Identification of candidate variants and genes associated with temperature tolerance in olive flounders by Genome-Wide Association Study (GWAS)

Abstract

The Republic of Korea is one of the largest producers of farm-raised olive flounder (Paralichthys olivaceus), accounting for nearly half of the global production. However, global warming has affected the aquaculture industry worldwide as it impacts survival, growth, and immunity and accelerates increases in pathogen load. In this study, we identified thermal stress-related genes in olive flounder using a genome-wide association study (GWAS) to provide a basis for marker-assisted selection and the development of temperature-resistant olive flounder in response to global warming. In total, 768 healthy olive flounder (weight of 159 ± 29.9 g and length of 25.42 ± 1.63 cm) were subjected to thermal stress (19.4–32.5 °C), and dead fish (537) were collected every 30 min. The fin tissues were isolated from all dead and surviving fish (231) and used for gDNA extraction. A high-quality 70 K SNP chip was used for genotyping, and 58,920 SNPs were obtained from 726 individuals after quality filtering. The GWAS identified 216 statistically significant SNPs at the Bonferroni cutoff (8.5 × 10−7). All significant SNPs were located on chromosome (chr) 18 (39 SNPs), chr 19 (176 SNPs), and contig 28 (AGQT02031776.1). After the SNP annotation, 13, 67, and 135 SNPs were identified in exons, introns, and intergenic regions, respectively. Gene and functional annotations revealed that almost all significant SNPs were directly or indirectly associated with the thermal stress response. Annotated genes were further categorized into the following functional groups: metabolic, neural and neuroendocrine, molecular and cellular, and physiological and behavioral responses. The significant SNP-harboring genes identified in this study could be used for marker-assisted genomic selection in future breeding programs.