Data from: Carotenoid pigmentation in salmon: Variation in expression at BCO2-l locus controls a key fitness trait affecting red colouration

Carotenoids are primarily responsible for the characteristic red flesh
colouration of salmon. Flesh colouration is an economically and
evolutionarily significant trait that varies inter- and
intra-specifically, yet the underlying genetic mechanism is unknown.
Chinook salmon (Oncorhynchus tshawytscha) represent an ideal system to
study carotenoid variation as, unlike other salmonids, they exhibit
extreme differences in carotenoid utilization due to genetic
polymorphisms. Here, we crossed populations of Chinook salmon with fixed
differences in flesh colouration (red vs. white) for a genome-wide
association study (GWAS) to identify loci associated with pigmentation.
Here, the beta-carotene oxygenase 2-like (BCO2-l) gene was significantly
associated with flesh colour, with the most significant SNP explaining 66%
of the variation in colour. BCO2 gene disruption is linked to carotenoid
accumulation in other taxa, therefore we hypothesize that an ancestral
mutation partially disrupting BCO2-l activity (i.e., hypomorphic mutation)
allowed the deposition and accumulation of carotenoids within Salmonidae.
Indeed, we found elevated transcript levels of BCO2-l in white Chinook
salmon relative to red. The long-standing mystery of why salmon are red,
while no other fishes are, is thus likely explained by a hypomorphic
mutation in the proto-salmonid at the time of divergence of red-fleshed
salmonid genera (~30 MYA).