| Summary: | <p>Abstract</p> <p>Background</p> <p>Red flesh colour is a unique trait found in some salmonid genera. Carotenoid pigments are not synthesized <it>de novo </it>in the fish, but are provided by dietary uptake. A better understanding of the molecular mechanisms underlying the cellular uptake and deposition of carotenoids could potentially be used to improve the low muscle deposition rate that is typically found in farmed Atlantic salmon. In addition, from an evolutionary point of view, the establishment and maintenance of this trait is still poorly understood. It has been demonstrated in several species that scavenger receptor class B, member 1 (<it>SCARB1</it>) is involved in intestinal absorption of carotenoids, which makes this gene a possible source of genetic variation in salmonid flesh pigmentation.</p> <p>Results</p> <p>In this study, a novel paralog of <it>SCARB1 (SCARB1-2) </it>was detected through screening for genetic variation in Atlantic salmon <it>SCARB1</it>. Full length <it>SCARB1-2 </it>encodes a protein with 89% identity to Atlantic salmon <it>SCARB1</it>, except for the C-terminal cytoplasmic tail that shows only 12% identity. The most prominent site of <it>SCARB1 </it>mRNA expression was in the mid gut, while a five-fold lower level was detected in Atlantic salmon skeletal muscle and liver. The <it>SCARB1-2 </it>mRNA was equally expressed in liver, muscle and mid gut, and at a lower level than <it>SCARB1 </it>mRNA. A total of seven different <it>SCARB1-2 </it>alleles comprising repetitive enhancer of zeste motifs (EZH2) were identified in the founding parents of a resource Atlantic salmon population. We mapped the <it>SCARB1-2 </it>paralog to a region on Atlantic salmon chromosome 1, containing a putative QTL for flesh colour. Addition of the <it>SCARB1-2 </it>marker increased the significance of this QTL, however the large confidence interval surrounding the QTL precludes confirmation of <it>SCARB1-2 </it>as a causative gene underlying variation in this trait.</p> <p>Conclusion</p> <p>We have characterised a novel paralog of <it>SCARB1 (SCARB1-2)</it>, have mapped it to Atlantic salmon chromosome 1 and have described its expression in various tissues. Mapping with <it>SCARB1-2 </it>alleles added further evidence for a QTL affecting flesh colour on this chromosome, however further studies are needed to confirm a functional role for this gene in flesh colour pigmentation.</p>
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