RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout

Authors: AHMED, RIDWAN - University Of Maryland; ALI, ALI - University Of Maryland; Leeds, Timothy - Tim; SALEM, MOHAMED - University Of Maryland

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/20/2023
Publication Date: 9/28/2023
Citation: Ahmed, R.O., Ali, A., Leeds, T.D., Salem, M. 2023. RNA-Seq analysis of the pyloric caecum, liver, and muscle reveals molecular mechanisms regulating fillet color in rainbow trout. BMC Genomics. 24:579. https://doi.org/10.1186/s12864-023-09688-5.
DOI: https://doi.org/10.1186/s12864-023-09688-5

Interpretive Summary: The color of rainbow trout fillets affects consumer preference. Fillet color can be manipulated by adding astaxanthin (a natural pigment) to the diet, but its inclusion increases feed costs and the uptake and retention of the pigment in the fillet can be variable. In this study, fish were fed a diet with astaxanthin, and those with divergent fillet coloration (red versus pale) were used to identify molecular mechanisms affecting uptake and retention by evaluating differences in gene expression in the pyloric caecum, liver, and muscle. Thousands of genes affecting ribosomal activities, mitochondrial functions, stress homeostasis, immune functions, and lipid/carotenoid metabolism, transport, and absorption were identified in these tissues as potential contributors to variation in fillet coloration. This study furthers our understanding of the mechanisms affecting variation in fillet color and informs strategies that can improve pigment retention in rainbow trout fillets.

Technical Abstract: The characteristic pink-reddish color in the salmonids 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 basis for the variation in fillet color when fish families were fed an astaxanthin-supplemented diet. We used RNA-Seq to study the transcriptome profile in the pyloric caecum, liver, and muscle from fish families with pink-reddish fillet coloration (Red) versus those with lighter pale coloration (White). More differentially expressed genes (DEGs) were identified in the muscle (5,148) and liver (3,180) than in the pyloric (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 cecum 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, liver, and muscle. The result from this study deepens our understanding of carotenoid dynamics in rainbow trout and can guide us on strategies to improve astaxanthin retention in the rainbow trout fillet.