Introduction
Fillet color is a key trait which determines the quality of farmed salmon, and has been identified as a polygenic trait in nature, with some QTL (quantitative trait loci) being associated with carotenoid and lipid metabolism genes. The Lochy strain of Atlantic salmon has shown high variation in fillet color between families and between males and females. Thus, identifying QTL associated with color could help improve the quality of this strain through the use of genomic selection. This study presents a genome-wide association study (GWAS) of fillet color in a domesticated population of the Lochy strain. Additionally, we assessed the potential to predict fillet color using genomic information for broodstock selection.
Materials and methods
1194 pit-tagged fish (from 200 full-sib families; 589 females and 605 males) were harvested from a marine fish farming center in Chile belonging to the salmon breeding program of Salmones Camanchaca company. Fillet color was digitally measured using the QMCOLOR software (Quality Metrics SPA), and expressed as a quantitative variable ranging from 20 (low color) to 34 (high color) (Figure 1). All fish were genotyped with a customized 62 K Affymetrix genome-wide SNP-chip. The genomic association analysis was conducted using the GMMAT package of R; then, breeding values were estimated using the Genomic Best Linear Unbiased Prediction (GBLUP) with the BGLR package of R. The predictive ability of GBLUP was obtained from a 5-fold-cross-validation with BGLR, while the ICSASG_v2 genome in the NCBI database was used to identify genes associated with color.
Results and Discussions
The average fillet color, measured in the belly region, was 24.2 ± 0.98 (Females: 24.4 ± 0.94; Males: 24.0 ± 0.98). A total of 35 SNPs were found to be significantly associated with belly color, distributed in Ssa26 (33 SNPs) and Ssa29 (2 SNPs) (Fig. 2). The heritability of this trait was 0.29, and the genetic variance explained by QTL markers ranged from 8.6%-26.4% in Ssa26 and from 6.8%-7.0% in Ssa29. Notably, Ssa26 harbors two genes, bco1 and bco1l, which are involved in the metabolism (oxidation) of carotenoids (Helgeland et al., 2019; Sae-Lim et al., 2022). The correlation between breeding value and phenotype varied from 0.72 to 0.79 for the training populations, but was only between 0.32 and 0.44 in the test populations.
Conclusion
In conclusion, two genomic regions were associated with fillet color variation in the Lochy strain of Atlantic salmon. The first, located on chromosome 26, has already been identified in other domesticated fish strains such as Mowi and Aquagen . A new chromosomal region was detected on chromosome 29 in the Lochy strain, but the explained variance was lower than that on chromosome 26. These results demonstrate that genomic selection can be used to accelerate the genetic progress of color measurement digitally in this strain.
Acknowledgment
Funded by the doctoral scholarship ANID N°21211159 to P. Rivera and Salmones Camanchaca SA .
References
Helgeland, H., Sodeland, M., Zoric, N., Torgersen, J. S., Grammes, F., von Lintig, J., Moen, T., Kjøglum, S., Lien, S., and Våge, D. I. (2019). Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color. Scientific Reports, 9(1): 20061.
Sae-Lim, P., Boison, S. and Baranski M. (2022). Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). 2347-2350