Solving the genetic mystery of the mosaic canary

Which genes are responsible for this peculiar plumage pattern?

Good scientific research resembles a thrilling mystery novel. Gathering clues, testing potential leads and critical thinking enable both detectives and scientists to solve the challenging questions. A recent study in the journal Science nicely illustrated this approach. The mystery: the genetic basis of mosaic plumage coloration in captive canaries. These red canaries are the result of crossing the Common Canary (Serinus canaria) with the Red Siskin (Spinus cucullatus). Bird breeders have selected for this color pattern – commonly known as the mosaic phenotype – by consecutive backcrossing the hybrids with “pure” Common Canaries. Over time, the genome of resulting red canaries is largely Common Canary-DNA with a dash of Red Siskin. And this dash of DNA probably contains the genes responsible for the red plumage color.

Consecutive backcrossing between the Common Canary x Red Siskin hybrid and “pure” Common Canaries results in a genome that mainly consists of Common Canary DNA (light green) with a bit of Red Siskin-DNA (dark green). From: Gazda et al. (2020) Science.

Zooming in

Using a series of genomic techniques, the researchers zoomed in on the Red Siskin-DNA in the mosaic canaries. They narrowed the search down to a genomic region (on scaffold NW_007931177) with 52 genetic variants that were different between canaries with yellow and red feathers. The mosaic phenotype is a recessive trait, meaning that mosaic birds have the same genetic variant on both chromosomes (in other words, they are homozygous). This insight provides another important clue to solve the mystery. Which of the 52 genetic variants are homozygous for the Red Siskin in the mosaic canaries? Focusing on these homozygous variants pointed to a genomic region of about 36,000 DNA-letters, containing three genes: PTS (6-pyruvoyltetrahydropterin synthase), BCO2 (b-carotene oxygenase 2), and TEX12 (testis-expressed protein 12).

The genetic basis of red coloration is homozygous for Red Siskin DNA. This knowledge allowed the researchers to zoom in on a particular region with homozygous variants (highlighted in the black box). From: Gazda et al. (2020) Science.

Gene Expression

Now that we have three main suspects (PTS, BCO2 and TEX12) we can explore a next lead: differential gene expression. Mosaic males and females show distinct plumage patterns. Males accumulate more red pigment in their feathers than females. Hence, we can expect that the genes controlling red color are differently expressed in males and females. The researchers took a closer look at the expression patterns of PTS, BCO2 and TEX12 in regenerating feather follicles. One gene showed decreased expression in males compared to females: BCO2. Did we find the culprit?!

We know that BCO2 codes for an enzyme that plays an essential part in the degradation of carotenoids, the pigments responsible for red coloration. In mosaic males, this enzyme is not very active and does not break down many carotenoids, resulting in the accumulation of red pigment in the feathers. The mosaic phenotype is thus the outcome of sex-specific differences in BCO2-activity, suggesting that it is controlled by other regulatory sequences (the genetic on-and-off switches). These regulatory elements remain to be identified. We might have found the murderer, but we are still looking for the brains behind the crime.

Two genes (PTS and TEX12) did not show significant differences in gene expression between males and females (top boxes). The third gene (BCO2), however, was less active in males compared to females. Interestingly, the difference in gene expression was only apparent in feather follicles (lower left box) and not in the liver (lower right box). From: Gazda et al. (2020) Science.


Gazda, M. A. et al. (2020). A genetic mechanism for sexual dichromatism in birds. Science368(6496), 1270-1274.

Featered image: A mosaic canary © Fernando Zamora Vega | Shutterstock

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