Olive flounder (Paralichthys olivaceus) is a prominent aquaculture species in South Korea, with over 50% of the national production originating from Jeju Island. Currently, approximately 90% of Korean olive flounder farms utilize moisture pellets (MP), processed from small fish. However, the instability of MP supply has increased due to challenges in securing fishery resources, driven by resource depletion and marine pollution. Additionally, the high moisture content of MP complicates storage and results in rapid disintegration in water, increasing the risk of disease. In response, the Korean government is pursuing a policy mandating the use of extruded pellet feeds (EP). Despite this, farmers hesitate to adopt EP due to the observed lower growth rates in fish fed with EP compared to MP. Thus, there is a critical need for breeding efforts to enhance growth rates under EP feeding regimes to maximize production efficiency. This transition is also essential for the future automation of the olive flounder aquaculture industry.
To track growth, 1,200 fish were tagged with passive integrated transponders, and the body weight of each individual was measured at two-month intervals from June to October 2023 under a commercial EP feeding regime. Additionally, weight gain rate and specific growth rate, calculated from body weight data, were also used as phenotypic data. Genotyping was performed using a custom 70K SNP chip designed by our laboratory. The collected data were then used to conduct a genome-wide association study (GWAS) and to develop an optimized genomic prediction model.
Heritability estimates ranged from low to moderate, with the highest value of 0.38 observed for final body weight. GWAS results revealed no significant SNP markers based on the Bonferroni cutoff, indicating a polygenic architecture for growth traits. Among the 10 algorithms used to develop the prediction models, the highest predictive ability (53.8%) was achieved with GBLUP using final body weight as the target phenotype. Furthermore, we observed an increase in prediction ability of up to 79.5% by utilizing the top SNP markers identified through GWAS.
These findings provide valuable insights for selecting superior broodstock to produce high-growth progeny, supporting the development of new olive flounder lines with enhanced growth performance under EP feeding regimes. This research can thus contribute to a successful shift from MP to EP diets within the Korean aquaculture industry.