Association between the Polymorphisms of fads2a and fads2b and Poly-Unsaturated Fatty Acids in Common Carp (Cyprinus carpio)

SIMPLE SUMMARY: Fishes are the major dietary source of polyunsaturated fatty acids (PUFAs) for humans. The limited availability of PUFAs derived from fish represents a critical bottleneck in food production systems, one that numerous research institutions and aqua-feed companies in this field are trying to overcome. This problem could be minimized by select-bred fish to be capable of more effectively producing endogenous PUFAs. Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in the synthesis of PUFAs. The common carp, one of the most important food and ornamental allo-tetraploid fish, encodes two fads2 genes (fads2a and fads2b). The PUFA contents among common carp individuals were numerous, suggesting that there might exist polymorphisms in fads2a and fads2b. However, selective breeding of common carp with high PUFA contents was hindered due to a lack of effective molecular markers. This study investigated the contents of PUFAs in common carp and identified polymorphisms in the CDS regions of fads2a and fads2b. The association study identified three cSNPs associated with the PUFA contents and suggested that fads2b might be the major gene responding for common carp PUFA contents. These cSNPs would be potential markers for future selection to improve the PUFA contents in common carp. ABSTRACT: Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in PUFAs biosynthesis. Compared with the diploid fish encoding one fads2, the allo-tetraploid common carp, one most important food fish, encodes two fads2 genes (fads2a and fads2b). The associations between the contents of different PUFAs and the polymorphisms of fads2a and fads2b have not been studied. The contents of 12 PUFAs in common carp individuals were measured, and the polymorphisms in the coding sequences of fads2a and fads2b were screened. We identified five coding single nucleotide polymorphisms (cSNPs) in fads2a and eleven cSNPs in fads2b. Using the mixed linear model and analysis of variance, a synonymous fads2a cSNP was significantly associated with the content of C20:3n-6. One non-synonymous fads2b cSNP (fads2b.751) and one synonymous fads2b cSNP (fads2b.1197) were associated with the contents of seven PUFAs and the contents of six PUFAs, respectively. The heterozygous genotypes in both loci were associated with higher contents than the homozygous genotypes. The fads2b.751 genotype explained more phenotype variation than the fads2b.1197 genotype. These two SNPs were distributed in one haplotype block and associated with the contents of five common PUFAs. These results suggested that fads2b might be the major gene responding to common carp PUFA contents and that fads.751 might be the main effect SNP. These cSNPs would be potential markers for future selection to improve the PUFA contents in common carp.