Project: Genomic Mapping
Exploring the Maize Genome
presented by Dr. Richard Whitkus
Objectives:
1. Apply collaborative problem solving strategies to a
bioinformatics problem.
- Gather necessary background through discussion with
presenter and utilize necessary resources.
- Determine presenter's desired outcome or goals and
define specific questions related to the problem.
- Break down the problem and develop approaches to
finding solutions.
2. Become familiar with mapping and extend the experience
gained in the exercise.
- Learn to use comparative mapping tools.
- Apply these tools to identify similarities in the
genomes of 2 or 3 grass species.
- Be able to analyze and evaluate the quality of your
results.
3. Gain experience making a scientific presentation and
short report.
Description of expectations on reporting your analysis,
along with presentations and discussion in class is given at
the end of this section. Points = 20. Due 10/9.
Readings:
The following link is required reading for this
section:
Gale,
M. D. and D. M. Devos, 1998. Comparative genetics in the
grasses. Proceedings of the National Academy of Sciences
(USA), 95:1971-1074.
The following paper provides additional information that
can be read for background information, but are not
required:
Paterson
et al., 2000. Comparative genomics of plant chromosomes. The
Plant Cell 12: 1523-1539.
A review paper on comparative genomics in
plants, focusing on comparative genomic mapping.
Background:
Comparative genomic mapping allows comparisons of genome
structure from one species to another (synteny
relationships). Within a species, comparative mapping among
chromosomes can reveal another aspect of evolutionary
history - the presence and degree of genomic duplication.
This ability allows us to make informed choices about genome
complexity and to select those genomes that would be more
efficient at locating genes of interest. Larger, more
complex genomes contain more "junk" DNA and more
duplications. Therefore much more sequencing would be
required to locate and characterize specific genes. In
smaller, less complex genomes, less effort would be needed.
Yet if two genomes show significant relatedness, a small
genome can potentially serve as a model for a larger genome,
as long as the smaller genome does not exhibit greater
complexity relative to the larger genome.
To completely sequence a genome requires a tremendous
effort. Linkage and/or physical mapping, however, can
characterize most genomes relatively quickly. If two or more
maps are constructed with the same probe set (linkage maps),
then homeologous loci are identified among the maps.
Therefore, comparing maps among genomes can provide insights
about genome complexity, synteny relationships, and possibly
insights into genome size. Given the amount of information
available in the grass family, the most important group of
food plants in the world, we can explore some aspects of
genome similarity and complexity and apply it to real
problems.
Independent of mapping, genome sizes in many grass
species have been estimated. For rice, it is 490 megabase
pairs (mbp). For sorghum it is 1190 mbp, and for maize it is
2670 mbp.
Finally, from the reading provided, you know that all
grass genomes show a surprising degree of synteny. Thus one
genome can serve as a model for studying genomics in the
others. The question becomes, which one? Choose carefully,
you are planning on a multi-year, multi-person,
multi-million dollar research program. As a major advisor
has been known to tell students "Don't screw up!"
Getting
started:
For this problem, there are two excellent comparative
mapping web sites for grasses:
Maize Mapping Project: http://www.maizemap.org/index.htm
Gramene: http://www.gramene.org/index.html
1. Begin at Maize Mapping Project:
- Select the "Maps" tab
- Select the "Comparative Maps" link
You need to be using either Netscape or Mozilla as your
browser and the Java Run Time Environment must be installed.
If your browser requests you to get the plug-in, do so. I do
not know if Internet Explorer will work for this site.
This tool allows you to specify a specific genetic cross
in maize, as well as one in rice and one in sorghum. To
start, choose "IBM2, Chr. 1" in the first 2 fields, and
"IBM2, Chr. 2" in the second two fields and select the "Get
Mapping" button. If Java is running, it may take a minute
for the graphic to be loaded. If it does not load (glitch in
the system or heavy use), do not worry since the required
information will come from clicking on the "List"
button.
2. This will replace the graphics page with a page for
each linkage group showing the name of the linkage group,
the total length (in cM) of the linkage group, the total
number of mapped loci, and the number of matched loci (6 in
this example). You now have basic information to generate an
estimate of the percent shared loci between these two
linkage groups (within a genome, due to duplication of
loci).
3. Repeat the exercise by replacing the second set of
fields with the rice ("RGP") map and "Chr. 1". The list of
matched loci is now 2.
Your Assignment:
Given the information and tools at hand, address the
following:
1. Which of the three genomes (rice, maize, sorghum)
would serve as the best model system of the three?
In attacking this problem follow these steps:
A. What criteria do you use to make the choice for a
model genome?
B. How do you evaluate the criteria identified in A?
C. Carry out your evaluation using the mapping tool.
RECOMMENDATION:
Use "RFLP" markers or maps in your evaluation. These
provide more comparative information.
(For a useful comparative site see the
Tree of Life.)
Another useful site
is the Plant C-value database maintained by
the Royal Botanic Gardens, Kew.
Discussion and report
summary:
1. For discussion on 10/7, be prepared to present
your results, including a brief summary of methods, results,
and conclusions. Include recommendations for further
extensions using these tools and strategies.
a. For visual aids, you may include overheads of results
or use a computer presentation, such as PowerPoint.
b. Be prepared to field questions from others.
2. Submit the following as a typed report by 10/9.
As a guideline, a finished report on the search should be
1-3 pages of text [12 pt standard font] and no more
than 2 pages of appended graphs, tables, images, etc.
[Final page length is to be determined by what the group
identifies as appropriate*]:
a. Name of the activity and names of the members in your
group.
b. A brief report in scientific format, including
abstract [100 word limit], introduction, methods,
results, discussion/conclusions, and citations. Include
figures as appropriate.
* Excessive length, either hoping to impress or due to
failure to filter and organize, will not be well rewarded.
Take the approach that you are submitting a professional
consulting report. The recipient expects concise accurate
information, which is clearly presented and well
documented.
Grading will be on content, organization, spelling, &
grammar.
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