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This page offers a demonstration of the use of DracoBase. It is intended for developers.

Please contact Paul Szauter with comments and questions.

Outline of DNA to Trait Projects

This is adapted from the shared document Outline of DNA to Trait Projects, April 2011.

DNA to Trait 2. Identifying the gene behind brown ( b or Tyrp1).

	B/*	b/b
m/m D/*
	Charcoal	Earth

Students will first encounter brown ( b) as an inherited phenotypic variation in scale color. It is already present in the current Master level challenge.

More detailed reports on the phenotype of brown and other scale-color variants can be fed to students as studies done by others. In the case of brown, microscopic examination of developing scales from drake embryos will reveal that drakes homozygous for brown have pigment granules that are smaller than those from wild type.

I don't think that simply feeding students information about coat color genes in the mouse would be the best method for guiding students to investigate this gene.

It is easy to follow brown in crosses. We need a collection of DNA markers that can be followed in a cross of B/b females. Once the genome sequence is available we can discover SNPs between Nightwing (B/B) and drakes from the Eastern Kingdom bearing brown (b/b).

DNA of sons from the cross of B/b females to any parental male will be collected by students. We can imagine each student saving twenty such males to a stable, then sharing their DNA with the class.

There is no getting around that this is a mapping experiment. As I have described it above, it is a "dumb" one. We can make it smarter by selecting for analysis sons that have had crossovers near brown by following other sex-linked markers.

The experiment will pin down the inherited phenotypic variation of brown to a candidate genomic interval defined by particular SNPs. The more sons analyzed, the smaller the interval. Students would then examine all the genes in the interval to see if any is a candidate gene for brown.

Students will have to confirm that they have selected the correct candidate gene by sequencing Tyrp1 from a brown drake, then use a simple database tool to compare the predicted amino acid sequence from the mutants with the standard sequence from a wild-type strain.

For the actual mutation, we would lift one of the ones that is easy to spot from mouse or human.

Let us assume that a student group would collect 200 males from B/b females. Each of these males is scored for brown, then typed using 160 SNPs spread out along the X chromosome. The position of each SNP is known on the assembly.

The SNPs are summarized in the SNPs report.

The generation of 200 X chromosomes is summarized in the Generation of Recombinant X Chromosomes 1 demonstration.

The results of scoring the 200 X chromosomes for SNPs are shown in these displays:

229313 - 11809831 bp
11988466 - 22951710 bp
23129485 - 34421914 bp
34883889 - 44736849 bp
45115585 - 55806965 bp
56036063 - 65690579 bp
66387131 - 69789351 bp

The results of scoring the 200 X chromosomes for brown and all SNPs are shown in these displays:

229313 - 11809831 bp
11988466 - 22951710 bp
23129485 - 34421914 bp
34883889 - 44736849 bp
45115585 - 55806965 bp
56036063 - 65690579 bp
66387131 - 69789351 bp

Within each display, you can select to view all chromosomes, or only those that have had crossovers within the interval that you are viewing.

These displays make it possible to find the SNP most closely linked to brown visually. Inspection of the report Gene Models with Coordinates will reveal genes very closely linked to the relevant SNP. With 200 crossovers, there is really only one candidate gene. The flanking genes do not seem promising in terms of being able to influence scale color. The obvious choice is Tyrp1.

Let us imagine that we have got students to the point that they are ready to take a drake homozygous for brown from their stable and send a DNA sample to a facility for sequencing. They ask that the Tyrp1 gene be sequenced. The computational biology and genomics in Geniverse are better than what we have in our world. The facilty returns the results to the student in the form of a link.

The link goes to a page that displays the sequence of the predicted transcript from the mutant drake. This is hard to interpret by itself, but such is the power of steampunk genomics that the sequence from the mutant drake is aligned to the standard sequence from Nightwing. In addition, a predicted protein sequence is generated and aligned to the standard sequence from Nightwing.

What would such a page look like? Click the link below.

Tyrp1 sequence from b/b

There is an alternative to the mapping strategy that I don't like as well (because I'd like to teach mapping). The Tyrp1 gene is called tyrosinase related protein I because the sequence is similar to Tyrosinase ( Tyr). The brown allele from the old mouse fancy is a missense allele in a cysteine residue only three amino acids away from a cysteine residue that causes albinism when mutated in the Tyr gene. Please see:

http://www.genetics.org/content/126/2/443.long

In mouse, the cDNA for Tyrp1 appears to have been first isolated when looking for Tyr cDNAs. Students would not need to do this, because they will have an annotated genome sequence. Let's try this with the mouse genome. I used MGI to find the Tyr protein sequence. I forwarded it to MouseBLAST, doing a BLASTP search on the UniProt Mouse data. The p score for the Tyr protein (query vs. itself) is 4.8e-306. For Tyrp1 protein, it is 7.9e-107, which is highly significant. In mouse, the amino acid identity between Tyr and Tyrp1 is 40%, similarity (conservative substitutions) is 58%.

Students might "discover" the Tyrp1 gene in the annotated genome sequence of drakes while looking for Tyr (see the outline of the analysis of colorless). We can give them a hint that it might be worth looking into.

From this outline, you can see that this requires us to: 1) devise ways to feed research information to students (easy), 2) introduce a lot of SNPs as genetic markers, 3) build a genomic database that supports simple queries, and 4) devise (or steal) a tool that allows the comparison of DNA and amino acid sequences.

Let us imagine that we have got students to the point that they are ready to take a drake homozygous for brown from their stable and send a DNA sample to a facility for sequencing. They ask that the Tyrp1 gene be sequenced. The computational biology and genomics in Geniverse are better than what we have in our world. The facilty returns the results to the student in the form of a link.

The link goes to a page that displays the sequence of the predicted transcript from the mutant drake. This is hard to interpret by itself, but such is the power of steampunk genomics that the sequence from the mutant drake is aligned to the standard sequence from Nightwing. In addition, a predicted protein sequence is generated and aligned to the standard sequence from Nightwing.

What would such a page look like? Click the link below.

Tyrp1 sequence from b/b