Enteromyxum leei (E.leei) infestation, belonging to the microscopic metazoans known as myxozoans, adversely affects fish health by suppressing appetite, hampering food metabolism, and causing growth impairment, ultimately leading to emaciation and cachexia. Additionally, it causes high mortalities and significant financial losses within South Korean aquaculture industries. In this study, our primary objective was to identify single nucleotide polymorphisms (SNPs) associated with resistance to E. leei in olive flounder using GWAS.
Initially, we obtained intestine samples from 752 olive flounders sourced from a farm naturally infected with E. leei. We utilized quantitative real-time PCR to quantify the infection levels, classifying them as high, medium, or low based on absolute copies using genomic DNA from the segment of mid-intestine. Furthermore, we established two indices using absolute copies and spores per cell. We performed SNP genotyping using the Affymetrix® Axiom® myDesign™ Array, leading to the discovery of 627 samples and 59,509 high-quality SNPs.
According to the GWAS conducted by the Gaston and ASReml R packages, several significant SNPs were mapped to chromosome 7. Functional annotations revealed that genes encoding nucleobindin-2-like and SET binding factor 2 were associated with regulating food intake and energy homeostasis, as well as cellular communication and the signaling network.
The heritability was estimated for two indices (absolute copies and spores per cell) range from 0.228 to 0.435. Additionally, we utilized a cross-validation approach to carry out genomic prediction employing various models, with the goal of estimating the prediction accuracy. Results revealed that Random forest(RF) (0.490~0.521) has higher genomic prediction accuracy than in GBLUP (0.472~0.479).
Collectively, this study has the potential to i ncrease the availability of E.leei resistant broodstocks, thereby reducing parasitic infection rates in South Korea aquaculture industry.