371B_PS3.html

Genetics 371B, Autumn 1999

Problem set 3 -- based on lectures 9-14

Due Fri Nov. 5 at the start of class

1. Coin production in a certain species (Species 1) of Money Tree is controlled by three linked genes: q⁺ (dominant over q) allows production of quarters; d⁺ (dominant over d) allows production of dimes; and n⁺ (dominant over n) allows production of nickels. The recessive condition is lack of coin production. A linkage map of the region is shown. A closely related species (Species 2) also has the same genes and alleles, but here the chromosome has been split in two such that locus n is on a separate chromosome as shown.

(a) Species 1: Homozygous dominant plants are crossed with homozygous recessive. If the F1 progeny are testcrossed and 2000 F2 plants are obtained, what phenotypes and ratios would you expect to see in the F2? (Show your calculations.)

(b) Species 2: If a similar experiment is done with Species 2 (and 2000 F2 progeny are counted), what phenotypes and ratios would you predict? (Show your calculations.)

(c) Trees of the two species look very similar; it takes an expert eye to tell them apart. An inexperienced young assistant, not realizing that the F2 progeny in (a) and (b) above came from separate species, combines the progeny numbers (i.e., he has 4000 progeny from what he thinks is a single species). If he constructs a map of the region based on these 4000 progeny, what would that map look like? (Show your calculations.)

2. (a)
A meiosis is considered to be informative for linkage if we can identify whether or not the gamete is recombinant. (Note that the gamete does not necessarily have to be recombinant; we just have to be able to tell whether it was recombinant.) Consider the four pedigrees below, which show inheritance of brachydactyly, an autosomal dominant trait in humans. The numbers in brackets refer to inheritance of alleles of a polymorphic site that is linked to brachydactyly at 12 cM. For each of the four pedigrees, state whether the meiosis in II-2 was informative or uninformative (with respect to brachydactyly and the polymorphic locus). If it was informative, was the gamete recombinant? BRIEFLY explain your thinking no need to explain on a case-by-case basis, just outline in one or two sentences what you looked for in making your decision.

(b) In Pedigree (iv), if II-1 and II-2 have a second child, what is the probability that the child will be an affected boy with genotype {21,23} at the polymorphic site?

3.
A map of Hind III restriction enzyme cut sites (H) flanking a polymorphic microsatellite repeat locus (CCTA)n is shown:

(a) DNA is obtained from a heterozygous individual of genotype {25,50} at the polymorphic locus. If the DNA is cut to completion with Hind III and hybridized to the indicated probe, what sizes of bands would be detected by the probe?

(b)
A Southern blot experiment was performed on Hind III-cut DNA obtained from a woman and her six children. The resulting image is depicted; the numbers on the side refer to the number of CCTA repeats at the polymorphic site. Which lane has the mother's DNA? What was the father's genotype for the polymorphic site? Explain BRIEFLY.

4. (a)
Continuing with the map shown in Question 3...

Homozygous {50,50} tissue culture cells in G1 phase of the cell cycle were exposed to the alkylating agent ethyl methane sulfonate. In one of those cells the middle Hind III site was alkylated at the G base indicated by the asterisk:

Starting with this DNA, diagram the products after one round of DNA replication and after two rounds . If you could do a Southern blot on each of the four cells (after two rounds of cell division) using Hind III and the same probe as before, what size fragments would you detect? Assume that only one homologue in the original cell was modified by EMS. Note that the recognition sequence for Hind III is 5'-AAGCTT-3'.

(b) The mutation described above is an example of a forward mutation changing a sequence from wildtype (functional) to mutant (nonfunctional). But, as you might imagine, reverse mutations are possible also, changing a mutated sequence back to wildtype. Which do you imagine is more probable, a forward mutation that destroys a Hind III site, or a reverse mutation that restores a Hind III site? Why?

5.
The graph shows LOD score curves for linkage between a disease gene and four different polymorphic loci (#s 1-4). Interpret the data for each polymorphic site, stating whether there is significant evidence for or against linkage. If there is significant evidence, also state the approximate minimum and/or maximum distance in cM between the polymorphic site and the disease gene, and give the most probable map distance if possible.

1.	Coin production in a certain species (Species 1) of Money Tree is controlled by three linked genes: q⁺ (dominant over q) allows production of quarters; d⁺ (dominant over d) allows production of dimes; and n⁺ (dominant over n) allows production of nickels. The recessive condition is lack of coin production. A linkage map of the region is shown. A closely related species (Species 2) also has the same genes and alleles, but here the chromosome has been split in two such that locus n is on a separate chromosome as shown.
	(a)	Species 1: Homozygous dominant plants are crossed with homozygous recessive. If the F1 progeny are testcrossed and 2000 F2 plants are obtained, what phenotypes and ratios would you expect to see in the F2? (Show your calculations.)
	(b)	Species 2: If a similar experiment is done with Species 2 (and 2000 F2 progeny are counted), what phenotypes and ratios would you predict? (Show your calculations.)
	(c)	Trees of the two species look very similar; it takes an expert eye to tell them apart. An inexperienced young assistant, not realizing that the F2 progeny in (a) and (b) above came from separate species, combines the progeny numbers (i.e., he has 4000 progeny from what he thinks is a single species). If he constructs a map of the region based on these 4000 progeny, what would that map look like? (Show your calculations.)