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This page offers some demonstrations 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 5: dilute |
DNA to Trait 5. Identifying the gene behind dilute ( d or Myo5a).
| D/* | d/d | |
| m/m B/* |  |
 |
| Charcoal | Dust |
Students will first encounter dilute ( d) as an inherited phenotypic variation in scale color. It is present in the current screens.
More detailed reports on the phenotype of dilute and other scale-color variants can be fed to students as studies done by others. In the case of dilute, microscopic examination of developing scales from drake embryos will reveal that drakes homozygous for dilute have pigment granules that do not disperse normally, resulting in clumps of pigment and a dilution of color.
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.
As in the case of brown, dilute is easy to follow in crosses. We need a collection of DNA markers that can be followed in a cross of D/d or D/dl females. We can imagine that students might carry out crosses on a fairly large scale to see if they could separate the sex-linked recessive lethal phenotype from the scale-color phenotype in sons from D/dl females.
This is a mapping experiment, which would be much improved through the use of flanking markers. We have very good markers already: brown ( b) and rostral horn ( rh).
Imagine a cross of b D rh/B d Rh females to any males. We save sons that inherit crossover chromosomes:
b d Rh
B D rh
b D Rh
B d rh
b d rh
B D Rh
If the cross involves dl, all sons getting dl die, so the crossover classes are:
B D rh
b D Rh
B D Rh
The experiment will pin down the inherited phenotypic variation of dilute 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 dilute.
Students will have to confirm that they have selected the correct candidate gene by sequencing Myo5a from a dilute drake, then using 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. The sequence of dl would reveal a total loss-of-function allele, while d could be a missense allele. One of the disease-causing alleles in humans is an insertion causing a frameshift; another is a big deletion that removes an entire exon (see OMIM).
This project has a bonus in that dl is pleiotropic.
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.
| Mapping dilute with SNPs |
Let us assume that a student group would collect 200 males from D/d or or D/dl females. Each of these males is scored for dilute, 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 dilute 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 dilute 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 Myo5a.
Let us imagine that we have got students to the point that they are ready to take a drake homozygous for dilute from their stable and send a DNA sample to a facility for sequencing. They ask that the Myo5a gene be sequenced.
We can also imagine that students can take the remains of a drake that has died from dl and send a DNA sample to a facility for sequencing. They ask that the Myo5a 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.