Download Linked Loci

Relationship between quantitative trait inheritance and
genetic markers ( A rationale for QTL mapping)
(1) Genes controlling quantitative traits are located in the genome
just like simple genetic markers.
(2) If markers cover a large proportion of the genome then there is
a chance that some genes controlling quantitative traits are
linked with the some of these markers.
(3) If genes and markers are segregating in a genetically defined
population, then the linkage relationship may be resolved by
studying the association between trait variation and marker
segregation pattern.
Genetic linkage
Parental
X
PP; LL
pp; ll
Flower color:
P, purple
p, red
F1
X
Pollen size:
Pp; Ll
L, long
l, short
F2
• excess of parental types
(and deficit of non-parental
types, i.e., recombinants)
reveals genetic linkage
phenotype
ratios
9
:
3
:
3
:
1
expected
240 :
80 :
80
:
27
296 :
19 :
27
:
85
observed
QTL and Molecular Markers
QQ / MM
x
qq / mm
Q
Q
q
q
M
M
m
m
P1
P2
Q
q
M
m
F1
Q
q
M
m
x
q
q
m
m
F1
P2
Expectation under free recombination r = 0.5
Q
q
Q
q
q
q
q
q
M
m
m
m
M
m
m
m
0.25
0.25
0.25
0.25
Expectation if r = 0.1
Q
q
Q
q
q
q
q
q
M
m
m
m
M
m
m
m
0.45
0.05
0.05
0.45
What is the probabilitiy (likelihood) of observing
Qq / Mm under the two models?
Likelihood if r = 0.1
Likelihood if r = 0.5
=
0.45
0.25
Likelihood
Ratio
recombination frequency
0.5 0.4
0.3
0.2
0.1
0
Qq/Mm
0.25
.30
.35
.40
.45
0.5
Qq/mm
0.25
.20
.15
.10
.05
0
qq/Mm
0.25
.20
.15
.10
.05
0
qq/mm
0.25
.30
.35
.40
.45
0.5
How do we assess the strength of the evidence for linkage?
(1) Calculate the likelihood ratio for each individual of the cross,
under a particular model of recombination. (denominator is null
hypothesis that r = 0.5)
(2) Take the logarithm of this odds ratio. This gives LOD.
(3) Sum all LODs to obtain the overall likelihood of the data.
For example:
If we examined 20 individuals with the following genotypes:
Qq/Mm = 10
Qq/mm = 1
qq/Mm = 1
qq/mm = 8
LOD (r=0.1)
.26
-.7
-.7
.26
N
x 10 = 2.6
x 1 = -.7
x 1 = -.7
x 8 = 2.1
Overall LOD
3.3
Single Marker Method
(Sax 1923)
r
A
(marker)
Q
(putative QTL)
Interval Mapping
(Lander and Botstein, 1986, 1989)
r
A
(marker)
r1
r2
Q
(putative QTL)
B
(marker)
Interval Mapping allows Independent Estimates of Location and Effect
QTL affecting tomato size or shape
How Many Genetic Differences Underlie
Evolutionarily Important Traits?
M. cardinalis
M. lewisii
Genetics of Speciation: QTL mapping of Mimulus
Parentals
F1’s
QTL
Mapping
Test for correlations between flower
characters and genetic markers
QTL Mapping: Detecting Associations
between genotype and phenotype
Schemske and Bradshaw (1999)
Bees preferred large flowers with moderate or
low amounts of yellow pigment.
Hummingbirds preferred nector-rich flowers with
high amounts of purple pigment
One genetic marker (QTL) for yellow pigment
reduced bee visitation by 80%.
Another QTL for nectar production doubled
hummingbird visitation.