The characteristic pink-reddish color in the salmonid fillet is an important, appealing quality trait for consumers and producers . The color results from diet supplementation with carotenoids, which accounts for up to 20-30% of the feed cost. Pigment retention in the muscle is a highly variable phenotype. In this study, we aimed to understand the molecular and microbiome basis for the variation in fillet color when fish families produced by the NCCCWA (YC 2020 ) were fed an astaxanthin-supplemented diet. We used RNA-Seq to study the transcriptome profile in the muscle, liver and pyloric caecum from fish families with pink-reddish fillet coloration (Red) versus those with lighter pale coloration (White). More DEGs were identified in the muscle (5,148) and liver (3,180) than in the pyloric caecum (272). Genes involved in lipid/carotenoid metabolism and transport, ribosomal activities, mitochondrial functions, and stress homeostasis were uniquely enriched in the muscle and liver. For instance, the two beta carotene genes (BCO1 and BCO2) were significantly under-represented in the muscle of the red fillet group, favoring more carotenoid retention. Enriched genes in the pyloric caecum were involved in intestinal absorption and transport of carotenoids and lipids. In addition, the analysis revealed the modulation of several genes with immune functions in the pyloric caecum, liver, and muscle.
In the same fish population, using 16S sequencing, we identified bacteria taxa showing differential abundance between the white versus the red fillet group . The red fillet group has enrichment (LDA score > 1.5) of taxa Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter chromiireducens. In contrast, the white fillet group has an enriched presence of mycoplasma, Lachnoclostridium, and Oceanobacillus indicireducens. The enriched bacterial taxa in the red fillet group have probiotic functions and can generate carotenoid pigments. Bacteria taxa enriched in the white fillet group are either commensal, parasitic, or capable of reducing indigo dye.
Separately , GWAS analysis was performed on unpigmented diet-fed fish families produced by the NCCCWA (YC 2010 & 2012) . SNP-harboring genes associated with fillet color are involved in carotenoid metabolism, myoglobin homeostasis, lipid oxidation, and maintenance of muscle integrity. Overall, o ur results revealed that fillet color is likely determined by carotenoid, lipid metabolism , and iron homeostasis.
This work extends our understanding of carotenoid metabolism in rainbow trout through the interaction between gene polymorphism, gene expression, gut microbiota and their relationship with fillet color. The genetic and microbial markers identified could be prioritized in breeding programs to enhance fillet color.