BCO2 = beta-carotene oxygenase 2
Coloration (beak)
Cis-regulatory,
Unknown
Geospiza scandens
(species) D
Geospiza fortis
medium ground-finch - (species) D
Geospiza conirostris
(species) D
Geospiza magnirostris
(species) D
Geospiza fuliginosa
(species) D
Camarhynchus parvulus
(species) D
Camarhynchus pauper
(species) D
Camarhynchus pallidus
woodpecker finch - (species) D
Geospiza difficilis
(species) D
Intraspecific
Association Mapping
Enbody ED; Sprehn CG; Abzhanov A ; et al. (2021)
A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation.
GP00002384
BCO2
Q9BYV7
Morphology
"By closely inspecting this region in a combined sample of all 456 finches of the two species we identified a single exonic SNP with a likelihood ratio test (LRT) statistic exceeding 166 (Figure 1C). It is also the only consistently elevated SNP in an analysis of each species alone (Figure S1), is the best fit variant under a recessive model (STAR Methods), and occurs on multiple haplotypes (Figure S1C). This SNP (chr24:6,166,878; p6166878 hereafter) leads to a synonymous change 32 bp into exon 4 of BCO2. "
"The functional importance of the observed synonymous change is uncertain, and the presence of an unidentified linked causal variant cannot be completely ruled out (see Conclusions). However, a functional explanation is possible because codon usage can be under strong selection30 and may have functional consequences on translation,30 RNA stability,31 and transcription.32 Notably, p6166878 changes the highest frequency valine codon (ƒGTG = 27.3%) to the lowest (ƒGTA = 7.6%) in the reference genome. This is in line with the observed phenotypic effect of the yellow mutation because a lower abundance codon is expected to be associated with lower protein expression.33 In this case, less BCO2 activity results in more carotenoid deposition in the yellow morph. In fact, we found that yellow homozygotes showed significantly lower BCO2 expression compared to pink homozygotes in the upper beak of developing embryos (Figure 1F) that were sourced from a variety of different species and islands (Table S1): small sample sizes prohibit species-specific analysis. Among the six heterozygous individuals, the pink allele was expressed more than the yellow allele in five samples tested using a droplet-digital PCR (Figure S2C). Differences in expression between the two alleles, and in the absence of alternative splice variants (STAR Methods), raise the possibility that the synonymous change alters transcription factor binding affinity in exon 4. Further research into tissue-specific expression and the specific transcription factors that regulate BCO2 is warranted."
Geospiza scandens
(species)
Geospiza fortis
medium ground-finch - (species)
Geospiza conirostris
(species)
Geospiza magnirostris
(species)
Geospiza fuliginosa
(species)
Camarhynchus parvulus
(species)
Camarhynchus pauper
(species)
Camarhynchus pallidus
woodpecker finch - (species)
Geospiza difficilis
(species)
Geospiza scandens
(species) D
Geospiza fortis
medium ground-finch - (species) D
Geospiza conirostris
(species) D
Geospiza magnirostris
(species) D
Geospiza fuliginosa
(species) D
Camarhynchus parvulus
(species) D
Camarhynchus pauper
(species) D
Camarhynchus pallidus
woodpecker finch - (species) D
Geospiza difficilis
(species) D
BCO2 = beta-carotene oxygenase 2
Geospiza scandens
(species)
Geospiza fortis
medium ground-finch - (species)
Geospiza conirostris
(species)
Geospiza magnirostris
(species)
Geospiza fuliginosa
(species)
Camarhynchus parvulus
(species)
Camarhynchus pauper
(species)
Camarhynchus pallidus
woodpecker finch - (species)
Geospiza difficilis
(species)
Published - Accepted by Curator