PBG 650 Advanced Plant Breeding
First Midterm 2013
Name
Please show your work.
1)
6 pts
Homozygous AABB individuals are crossed to homozygous aabb individuals. The F1
generation is selfed to produce the F2 generation. The A and B loci are 20cM apart.
a.
What would be the initial value of disequilibrium (D) for these two loci in the
gametes that form the F2?
6 pts
b. Based on the expected rate of decay of disequilibrium, what would the value of D be for
these two loci after one generation if the F2 plants are allowed to mate at random?
6 pts
c. Consider another locus ‘E’ in this population that is not on the same chromosome as the
A and B loci. Would you expect there to be any disequilibrium between the A and E loci
in the gametes that form the F2 generation? Explain your answer.
1
2) An heirloom variety of carrots has been maintained by several members of a gardener’s
cooperative. Every year they each plant a small patch in their gardens, and allow it to crosspollinate, taking care that there is no other variety of carrots pollinating nearby. You plant
small quantities of seed from each gardener and score them for an SSR marker in the
laboratory. You tally the frequency of genotypes across all of the samples:
A1A1
22
8 pts
6 pts
A1A2
36
A2A2
42
What is the inbreeding coefficient for this variety?
3) In an open-pollinated landrace of corn, the purple stem characteristic is determined by a
single recessive gene. You grow a sample of this landrace in your garden and observe that 32
plants have purple stems and 168 plants have green stems.
a. Assuming that the population is in Hardy-Weinberg Equilibrium, what is the initial gene
frequency of the allele for purple stems?
8 pts
b. If you remove all of the plants with purple stems and allow the remaining plants to
intermate, what is the new frequency of the allele for purple stems that you would expect
in this population?
2
4) Assume that all parents of individuals C and D in the following pedigree are not inbred.
A
B
C
D
X
Y
Z
8 pts
a) What is the inbreeding coefficient (F) for individual Z?
6 pts
b) What does the inbreeding coefficient that you calculated for Z (previous question) tell
you about the coancestry of X and Y?
8 pts
c) Calculate the coancestry of X and Z. How does your result compare to the coancestry of
parent and offspring for individuals A and C? How would you explain the difference, if
any?
3
5) You collect a random sample of 30 individuals from a population and determine that there
are 12 AA and 18 Aa genotypes. You perform a Fisher’s Exact test and obtain the following
probability values for each of the possible outcomes for the observed numbers of alleles.
AA
21
20
19
18
12
17
13
16
14
15
10 pts
Aa
0
2
4
6
18
8
16
10
14
12
aa
9
8
7
6
0
5
1
4
2
3
Probability
0.0000
0.0000
0.0003
0.0055
0.0245
0.0427
0.1442
0.1611
0.3091
0.3125
1.0000
Total
a) Would you accept or reject the null hypothesis that the population is in Hardy-Weinberg
equilibrium (using =0.05)? Explain your reasoning.
6) What is meant by the “average effect of a gene” in quantitative genetics?
8 pts
4
7) Assuming that there is complete dominance for a locus ‘A’, then the average effect of an
allele substitution (replacing A2 with A1) will be greatest when (choose one answer)
6 pts
a)
b)
c)
d)
The coded genotypic value a is large and the frequency of A1 (p) is high.
The coded genotypic value a is large and the frequency of A1 (p) is low.
The coded genotypic value a is small and the frequency of A1 (p) is high.
The coded genotypic value a is small and the frequency of p = q = 0.5.
8) The graph below plots the genotypic values for the Z locus on the Y axis as a function of the
number of favorable Z1 alleles on the X axis.
12
10
Value
8
6
4
2
0
0
1
Z 2Z 2
Z 1Z 2
2
Z 1Z 1
8 pts
a) Without doing any calculations, plot the approximate breeding values for the three
genotypes on the graph above.
6 pts
b) Based on the appearance of the graph, circle the answer below that best describes the
observed level of dominance at this locus.
i.
ii.
iii.
iv.
No dominance
Partial dominance
Complete dominance
Overdominance
5