Linkage and Gene Mapping
Objectives:
After completing this section, you should be able to..
1. Define linkage, loci, locus and crossover.
2. Contrast the inheritance of genes that are linked vs. those that are
independent.
3. Define a map unit and calculate map distance.
4. Describe the relationship between map unit or linkage distance and
physical distance between loci.
5. Assemble linkage maps from inheritance data in test cross and F2
families.
6. Predict the frequency of offspring with specific trait combinations or
genotypes using mapping information.
7. Define a genetic marker, linkage group, and genome map.
8. Describe why DNA markers are valuable in gene mapping.
Key Terms:
Recombination frequency
Recombinant gamete
Parental gamete
2 point cross
3 point cross
Linkage map
Linkage group
Genome map
Locus
Loci
Crossover
Double crossover
DNA marker
Online Lessons:
Linkage Part I
Linkage Part II
(http://plantandsoil.unl.edu)
Linkage
Test Cross: Genetic test to detect linkage
Key questions:
1) What types of gametes are produced?
2) In what frequencies are the different kinds produced?
Answers: Classify gametes on the basis of phenotypes the zygotes produce.
Why? Each type of gamete produced by the heterozygote produces a unique
phenotype if there is no epistasis.
AaBb
ab
ABb
Ab
aB
ab
both dominant
A dominant
B dominant
both rescessive
AaBb
Aabb
aaBb
aabb
Testcross example in corn:
I_
ii
G_
gg
Are the genes for iojab and glossy linked?
solid green leaf, dominant
iojap, recessive
normal leaf surface, dominant
glossy leaf surface, recessive
cross two true breeding plants:
solid green, normal IIGG
F1 solid green, normal
Testcross IiGg
Phenotype
solid, normal
solid, glossy
iojap, normal
iojap, glossy
x
x
iojap, glossy iigg
IiGg
iigg
heterogamete
IG1
ig2
iG2
ig1
observed
508
94
98
500
expected if independent
1/4
1/4
1/4
1/4
300
300
300
300
The observed results vary from the 1:1:1:1 ratio expected if the genes were
independently assorting, therefore linkage is suggested.
Linkage
What types of gametes are produced?
1. parental types – The same gene combinations that united to form the
heterozygotous parent.
2. recombinant types – Gene combinations that differ from those that united
to form the heterozygous parent.
In what frequencies are the different gametes produced?
Parentals
IG
508
Ig
500
1008
Recombinants
Ig 94
iG 98
192
Convert each to % of total gametes:
Parental gametes 1008/1200 = 84%
Recombinant gametes 192/1200 = 12%
The deviation from equal frequencies indicates linkage. These two genes are on
the same chromosome pair (#7).
Why aren’t all the gametes parental type, if the genes are on the same
chromosome?
What would be the result of the test cross if the heterozygous F1 had been
produced another way?
Parents:
solid, glossy
I
g
x
iojap, normal
i
G
I
g
i
G
Gametes:
I
g
i
G
F1
I
g
i
g
i
G
i
g
x
Testcross results:
gametes from
heterozygote
IG
Ig
iG
ig
phenotype
solid, normal
solid, glossy
iojap, normal
iojap, glossy
classification
of gamete
recombinant
parental
parental
recombinant
frequency
8
42
42
8
Recombination Frequencies – same as the other experiment
Parental:
Ig
iG
42
42
84%
recombinant
IG
ig
8
8
16%
Frequency of recombinant gamete production…
__A. Depends on which alleles are found at two linked loci (ie. Crossovers
happen more between two dominate alleles)
__B. Depends on the distance between loci, not the alleles at two loci.
Linkage
Parentals -- The most frequent class of gametes
Recombinants -- Those that result from crossover
Features of Crossing Over:
*Reciprocal exchange of chromosome segments, break and rejoin
*Occurs during prophase I of meiosis
*Random event, probability increases with increasing distance between loci.
________________________________________________________________
Parental gametes from a dihybrid can have either dominant genes, recessive
genes, or both depending on the status of the initial parents.
Cis (coupling) – condition in a dihybrid in which 2 dominant liked genes came
from one parent and their recessive alleles came from the other parent.
I
G
i
g
Cis heterozygote
Trans (repulsion) – condition in a dihybrid in which a dominant gene and a linked
recessive came one parent and their alleles came from the other parent.
i
G
Trans
heterozygote
I
g
________________________________________________________________________
When parental type gametes are significantly more frequent than recombinant
gametes we can suspect linkage.
Steps in Determining Linkage
1) Produce a dihybrid (AaBb)
2) Determine what gametes are produced by the heterozygote and the
frequency of each.
Testcross: Direct method (why?)
F2: More complex results (why?)
F2 Segregation Data with Linkage
I
G
I
G
Coupling
x
i
g
i
g
Parents
F1
F2
IG .42 Ig .08
I
G
i
g
iG .08
ig .42
.42 IG
0.1764 0.0336 0.0336 0.1764
IIGG
IIGg
IiGG
IiGg
.08 Ig
0.0336 0.0064 0.0064 0.0336
IIGg
IIgg IiGg
Iigg
.08 iG
0.0336 0.0064 0.0064 0.0336
IiGG
IiGg
iiGG
iiGg
.42 ig
0.1764 0.0336 0.0336 0.1764
IiGg
Iigg
iiGg
iigg
I_G_
.1764
.0336
.0336
.1764
.0064
.0064
.1764
.0336
.0336
.6764
I_gg
.0336
.0064
.0036
.0736
iiG_
.0336
.0064
.0036
.0736
iigg
.1764
Repulsion
F2
IG .08
Ig .42
iG .42
ig .08
IIGG
IIGg
IiGG
IiGg
IIGg
IIgg
IiGg
Iigg
.42 iG
IiGG
IiGg
IiGG
iiGg
.08 ig
IiGg
Iigg
iiGg
iigg
.08 IG
.42 Ig
How would you calculate gamete frequency if you had collected
Phenotype data on the F2 offspring?
F2 Linkage problem
B_is normal eyes
G_is grey
bb is blind
gg is white
BBGG X bbgg --------- give BG / bg
BG / bg
X
BG / bg
F2 phenotypes :
give the F2
grey, normal 622
grey, blind
128
white, normal 127
white, blind
123
F2 Linkage problem
BBgg X bbGG --------- give Bg / bG
Bg / bG
X
Bg / bG
F2 phenotypes:
BG / bg
X
give the F2
grey, normal
grey, blind
white, normal
white, blind
bbgg:
523
227
228
22
grey, normal
grey, blind
white, normal
white, blind
381
162
168
389
Lean Angus
Assume that in angus cattle…
B___ black
F___ fatty
bb
red
ff lean
1) Red lean
F1 BbFf
x
Black fatty
x
red lean
B (10 map units) F