Enteromyxum leei resistance in a flounder population using a high-density single-nucleotide polymorphism (SNP) panel. Fish were categorized based on infection severity, and disease-related traits, such as absolute parasite copies, spores per cell, their log-transformed values (Abs_log and Spc_log), and relative condition factor (rCF), were used as phenotypes. After quality control, 61,024 SNPs were retained for GWAS analysis. Linkage disequilibrium (LD) analysis revealed a rapid decline in LD with increasing genomic distance. GWAS identified 20 SNPs suggestively associated with disease traits and rCF (p&#xa0;<&#xa0;1&#xa0;&#xd7;&#xa0;10), although none reached genome-wide significance (p&#xa0;<&#xa0;8.19&#xa0;&#xd7;&#xa0;10). These SNPs were mapped to candidate genes involved in key biological processes such as protein catabolism and signal transduction. GP using GBLUP and Bayesian C models demonstrated higher predictive ability for disease traits and rCF, especially when SNPs selected from GWAS were included, compared to randomly selected markers. Both prediction methods showed the highest predictive abilities for log-transformed derivative traits, particularly when 500-5000 GWAS-selected SNPs were used. Overall, this study provides evidence supporting the application of genomic selection to enhance resistance to E. leei in flounder. Our findings serve as a step toward developing resistance to emaciation diseases, ultimately contributing to improved productivity of flounder aquaculture.