First Exam:
Total 100
2/8/02
90 min
Part I:
Answer only 1 or 2, and 3
Total mark 30
1. What are the five most contentious issues reviewed by Fairbanks and Rytting (2001)? Which
one do you think to be the most important one and why?
15
2. What are the possible reasons for Mendel’s failure to report linkages?
15
3. Two of the traits studied by Mendel are now investigated at the molecular level. Based on the
results reported for one of these molecular studies on seed shape and stem length explain:
a. how a mutant phenotype is developed, and
10
b. how a wild-type gene functions as a dominant one, while a mutant gene as a
recessive one?
5
Part II
Answer one only
Total Mark 20
4. Draw the Synoptonomal complex and label its different parts. Where are the recombination
nodules (RN) detected? What is interference and what is the proposed model for the basis of
interference?
10+3+3+4= 20
5. Draw a ring bivalent of a pair of homologous chromosomes with their inner chromatids
exchanged through the crossing over event in both of their arms. Consider the gene order in
one chromosome is AAbbCCDD, while in the other homologous chromosome is aaBBccdd.
•
The centromere is located in between ‘B’ and and ‘C’ loci.
•
Assume that two crossovers occurred: one between A and B and the other between C and D.
Based on these information show the equational and reductional divisions for these loci at the
end of:
a) anaphase I, and
15
b) anaphase II.
Part III
5
Answer one only
Total Mark 20
6. You have just joined as a maize molecular geneticist position after completion of your
graduate studies. In your graduate studies you developed a high-resolution recombination
nodule map for the maze genome.
How will this knowledge help you in the current maize genomics position (which requires
mapping and cloning genes that govern traits of agronmic importance)? Justify your answers with
advantages that you will get from the maize RN map for identifying and isolating regions that
may carry your genes of interest.
7. What is an RN map? How do you develop it? Why is it a better cytogenetic map than a map
constructed based on the chiasmata? What are the possible reasons for the total genetic
distance in an RN map to be smaller than that in a molecular map?
5 x 4 = 20
Part III
Answer one only
Total Mark 30
8. As a graduate student you are to determine the inheritance of flower color in green beans.
Your major professor has provided with you the materials and data of the previous year to
investigate the issue.
-
He made several crosses using distantly related lines that carry either red or
white flowers.
-
He crossed a specific red flower carrying line only once with a specific line
carrying white flowers. He used four independent red flowering lines to cross
with four independent white flowering lines.
-
He thinks that red color is dominant over white and the flower color is
governed by a single gene.
-
The F2 segregations are shown below:
Cross
Red Flower
White Flower
I
77
25
II
60
40
III
80
27
IV
62
47
======================================
i)
What would be the null hypothesis to test major professor’s assumption?
Test the goodness-of-fit of these data and determine if this hypothesis is
correct. Are the segregation data heterogeneous? If so, explain the cause(s)
of variability among crosses.
15
ii)
Based on the results from the analysis in the previous step
develop your hypothesis to determine the number of genes
involved in the development of flower colors in green beans by
carrying out the goodness-of-fit test.
15
Midterm Exam. (3/15/02)
Total 100
Time 2 hr
Expected to use the formulae that are provided!
Q1. (30=15 +3+12) Using a simplex quadrivalent diagram show the segregation of two
loci, one (Aaaa) is next to the centromere, and the other (Bbbb) away from the
centromere. Why do you see the double reduction in autotetraploid but not in diploid
segregation? What are the requirements for double reduction?
Q2. (15=5 x 3) Describe the following terms
i) telomeres; ii) centromeres; iii) retrotransposons.
Q3. Considering θ as the recombination fraction between two genes A and B write the
frequency of gametes that will be produced in a double heterozygous plant:
(2.5) if the genes are in the repulsion phage linkage?
(2.5) if they are in coupling phase?
Q4. In a dihybrid segregation between resistance to powdery mildew disease and seed
shape in peas the following classes were observed.
• Round and resistant = 753
• Round and susceptible = 292
• Wrinkled and resistant = 351
• Wrinkled and susceptible = 19
Round (R-) is dominant over wrinkle (rr).
Resistant (Rpm-) is dominant over susceptible (rpmrpm).
Both traits are governed by single genes.
(15) Is there any linkage between these two traits?
(15) Develop a suitable maximum likelihood equation to determine the value of
the recombination fraction θ between these two traits.
Q5. (10) a) Describe G and Z statistics that are applied to test the significance of linkages
between two loci. Write the null hypothesis for each statistic.
(4+4+2) b) How does the map unit relate to the recombination fraction? What are
mapping functions? What are the assumptions in Morgan’s and Kosambi’s functions?
What is the limitation of the most commonly used Kosambi’s function?
===============================================================
χ2 values (p=0.01)= 1 df: 6.64; 2 df: 9.21; 3 df: 11.34; 4 df= 13.28
ln L = Constant + n1ln (¼(2+θ)2) + (n2+n3) ln (¼(1-θ)2+ n4 ln (¼ θ2)
lnL = C + aln
2+θ 2
1− θ 2
θ2
+ (b + c)ln
+ d ln
4
4
4
d lnL
2θ
2θ
2θ
=a
− (b + c)
+d 2 = 0
2
2
dθ
2+θ
1− θ
θ
(n1+n2+n3+n4)θ4 – (n1-2n2-2n3-n4)θ2 –2n4=0
x=
−b ± b2 − 4ac
2a
I(θ$) = n
2(1+ 2θ 2 )
(2 + θ 2 )(1− θ 2 )
1
V(θ$) =
I(θ$)
= n*i
SE(θ$) = V(θ$)
 L(θ ) 
Z(θ ) = log10 
 = log10 L(θ ) − log10 L(0.50)
 L(0.50) 
 L(θ$i ) 
Gi = 2 ln
 = 2 ln L(θ$i ) − lnL(0.50)
 L(0.50) 
[
x = 21 tanh−1(2θ ) = 41 ln
[
1
x = 21 N 1− (1− 2θ ) N
1+ 2θ
1− 2θ
]
x = − 21 ln(1− 2θ )
]
Agron 527
April 10, 2002
Exam III
Total 100
Developing Molecular Maps:
Q.1: 10 (5 + 5). Use a diagram to explain the linkage disequilibrium (LD). Between soybean and
maize, which one is under linkage equilibrium for a given genomic region if soybean parents are
highly diverse for the region, and maize parents selected from an open pollinated synthetic line.
Support your answers with reasons.
Q.2: 20 (4 x 5= 15) Describe any four the following molecular markers: AFLP, RAPD, RFLP,
and CAP and SSR markers with suitable diagrams.
Q.3: 15 (15) Describe how one can develop a molecular map for a polyploid species. Describe
the strategy considering segregation of two linked molecular markers in an F2 population of 16
plants.
Comparative Mapping
(only one question to answer from this section)
Q.4: (20) Comparative mapping can facilitate positional or map-based cloning of genes in a
complex species. With a suitable diagram describe how it can help us to develop a high density
molecular map for the region that carries the gene of our interest.
Or
Q.4: 20 (4 x 5 =20) Describe with suitable diagrams the following terms. i) Colinearity or
synteny; ii) microsynteny or microlinearity; iii) Orthologous; iv) Paralogous.
Male Sterility
Q.5: 15 (3 + 12) Name the genes that regulate the expression of the gene-cytoplasmic male
sterility (CMS) in maize lines carrying T-cytoplams. Describe how (the mechanism) the male
sterility is developed. Describe with suitable diagrams to explain the process of male sterility
development.
Q.6: (10) How does the male sterility restored in maize lines that carry T-cytoplam? With
suitable diagrams describe the mechanisms or possible mechanisms of fertility restoration in Tcytoplam.
Self-incompatibility
Q.7: 10 (4 + 6) Distinguish gametophytic self-incompatibility from the sporophytic selfincompatibiltiy. Draw diagrams to distinguish the hetermorphic from the homomorphic selfincompatibilities.