Genomics of omega-3 in Atlantic salmon

Marine oils constitute an important source of the omega-3 fatty acids EPA and DHA that are essential components in both human and fish diets. Marine oils are, however, a limited resource. In OMEGA3GENOMICS, we focused on the individual genetic capacity of the fish to synthesize and deposit of EPA and DHA in different organs while maintaining good health. The genetic basis of the EPA and DHA trait was studied in a selective breeding population using a combination of genomic methods with the aim of revealing the complex genetic mechanisms regulating the omega-3 fatty acid metabolic pathway. Results: 1. The heritability of the relative amounts of EPA and DHA in salmon fillet has a heritability of 9 and 26%, respectively. This shows a genetic potential of the Atlantic salmon to increase the contents of these two important fatty acids, which enables selection for increased contents of EPA and DHA in the filet by the breeding companies. 2. We evaluated the use of the fast method «near-infrared» NIR spectroscopy could be used to measure the contents of EPA and DHA in muscle. Results show that the method does not have enough precision, due to a large co-variation between the EPA, DHA and total fat contents. It was therefore difficult to detect individual differences in EPA and DHA contents in the muscle. 3. We have shown that EPA og DHA levels in Atlantic salmon muscle are associated with the expressions of genes related to carbohydrate metabolism, including insulin, and genes related to muscle function. Increased levels of EPA and DHA in muscle could not be explained by up- or down regulation of genes related to elongation and desaturation of omega-3 fatty acids in our experiment. 4. We found a negative effect of methylation of individual CpG loci in the delta6fad_b gene on both expression of the delta6fad_b gene and contents of EPA and DHA in liver, but not muscle. We also found less methylation of the delta6fad_b gene in salmon fed a diet with a high level of fish oil. However, no effect of diet was found on the methylation of the delta5fad, Elovl2 or Elov5_b genes in neither liver or muscle. These genes are central in fatty acid metabolism. 5. In a gene association study, we found genetic markers on chromosome 21 in the Elov2 gene on chromosome 19 with effect on contents of omega-3-fatty acids in salmon muscle. 6. Genomic selection is a method, where large numbers (10000-100000) of genetic markers are used to estimate breeding values of selection candidates of breeding programs. Here, we tested the accuracy of selection when using only 400 genetic markers in genes with known differences in gene expression of salmon with different marker alleles. The accuracy of these breeding values was 15% lower compared to a dataset with ~50000 genetic markers for relative content of DHA in muscle, but for relative content of EPA in muscle and muscle fat content, we found no differences between the two data sets in the accuracy of the genomic breeding values.

-

The omega-3 fatty acids are essential components in both human and fish diets. The health beneficiary very long chain omega-3 fatty acids EPA and DHA are only found in marine ingredients, while the shorter chain alfa-linolenic acid (ALA) are found in several plant oils. There is a global lack of marine oils for use in fish diets due to an increased demand from the aquaculture industry and human consumption sectors. The overall aim of OMEGA3GENOMICS is to increase the genetic capacity of Atlantic salmon to synthesize, utilize and deposit omega-3 fatty acids while maintaining good health. We have in earlier projects shown a significant genetic variation in the capacity of Atlantic salmon to synthesize the omega-3 fatty acids EPA and DHA from ALA, and that this variation impacts the capacity of the fish to cope with different diets, lipid storage, survival and inflammatory status. The EPA and DHA contents in the muscle does not only depend on the capacity to synthesize EPA and DHA in the liver, but the omega-3 fatty acid bioconversion also includes uptake, transport, deposition, mobilization, oxidation in other tissues and organs including muscle. In OMEGA3GENOMICS, this complex genetic basis of this trait will be approached by a combination of genome-wide association, transcriptomics, epigenetics and genomic prediction studies. Results aim to be directly relevant for the aquaculture selective breeding, feeding and production industries in their work to reduce the dependence on marine oils.