| Summary: | Fatty acid desaturase 2 (<i>fads2</i>) is one of the rate-limiting enzymes in PUFAs biosynthesis. Compared with the diploid fish encoding one <i>fads2</i>, the allo-tetraploid common carp, one most important food fish, encodes two fads2 genes (<i>fads2a</i> and <i>fads2b</i>). The associations between the contents of different PUFAs and the polymorphisms of <i>fads2a</i> and <i>fads2b</i> have not been studied. The contents of 12 PUFAs in common carp individuals were measured, and the polymorphisms in the coding sequences of <i>fads2a</i> and <i>fads2b</i> were screened. We identified five coding single nucleotide polymorphisms (cSNPs) in <i>fads2a</i> and eleven cSNPs in <i>fads2b</i>. Using the mixed linear model and analysis of variance, a synonymous <i>fads2a</i> cSNP was significantly associated with the content of C20:3n-6. One non-synonymous <i>fads2b</i> cSNP (fads2b.751) and one synonymous <i>fads2b</i> 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 <i>fads2b</i> 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.
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