Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)

• Published in: BMC Genomics
• Main Authors: Thu Thi Minh Vo, Tuan Viet Nguyen, Gianluca Amoroso, Tomer Ventura, Abigail Elizur
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2021
• Subjects: RNA-Seq; TruSeq; 3’ mRNA-Seq; Lexogen QuantSeq; Flesh discoloration; Atlantic salmon; Biotechnology; TP248.13-248.65; Genetics; QH426-470; Salmo salar
• Online Access: https://doi.org/10.1186/s12864-021-07884-9; https://doaj.org/article/8ad1276abf214c5fbb7a7702ff9d5dea

Abstract Background The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3’ mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3’ mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes. Results In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR. Conclusions Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding ...