Teaching Genetic Linkage and Recombination through Mapping with Molecular Markers
Lisa McDonnell and Jennifer Klenz
Student Name:
Student #:
Post-test (tutorial quiz) 16 marks total, 20-25 minutes FOR STUDENTS
Recently scientists working with a modern-day corn variety, called “Brocade” have found a “lazy” corn
mutant that grows by laying along the ground, rather than with an upright stalk. Researchers want to
determine the gene involved in creating the recessive lazy phenotype. To map the mutant gene found in
the “Brocade” background they crossed it to another line “Merit” that differs from “Brocade” in terms of
band size for many different microsatellite (microsat) molecular markers given simple numbers in the
table below.
Brocade alleles
Lazy (LZ)
lz
Prostrate stalk (laying
on ground)
LZ
phenotype/gel
banding pattern
Upright stalk
Microsat 1
Microsat 2
Microsat 3
Microsat 4
200 bp
50 bp
75 bp
400 bp
high band
low band
low band
high band
100 bp
250 bp
150 bp
275 bp
low band
high band
high band
low band
Locus
phenotype/gel
banding pattern
Merit alleles
a) Why do you need different microsatellite markers in the two varieties of corn? (1 mark)
b) The Brocade B1 allele is different from the Merit M1 allele for Locus 1. Also the B2 allele is different
from the M2 allele for Locus 2. Describe what these differences actually are at the DNA level. (2 marks)
c) Draw the homologous pairs of chromosomes in the F1, labelled with all of the molecular markers (assume
all the loci are on one chromosome when you draw your chromosomes). Include the lz vs LZ alleles in
your drawing even though you don’t know where the LZ locus is actually located on this chromosome
yet. (3 marks)
d) For the mapping experiment you allow the F1 hybrid to self and you will only isolate DNA from the
homozygous F2 lz/lz mutants. What ratio of band types would you expect to see for independent
assortment? What would you expect to see for linkage? (2 marks)
Teaching Genetic Linkage and Recombination through Mapping with Molecular Markers
Lisa McDonnell and Jennifer Klenz
Student Name:
Student #:
e) You would isolate DNA from a number of F2 homozygous lz mutants and then perform PCR reactions for
various markers and score their segregation patterns. Data is shown below for 20 different F2 lz/lz plants for
two different markers. Fully explain what each dataset below indicates. (8 marks)
A. Marker 1.
B. Marker 2
Teaching Genetic Linkage and Recombination through Mapping with Molecular Markers
Lisa McDonnell and Jennifer Klenz
Student Name:
Student #:
Post-test (tutorial quiz) 16 marks total, 20-25 minutes ANSWERS
Recently scientists working with a modern-day corn variety, called “Brocade” have found a “lazy” corn
mutant that grows by laying along the ground, rather than with an upright stalk. Researchers want to
determine the gene involved in creating the recessive lazy phenotype. To map the mutant gene found in
the “Brocade” background they crossed it to another line “Merit” that differs from “Brocade” in terms of
band size for many different microsatellite (microsat) molecular markers given simple numbers in the
table below.
Brocade alleles
Lazy (LZ)
lz
Prostrate stalk (laying
on ground)
LZ
phenotype/gel
banding patternd
Upright stalk
Microsat 1
Microsat 2
Microsat 3
Microsat 4
200 bp
50 bp
75 bp
400 bp
high band
low band
low band
high band
100 bp
250 bp
150 bp
275 bp
low band
high band
high band
low band
Locus
phenotype/gel
banding pattern
Merit alleles
e) Why do you need different MICROSATELLITE markers in the two varieties of corn? (1 mark)
1 mark for explaining that (just like crosses using morphological traits) in order to map we need to cross
individuals that have different alleles for several genes in order to observe independent assortment (or not) for
the gene of interest. We need two different alleles for every molecular marker and they need to segregate to
observe whether independent assortment is occurring. The two different varieties have differing alleles for all
the molecular markers (1)
f) The Brocade B1 allele is different from the Merit M1 allele for Locus 1. Also the B2 allele is different
from the M2 allele for Locus 2. Describe what these differences actually are at the DNA level. (2 marks)
2 marks for explaining that band size given above relates to insertions/deletions between the primers for
different alleles.
The B1 allele has more nucleotides than the M1 between the PCR primers used to amplify Locus 1.(1) The B2
allele has fewer nucleotides than the M2 allele between the primers used to amplify Locus 2.(1)
g) Draw the homologous pairs of chromosomes in the F1, labelled with all of the molecular markers (assume
all the loci are on one chromosome when you draw your chromosomes). Include the lz vs LZ alleles in
your drawing even though you don’t know where the LZ locus is actually located on this chromosome
yet. (3 marks)
1 mark for having all the B alleles on on chromosome and all the M alleles on the other.
1 mark for having the lz allele with the B alleles somewhere and the LZ allele with the M alleles.
1 mark for lining them up so that the loci correspond correctly B1 is in same position as M1 etc.
Teaching Genetic Linkage and Recombination through Mapping with Molecular Markers
Lisa McDonnell and Jennifer Klenz
Student Name:
Student #:
h) For the mapping experiment you allow the F1 hybrid to self and you will only isolate DNA from the
homozygous F2 lz/lz mutants. What ratio of band types would you expect to see for independent
assortment? What would you expect to see for linkage? (2 marks)
1 mark for ind. assortment prediction of 1:2:1.
1 mark for linkage prediction.
1 high:2 heterozygous (both bands): 1 low for independent assortment. (1)
More B bands (variety carrying lz mutation) when linked. Few M bands, fewer hets. (1) Note based on
experience: Most students will probably say that you will see All B bands and no M bands ie complete
linkage. This could be marked correct because the question doesn’t specify the degree of linkage, but it would
be important to remind them what less than complete linkage would look like ie Marker 2.
e) You would isolate DNA from a number of F2 homozygous lz mutants and then perform PCR reactions for
various markers and score their segregation patterns. Data is shown below for 20 different F2 lz/lz plants for
two different markers. Fully explain what each dataset below indicates. (8 marks)
A. Marker 1.
2 marks for writing out data in terms of different alleles
2 marks for explaining that it is assorting independently
You observe 5 plants homozygous for the B allele and 5 plants homozygous for the M allele and 10
heterozygotes B/M. This 1:2:1 pattern shows that this marker is assorting independently from the lz mutation.
If it was linked you would expect to see more B alleles (parental) and fewer M alleles (recombinant).
Note they could also just classify the data in terms of B vs. M alleles (20 parental vs. 20 recombinant) which
similarly indicates independent assortment.
B. Marker 2
2 marks for writing out data in terms of different alleles and parentals vs. recombinants
1 mark for explaining that this is not independent assortment (and suggests linkage)
1 mark for calculating the map distance between Marker 2 and the lz mutation.
(-0.5 marks if indicate formula for map distance, but make mistake in calculation)
Teaching Genetic Linkage and Recombination through Mapping with Molecular Markers
Lisa McDonnell and Jennifer Klenz
Student Name:
Student #:
There are 13 B homozygotes, 1 M homozygote and 6 B/M heterozygotes. (1) This is not a 1:2:1 ratio.
(1)
OR
There are 34 B alleles vs. 8 M alleles (1) indicating there are more parentals vs. recombinants. (1)
The map distance 8/40 (recombinants/total) =0.2 (1)
This indicates that the lz mutation is 20 map units away from marker 2. (1)