Genome-wide association study (GWAS) of growth traits in olive flounder (Paralichthys olivaceus)

Abstract

Traits linked to growth performance in farmed fish are major drivers of profitability in aquaculture systems. Given the importance of growth-related traits, there have been efforts to unravel the genomic architecture of growth traits and to identify key genes or genomic regions useful as selection markers in various species. Such markers would increase the accuracy of selection and improve rates of genetic progress for growth improvement in breeding programs. Olive flounder (Paralichthys olivaceus) has a considerable market value in Asia and is mainly cultured in South Korea. To facilitate a breeding program for this species, a genome-wide association study (GWAS) was conducted to identify single nucleotide polymorphisms (SNP) associated with growth traits. In total, 1800 fish were measured for body weight (BW), total length (TL), and maximum body depth (BD). Fish were genotyped using the Affymetrix® Axiom® myDesign™ Genotyping Arrays; 1009 fish and 58,756 SNPs remained after the final quality control check. According to the phenotypes, female fish recorded higher BW, TL, and BD than male counterparts of the same age, revealing a sex-dependent growth pattern. There was a strong positive phenotypic correlation (0.945–0.965) and a moderate genotypic correlation (0.286–0.332) between the three growth performance traits of the 1009 fish. Eight SNPs were identified above the significant (p < 8.5 × 10−7) and suggestive (p < 1 × 10−5) thresholds for all traits, and they were mapped primarily onto chromosomes 23 and 24. According to the GWAS analysis, genotypes at loci AX-419206420 and AX-419307742 significantly affected the growth performance of the population. Gene ontology (GO) analysis was performed on 30 candidate genes with notable growth performance effects (p < 1 × 10−4) and GO terms related to neuron development, molecule binding and cytoskeleton organization were highly enriched. Our findings may contribute to understanding of the molecular basis of growth regulation and promote the use of SNP-based genomic selection in flounder culture.