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2015 C. elegans problem set
I. Basic concepts of diploid genetics and linkage
You cross a dpy-5(e61) male (“dumpy” body shape phenotype, recessive mutation) with an
unc-13(e51) hermaphrodite (“uncoordinated” movement phenotype, recessive mutation).
a. What phenotype(s) do expect to see in F1 cross progeny? Sex ratio?
b. You single (i.e. move individual worms onto separate plates and let them self) several of
the F1 cross progeny at a stage that you are certain they have not mated with their siblings.
What genotypic and phenotypic ratios do you expect to see in the F2 if the two mutations are
unlinked? (Draw out the dihybrid cross). How do these ratios change if the mutations are
linked?
c. At this point, let’s assume that the specific Dpy and Unc genes are linked. From the F2
progeny plate (see above) you single out several Dpy animals, 1 per plate (again, you are
certain that they have not mated). What do you expect to see phenotypically in their
progeny (F3 relative to the starting cross)?
d. Of the 32 Dpy F2 animals that you single, 2 of the worms give rise to progeny (F3) that are
¼ DpyUnc. How many map units are Dpy and Unc apart?
2. Mapping using polymorphisms (SNPs)
You have isolated a mutation that appears to be due to inactivation of a single locus. Your
screen was started in the N2-Bristol background strain. To identify the mutated gene, you
cross your mutant to the CB4856 Hawaiian mapping strain. You pick F1 cross progeny, allow
them to self, and from their progeny (F2), you pick animals that once again display the
mutant phenotype. You pick 20 such animals. These animals are then placed individually on
separate plates and allowed to lay eggs. About a week later, all 20 plates are filled with
animals. From each plate you wash some of the animals away for DNA extraction and retain
the plates (each plate will still have lots of animals). Using SNP mapping, you generate the
following results (a gel showing the SNIP-SNP patterns for each chromosomal marker are
shown. Lanes one and two show the band patterns for the N2 and CB strains as controls, and
lanes 1-10 show the band patterns for each of 10 F2 clones that are tested):
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Chrom. I
N2 CB
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Chrom II
N2 CB
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Chrom III
N2 CB
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Chrom IV
N2 CB
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Chrom V
N2
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CB
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Chrom X
N2 CB
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a) Which chromosome does this mutation map to? Why?
b) What is a rough estimate of map position of your mutation in relation to the SNP on that
chromosome?
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3. Epistasis analysis and pathway building:
During programmed cell death cells are killed off and the corpses are engulfed and cleared
by neighboring cells. From your first worm discussion paper, you know:
ced-9 --| ced-4  ced-3  programmed cell death
Once a cell has undergone programmed cell death, its corpse is quickly engulfed and cleared
away. Corpse engulfment genes of programmed cell death are identified as mutations in
which cell death still occurs leaving a visibly identifiable cell corpse but one that is not
cleared away. Consider:
Genotype
ced-1(lf)
ced-3(lf)
ced-1(lf), ced-3(lf)
phenotype
cells die, but leave ugly corpses
cells do not die
cells do not die
a) What is the epistatic relationship of ced-3 and ced-1?
Loss of function mutations in ced-1, ced-2, ced-7, and ced-10 were identified as engulfment
genes as null mutations in each of these genes left, on average, one corpse per pharynx (C.
elegans feeding organ). However, more than one cell undergoes programmed cell death in
the pharynx, implying that some corpse engulfment is still occurring in each of the single
mutant backgrounds. The following results were obtained from mutant combinations (all
cases are null alleles):
ced-1; ced-2: average four corpses/pharynx
ced-1; ced-7: average one corpse/pharynx
ced-1. ced-10: average four corpses/pharynx
ced-2; ced-7: average four corpses/pharynx
ced-2; ced-10: average one corpse/pharynx
ced-7; ced-10 average four corpses/pharynx
b) What can you conclude about relationships between these four ced genes?
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