PBGMCB 621 – Genetic Mapping
Fall 2012
Homework Problem
Due Date:
A testcross population was produced to localize the gene for purple plant color (Pl Pl) in
maize relative to two cytological landmarks (heterochromatic knobs) on chromosome 6.
Stock A, a maize stock that is homozygous for two distinctive large knobs, K1 and K2, in
the long arm of chromosome 6 (6L), was crossed to Stock B, a pigmented (Pl Pl) line that
had two prominent chromomeres (k1 and k2) instead of the two knobs, but at the same
positions (see the figure below for the pertinent karyotypes). The F1 (Stock A X Stock B)
was then testcrossed to a pl pl knobless stock. Microsporocytes, for cytological analysis,
were obtained from the 85 testcross progeny and notes on pigmentation (Pl) were taken
later on the remaining tillers. A crossover between K1 and K2 was identified
cytologically by the presence of one of the two large knobs and a prominent chromomere
at the position of the other knob.
Stock A
Stock B
Knobless
Short arm - 6S
centromere
K1
Long arm - 6L
K2
not pigmented
pl pl
pigmented
Pl Pl
not pigmented
pl pl
The linkage data are presented in the following table.
Frequency of phenotypes in a three-point linkage test between the purple plant color
gene (Pl) and two knobs (K1 and K2) in chromosome 6.
pl K1 K2
Pl k1 k2
pl k1 k2
Pl K1 K2
30
36
8
7
pl K1 k2
Pl k1 K2
pl k1 K2
Pl K1 k2
1
2
0
1
Using the linkage data perform the following analyses.
1. Determine if there is segregation distortion for the three loci (Pl, K1, and K2) using log
likelihood ratio (G) statistics. Explain your results.
2. Determine if the three loci (Pl, K1, and K2) are genetically linked using log likelihood
ratio (G) statistics. Explain your results.
3. Calculate all possible recombination fractions.
4. Determine the position of Pl in relation to the two knobs (K1 and K2).
a. Show that the correct order will result in the minimum sum of adjacent
recombination fractions.
b. Show that the correct order minimizes the number of double-crossovers.
5. Draw a map with Pl, K1, and K2 using:
a. the Kosambi mapping function; and
b. the Haldane mapping function
6. Calculate the coefficient of coincidence for the order you obtained in 4. Is interference
positive or negative? What does this mean?
NOTE – Show your calculations or strategy for every step. You may use any computing
device or software for calculations except one that is specifically designed to do genetic
mapping.