Genome-wide association study of tolerance to acute hypoxia in the olive flounder (Paralichthys olivaceus) using individual blood cortisol levels as a physiological phenotype.

Hypoxia, caused by reduced dissolved oxygen (DO) levels in water, is a critical challenge in aquaculture and often results in stress, anorexia, and mass mortality in fish. The olive flounder (Paralichthys olivaceus) is a key species in South Korea's global aquaculture exports. However, aquaculture production of P. olivaceus experiences significant economic losses caused by hypoxia-induced fish mortality, highlighting the critical need for developing genetically improved hypoxia-tolerant strains. In this study, a genome-wide association study (GWAS) was performed to unveil single-nucleotide polymorphisms (SNPs) associated with acute hypoxia tolerance and elucidate underlying regulatory mechanisms. A total of 382 P. olivaceus fish were measured for blood serum cortisol level using enzyme-linked immunosorbent assay (ELISA) upon acute hypoxia stress. Blood plasma cortisol levels were used as a proxy phenotype of hypoxia tolerance, with the hypothesis that elevated concentrations indicate low tolerance, and minimized concentrations indicate high tolerance to acute hypoxia stress. Then, fish were genotyped using the Affymetrix® Axiom® myDesign™ genotype array, and 57,651 SNPs were retained after quality control filtering. A significant SNP was identified on chromosome 15 of the P. olivaceus genome, above the suggestive threshold (p < 1 × 10-4) for the stress cortisol level trait. A strongly associated SNP with accession number AX-419149718 was located in the zona pellucida-like domain-containing protein 1 (Zpld1) gene. Gene ontology (GO) analysis suggests that Zpld1 is involved in signaling pathways, including the integrin-mediated signaling pathway, thereby contributing to the mitigation of hypoxia stress effects. Collectively, this study provides insights into the genetic basis of acute hypoxia tolerance in P. olivaceus and may serve as a foundation for establishing genomic selection of olive flounders with acute hypoxia stress tolerance in aquaculture breeding programs.