November 24, 2018
This assignment is worth 5% of the course grade. Due Tue. Dec. 4
To make your job easier, a template for the report is available for
1. (2 points) Differences
between maize lines.
Many maize lines have heterochromatic knobs which are easily
distinguishable in C-banding. A karyotype of the South American
line 441123 is shown in A.
The somatic karyotypes are shown for a South American maize line
441311* (B), and F1 progeny from a cross between 441311 and the
North American breeding line KYS (F). To provide landmarks
useful in identifying chromosomes, three FISH probes were used:
*Lines 441123 and 441311 are very closely-related and their
chromosomes can be considered comparable for our purposes.
- green - 180 bp repeat sequence found in heterochromatic knobs
- red - subtelomeric repeat 4-12-1
- white - 5S rRNA
Briefly describe the most obvious differences between lines 441311
2. (2 points) Use
of pachytene chromosomes for measuring long arm to short
|Figure 3 at right shows carmine-stained
pachytene chromosomes from a cross of two closely-related
lines, 441123 x 444331. Chromosomes are shown as follows:
Arrows - centromere
Heterochromatic knobs appear as dark spots on the
chromosomes eg. at the end of the short arm of chromosome 9
The long arm/short arm ratios were measured in both in metaphase
chromosomes (eg. as in part 1, panel A) or in pachytene chromosomes
as in Figure3. The results are shown below:
a) What can you generalize about measuring arm ratios (AR) in
metaphase, vs. pachytene chromosomes?
b) Can you think of a molecular mechanism that might account for the
differences in results seen between the two methods of chromosome
measurement? To answer this question, it will help to compare
chromosome 7 as seen in Fig. 3G with chromosome 7 as seen in part 1.
3. (1 point) Changes
in knob loci.
|Most chromosomal knobs in maize consist of
many tandem repeats of two satellite sequences: the 180 bp
knob repeat, and the 350 bp TR-1 repeat.
The figure at right illustrates differences in knob loci
that might be found in two different maize lines, one with a
very large number of repeats (A) and the same chromosome
with a small number of repeats (B).
Based on what you know about crossing over, briefly describe
a simple molecular mechanism to account for the differences
seen between lines 441311 and KYS, from the results in part
- Rename the template file something different from
- Make sure your assignment report includes your name, student
number and UM email address.
- Feel free to include graphs, figures, tables, anything that
gets your point across.
- Save your assignment report as a PDF file, and upload it to
the PLNT3140 UMLearn dropbox site in the Assignment 4 folder.
Files in word processing formats (.doc, .docx, .rtf, .odt) are NOT
Note on grading: In assigning a grade, some consideration
may be given to how the answer communicates your ideas. Keep in
mind the following:
Note on academic integrity: The results shown in this
assignment may be derived from the research literature. It will be
considered a breach of academic integrity to search for the paper on
the Internet and simply copy the author's conclusions from the
- Use precise and appropriate biological terms.
- Organization the ideas in your answer, so that a clear chain
of logic is apparent. Formatting tools such as s subheadings or
bullet points help to show the reader the structure of your
- Ambiguity: Try to read your answers from the viewpoint of your
reader. Are there several possible ways to interpret what you
- Feel free to use figures or tables in cases where they will be
useful get across your ideas.
- Your first step should NOT be to go into the literature and
find papers on the topic. I want to see your
interpretation of the data, not someone else's. All the
information you need is given in this assignment.
- Be careful not to go beyond what the data is telling you. In
other words, state only those conclusions that are actually
supported by the data given here. It's perfectly legitimate to
include sentences like "These results are consistent with what
we know about glucocorticoid receptors...." but make it clear
what you can actually conclude from this data, versus other
points you wish to bring in.
Notes: If you have questions, it may help to
send me a
messge at firstname.lastname@example.org.