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Identifying genetic markers to improve Atlantic salmon fillet color

St. Andrews, New Brunswick, Canada – November 5, 2024 

Fillet color is perhaps the most important sensory characteristic that influences consumer purchasing at a fish market. The highest quality salmon fillets possess a consistent redness color tone, which results from binding unmetabolized carotenoid pigments, such as astaxanthin, to muscle tissue. Astaxanthin is supplemented within cultured Atlantic salmon diets but this is the same compound from planktonic crustaceans consumed by wild Atlantic salmon. Supplemented astaxanthin accounts for 10-15% of Atlantic salmon feed costs making it imperative to understand fillet color variability within a population and ensuring optimal uptake across all farmed Atlantic salmon. 

“We have completed harvest evaluations since our 2011 year class, and now into our third generation, from a commercial North American origin Atlantic salmon broodstock program, including fillet color assessments with tissue sampling from each assessed salmon over this time,” explains Dr. Amber Garber, a Huntsman Marine Research Scientist and anchor co-author on a recently published research study in the peer-reviewed journal Frontiers in Genetics. 

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Previous genomic and functional studies have linked fillet color redness with specific genes in Atlantic  salmon of European origin. “Unfortunately, Atlantic salmon originating from North America experienced  chromosomal rearrangement from its European counterpart during the last ice age causing both major populations of Atlantic salmon to be genomically distinct,” states Dr. Barbara Langille, also a Research Scientist with Huntsman Marine and lead author on the recent publication. This rearrangement means that studies focused on European origin Atlantic salmon must be repeated when trying to identify genomic markers for selection with North American origin Atlantic salmon as different or additional genomic regions may be involved for the trait of interest, in this specific case fillet color.

Fin clips collected from assessed Atlantic salmon comprising the 2018 & 2019 year classes (representing 83 & 207 families, respectively) were sent to IdentiGEN (Ireland) for genotyping using an array with 55,725 single-nucleotide polymorphism (SNP) markers distributed evenly across the 27 chromosomes of the North American origin Atlantic salmon genome. The resulting genotyping data was used to complete a genome-wide association study focused on fillet color to identify genomic regions of interest coupled with specific associated genes having a known purpose.

In this case, chromosome 26 displayed the same consistently elevated genomic region for both year classes associated with fillet color redness and yellowness while no significant markers were observed for measured fillet lightness. Numerous specific genes were identified close to this peak of interest on chromosome 26, most notably including beta-carotene oxygenase 1 (bco1), which is known for its function in carotenoid metabolism. “We were excited to discover the first known linkage between the bco1 gene with not only the redness trait in Atlantic salmon but also the measured yellowness trait as well when aspects of color were quantified,” added Langille. Six additional genes were identified that may be involved in or closely linked with the pigmentation of Atlantic salmon muscle. Known functions for these specific genes include thermogenesis, immune function and pathogenic responses thereby providing further validation to the readily accepted knowledge that muscle color and presence of carotenoids are highly correlated with boosting immunity in Atlantic salmon and other animal species.  

This specific study measured fillet color traits of two year classes of Atlantic salmon from the same commercial broodstock program. The pedigree-based heritability of lightness was the lowest among the color traits in both yea classes (between 0.21 and 0.30), while the heritability of redness and yellowness was consistently higher ranging from 0.32 (2018 yellowness) to 0.59 (2019 redness). These moderate-to-high pedigree-based heritability estimates suggest selective breeding can potentially improve these traits to produce consistent and high quality product for the marketplace. Genomic-based heritability for these same traits was slightly higher in the 2018 year class of salmon but slightly lower in the 2019 year class. A previous publication by the Huntsman Marine researchers described the 2011 year class, which were the grand-parental generation of the 2019 year class. Unsurprisingly, the earlier 2011 year class displayed similar heritability values between 0.42 and 0.58 for these same color traits. 

One final aspect of the present publication validated use of the SalmoFan method to characterize color in Atlantic salmon fillets. A SalmoFan has blades that are arranged in an ordered gradient of color from pale pink/peach to a deep red/yellow for salmonids. The SalmoFan is widely used to visually assess fillet color in the industry given its low cost for adoption but collected data depends on the color-perceiving ability of the assessor and, therefore, may be subjected to bias. This is in contrast to the Chroma Meter used by Huntsman Marine researchers to objectively measure individual aspects of colour, such as its lightness, redness and yellowness. 

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Color measured using a SalmoFan in the published study provided the same levels of moderate-to-high pedigree- and genomic-based heritabilities. SalmoFan measurements had at least moderately positive correlations genetically with quantified redness and yellowness traits using the Chroma Meter but moderately negative correlation with lightness measurements. The same region on chromosome 26 was also elevated genomically for SalmoFan data as described earlier Chroma Meter measured redness and yellowness. These results overall were not surprising as the quantified redness, yellowness and lightness measured with the Chroma Meter in theory make up the perceived color observed using a SalmoFan.  

This study provides insights into the genomics of the color traits in North American origin Atlantic salmon fillets and will aid in the selection to obtain a desired fillet color. “The absence of lightness within the elevated region of chromosome 26 requires further study to reveal its genetic architecture and ensure appropriate selection is completed across the broad perception of fillet color,” concludes Langille.

The research publication was co-authored by geneticists with Mowi Genetics AS (Bergen, Norway). Various aspects of this project were funded by the Government of Canada through Genome Canada and Genome Atlantic, the Atlantic Canada Opportunities Agency (ACOA) – Atlantic Innovation Fund, the New Brunswick Innovation Foundation – Research Innovation Fund and industry partners MOWI Canada East and formerly Northern Harvest Sea Farms. 

Research Publication: 

Langille, B.L., P. Sae-Lim, S. Boison, P.G. Wiper and A.F. Garber. 2024. Genome wide association identifies genomic regions influencing fillet color in Northwest Atlantic salmon (Salmo salar Linnaeus 1758). Frontiers in Genetics 15: 1402927.  https://doi.org/10.3389/fgene.2024.1402927
www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1402927/full

Image 1: Harvest evaluation completed in a commercial processing plant facility.

Image 2: Comparing use of the Chroma Meter versus SalmoFan to measure characteristics of fillet color. 

 

Story by Bud Adams, The Huntsman Marine Science Centre.  

For additional information or images relating to this article, please email huntsman@huntsmanmarine.ca. 

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