1] PCB5065 Fall 2014 - Exam 4 – Chase-McCarty Name :

I – Non-Mendelian inheritance – 50 pt.

1 (15 pt) This question pertains to our discussion of organelle genetics.

1a) Define heteroplasmy.

1b) Indicate whether each of the organisms or cell-types listed below is heteroplasmic or homoplasmic and explain how the heteroplasmy or homoplasmy arises in each example.

A yeast diploid zygote recovered immediately after crossing a mating type a strain with a mating type alpha strain, where each strain carries a different mitochondrial genome point mutation

A chlamydomonas haploid spore recovered after crossing a mating type plus strain with a mating type minus strain, where each strain carries a different plastid genome point mutation

A man suffering from myoclonic epilepsy and ragged red fiber (MERRF) due to a mitochondrial tRNALys A8344G mutation

A variegated pelargonium (geranium) plant resulting from the cross of a green seed parent by a variegated pollen parent

2) (15 pt) The Arabidopsis seth mutations were named after the brother and murderer of the Egyptian god Osiris. Recall that Arabidopsis pollen carrying the seth6 mutation does not function. For simplicity, assume that the penetrance of this mutation is 100% such that no seth6 pollen functions.

2a) Fill out the expected progeny genotypes and the expected progeny genotype ratio (e.g. 1:1, 3:1, etc.) for each of the three crosses below :

seed parent genotype / pollen parent genotype / progeny genotypes and ratios
cross 1 / + / seth6 / + / +
cross 2 / + / + / + / seth6
cross 3 / + / seth6 / + / seth6

2b) Is the seth6 mutation dominant or recessive? Explain your answer.


3. (20 pt) In the human pedigree shown left, shaded individuals have vision loss in young adulthood. Squares represent males and circles females. Roman numerals indicate generations and Arabic numerals individuals.

3-a) Based upon the pedigree shown, could this vision-loss trait be the result of a recessive nuclear autosomal mutation that exhibits Mendelian inheritance? Explain why or why not.

3-b) Based upon the pedigree shown, could this vision-loss trait be the result of a genetic mutation in a maternal-effect gene? Explain why or why not.

3-c) Based upon the pedigree shown, could this vision-loss trait be due to a mitochondrial gene mutation? Explain why or why not.

3-d) Based on the pedigree shown, could this vision-loss trait be due to an imprinted nuclear gene? Explain why or why not.

II. Developmental Genetics (50 pts)

1. (10 pts) A key test of the ABC model for floral homeotic gene action was successful prediction of double mutant phenotypes. The ABC model is summarized in this diagram.

First, diagram the phenotypes (i.e. organ identities found in each of the four whorls) for the three classes of single mutants:

a

b

c

Based on the model, what phenotype would you expect for the following double mutants:

a b

b c

2. (40 pts total) You identify mutants in four genes (A, B, C and D) that control development of specialized venom barbs on limbs of the giant carpathian zombie spider (Z. apocalypses).

You determine that A, B and C genes encode transcription factors with distinct DNA binding specificities. A is expressed during early limb development in a diffuse gradient along the proximal distal axis. By contrast B is expressed in a sharply defined region in the proximal half of the limb, whereas C is expressed exclusively in the distal half of the limb. D encodes a small peptide containing a signal peptide that is distributed in diffuse pattern over the proximal 2/3 of the limb. The phenotypes of the mutants are shown above. Assume you have capability for making transgenic spiders using GFP reporters, etc.

a) (14 pts) Sequencing of a upstream regulatory region of the B locus that confers faithful expression of a GFP reporter gene in the proximal region reveals a cluster of five A binding sites, two B binding sites but no C binding sites. Based on known principles of gene interaction, propose a mechanism that can account for formation of the sharply defined domain of B expression in the proximal half of the limb (Hint: the mechanism has two distinct components.). What are the two essential components of the mechanism? What specific role is played by the clustering of A binding sites? How would you test their importance in vitro and in vivo? What is the role played by the B binding sites? How would you test their significance in vivo? Which protein (s) would you expect to exhibit sigmoidal binding kinetics for DNA binding in vitro? Which is more likely to show hyperbolic kinetics?

b) (10 pts) Given the in situ data shown above and known principles of regulatory gene action, propose a mechanism that can account for the expression of D mRNA in the proximal domain? I.e. which gene(s) act as positive regulators of D? Which if any act as negative regulators? Using transgenic reporter constructs, you localize a 500 bp upstream enhancer sequence in the D locus that faithfully confers proximal expression pattern. What specific sequence features would you look for in the enhancer sequence? How do you account for the fact that D influences differentiation of cells in the distal domain? Based on the observed phenotypes is D also required for differentiation in the proximal domain?

d) (6 pts) Which gene (s) would you predict would be the most likely to directly regulate or signal downstream genes involved in barb formation (e.g. the venom biosynthetic pathway)? Which if any are positive regulators? Which if any are negative regulators? Explain.

e) (6 pts) You hypothesize that other genes in addition to the four play essential roles in generating the venom barb distribution in the limb. However, saturation mutagenesis and screening for venom barb phenotypes failed to identify any additional mutants in this pathway. Suggest two possible reasons why other mutants have not been detected. Suggest an example of a missing function in this pathway.

f) (4 pts) You discover that in addition to affecting limb development, the a mutant also has a discernible phenotype in the embryo (small embryo). You perform the following crosses (female on left):

embryo phenotypes embryo genotypes

AA X aa 100 % normal 100% Aa

aa X Aa 100% small 50% Aa 50% aa

Aa X aa 100% normal 50% Aa 50% aa

Where and at what stage of development would you look for expression of A that might account for these results. Explain.