Problem Set 12, Spring 2017
8 points total
Name:
1. A rare autosomal recessive disorder causes pink hair. A non-carrier male and an affected
female marry. Consider the following pedigree and RFLP analysis prepared using HindIII,
Southern blot, and a probe with a human sequence known to hybridize to sequences closely
linked to the gene responsible for this disorder.
a. Diagram each of the different haplotypes (group of markers that tend to be transmitted
together because of linkage) of I-1 and I-2 showing the restriction map and fragment lengths.
Show all HindIII restriction sites on each map.
Note several
arrangements are
possible. This shows
one of those.
Note that I-1 is heterozygous for the
pattern shown whereas I-2 is
homozygous for a pattern of sites as
shown.
Probe is somewhere in
the region shared by
these three fragments.
b. On the restriction map, indicate the area to which the radioactive probe must hybridize in
order to detect the fragments seen by Southern analysis.
Shown above
c. To which haplotypes (essentially pattern of each chromosome) does the mutant allele of
the gene seem to be linked in this family.
The mutation appears linked to the 2.5 kb polymorphism
d. Why does individual III-1 only show one band in the RFLP analysis?
She’s homozygous for a pattern of HindIII sites that produces the 2.5 kb fragment.
e. Which individuals are probably carriers? II-1, II-2, II-3, II-4, III-2
III-1
II-1
II-2
I-1 II-3 I-2
II-4
II-5
III-2 III-3 III-4 III-5
4.0kb
3.5kb
2.5kb
2.0kb
1.0kb
1
0.2kb
Problem Set 12, Spring 2017
8 points total
Name:
2. Your friend just got a new job in a research lab in Brazil studying tropical butterflies. She has
recently isolated a new mutant butterfly that produces fluorescent blue wings. She calls the
mutation flb. While attempting to establish a line of these butterflies for her lab, she crosses an
flb female with a wild type male and all of the progeny have fluorescent wings. When she
performs a reciprocal cross between a wild type female and an flb male the progeny are all wild
type. Suggest three plausible explanations for these results. How would you distinguish between
these possibilities?
Maternal effect, Extranuclear inheritance, or Genomic Imprinting
A cross of mutant female with wild type male followed by a cross of F1s would distinguish
between these possibilities. If maternal affect, all the F2 will be phenotypically wild type. If
extranuclear all the F2 will be phenotypically mutant. If imprinting, half the F2 will be
phenotypically mutant and half will be wild type.
3A. In general as we have seen this semester, reciprocal crosses produce the same results.
However, we have encountered several exceptions to this general rule. Provide 4 examples
where reciprocal crosses produce different results. Please include an example of such a cross and
an explanation for the reason for the difference.
X linkage
genomic imprinting
extranuclear inheritance
maternal effect
Drosophila linked genes (because males suppress recombination)
You’ve seen many examples of the above this semester so I won’t bother writing any here.
B. In your studies of the poison dart frog A. farlowae you discover that there are two true
breeding populations in the wild. The first population has bright red skin and the second has
brilliant blue skin. You wish to understand the genetic basis of skin color in A. farlowae, so you
cross frogs from population 1 with frogs from population 2 (i.e. red frogs X blue frogs). The F1
progeny all have purple skin. You cross purple F1’s to produce F2’s, and obtain the results shown
below.
307 red frogs
298 blue frogs
883 purple frogs
92 white frogs
1580
rrB–
R–bb
R–B–
rrbb
You see from the numbers
that we have a 9:3:3:1 ratio,
which says that the results
are due to segregation of
two alleles of two genes.
i. What are the genotypes of the F2 frogs?
ii. If you cross red F2 frogs X white F2 frogs, what is the probability of getting white
offspring?
1/3 are rrBB X rrbb => rrBb
2/3 are rrBb X rrbb => ½ rrBb and ½ rrbb
Therefore the probability of white offspring is 2/3(1/2) = 1/3
2
Problem Set 12, Spring 2017
8 points total
Name:
4. In your travels through the tropics you isolate a strain of poison dart frogs that has the
following unusual features. Every generation you are able to identify a high frequency of
mutations. Unfortunately, these mutations are not stable and often revert in the next generation
(even thought kept under identical conditions) making them difficult to map genetically. Provide
a plausible molecular explanation for the high frequency of reversion seen in this population.
Instability is a characteristic of transposable elements. The high frequency of reversion is
due to the transposable element excising from the gene, restoring gene function and
therefore the wild-type phenotype.
5. You are studying a rare mutant phenotype and perform PCR to analyze the suspected gene that
is associated with the phenotype. You notice that the allele found in mutants is much longer than
the wild type allele. You also notice a high frequency of reversion among mutants.
a. What caused the mutant allele?
As in #4, a high frequency of reversion is suggestive of a transposable element.
b. What are two mechanisms by which it could have moved into the gene (depending
upon what type of transposable element it is)?
It could have moved via replicative transposition, which is utilized by
retrotransposons, or by conservative transposition, utilized by some DNA elements.
6. You wish to study development, the process by which an embryo develops to produce a
mature animal. Which organism would you choose? Justify your answer.
Many choices are possible. You might utilize nematodes, Drosophila or zebra fish. Others
are possible but perhaps more difficult to justify. Justification would include some of the
advantages offered by each. For example, if you chose zebra fish you might point out that
they are genetically tractable, easy to store long term as frozen sperm, easy to house, have a
relatively short generation time, have transparent embryos and are vertebrate.
7. You study a rare, but evolutionarily interesting species of tunicate. You want to write a grant
in which you propose to sequence this animal’s genome. Please describe the general approach
that you will use to sequence the genome. Assume that the genome contains many repetitive
DNA sequences.
The strategy that’s been used for animals with much repetitive DNA involves preparing a
YAC library of large genomic pieces and then figuring out where in the tunicate genome
each large fragment came from. You then use the YAC library to order the clones made in
a cosmid library, which have much smaller fragments of the genome (~50,000 base pairs vs.
hundreds of thousands or more base pairs in YAC). You then determine the sequence of
~1,000 base pair bits of the cosmid clone and, once finished with each cosmid, assemble the
sequence. Sequence all of the DNA in each of the cosmids and assemble to determine the
final DNA sequence of the tunicate.
3
Problem Set 12, Spring 2017
8 points total
Name:
8. Reggaephilia, which causes a great fondness for Reggae music, is inherited as an autosomal
dominant. Below is the pedigree analysis of reggaephilia in a single family. You perform a
Southern blot analysis of DNA from family members, using a probe that recognizes a specific
polymorphism.
a. Based on the blot shown above, are any of the polymorphisms likely to be linked to
reggaephilia? If so, which one(s)? Numbers on the left show the sizes in kilobase pairs of
bands detected.
It’s difficult to say for
sure because of the
small sample size but
it looks like the 4.5 kb
band is cosegregating
with the disorder and
therefore likely to be
linked to the mutation
that produces it.
b. Draw a map showing the bands in the original parents. Please indicate the approximate
location of the nucleic acid probe that was used to detect the bands
that were seen on the blot.
Note several
arrangements are
possible. This shows
one of those.
Note that I-1 and I-2 are both
heterozygous for a pattern of
restriction endonuclease
recognition sequences that
produces the bands shown.
Probe is somewhere in
the region shared by
these four fragments.
c. How would linked polymorphisms help you to clone the gene?
You could use a positional cloning strategy using the hybridization probe shown
above as your starting probe. This would be viable as long as you could show tight
linkage between the polymorphism and the mutation that produces the disease.
4