The Promoter SNPs Were Associated with Both the Contents of Poly-Unsaturated Fatty Acids (PUFAs) and the Expressions of PUFA-Related Genes in Common Carp

Simple Summary Fish is an important PUFA source for human diet. Much research has focused on increasing the PUFA products of fish. Improving the biosynthesis of PUFAs would also be a way to contribute to nutrition supplement for human health. Aquaculture selective breeding by genetic markers is essential for increasing the content of PUFAs. Fatty acid desaturase 2 (fads2) and elongase 5 (elovl5) have been proven key rate-limiting enzymes in the synthesis of PUFAs for bony fishes. These genes’ coding SNPs (cSNPs) were reported to be significantly associated with the PUFA contents in common carp. However, the promoter SNPs (pSNPs) effectiveness for the PUFA contents has not been evaluated yet. This study identified the genetic variants in the promoter regions of fads2a/2b and elovl5a/5b. Moreover, the joint effects of multiple cSNPs and pSNPs in fads2b and elovl5b, two major genes related to the PUFA biosynthesis, were evidenced by the higher explained percentages of phenotype. Furthermore, the gene expression level of fads2a and fads2b showed significant positive correlation with the contents of multiple PUFAs. These SNPs would be potential markers for future selection to improve the PUFA contents in common carp. Abstract The allo-tetraploid common carp encodes two duplicated fads2 genes (fads2a and fads2b) and two duplicated elovl5 genes (elovl5a and elovl5b). The coding SNPs (cSNPs) of these genes were reported to be significantly associated with the PUFA contents. Whether the promoter SNPs (pSNPs) were associated with the PUFA contents has not been reported yet. In this study, after sequencing the promoters of these four genes, we identified six pSNPs associated with the contents of PUFAs in common carp, including one elovl5a pSNP, one elovl5b pSNP, and four fads2b pSNPs. The pSNPs were predicted in the locations of transcriptional factor binding sites. Together with previously identified cSNPs in fads2b and elovl5b, the pSNPs and cSNPs of these two genes had the joint effects on the PUFA contents with higher explained percentage of phenotypic variation of the PUFA contents than single gene. The expression levels of both fads2a and fads2b were significantly positively correlated with the contents of six PUFAs. The fads2b pSNPs corresponding to higher fads2b expression levels were associated with higher PUFA contents. The pSNPs and cSNPs will be useful for the future selection breeding of common carp with higher PUFA contents.