1. Relationship between quantitative trait inheritance and
genetic markers ( A rationale for QTL mapping)
Genes controlling quantitative traits are located in the genome
just like simple genetic markers.
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.

2. Genetic linkage X X Flower color: P, purple p, red Pollen size:
Parental F1
Pp; Ll X
PP; LL
pp; ll
Flower color:
P, purple
p, red
Pollen size:
L, long
l, short F2 X
• excess of parental types
(and deficit of non-parental types, i.e., recombinants)
reveals genetic linkage 9 3 1 :
phenotype ratios
expected
240 80 27
296 19 27 85 :
observed

3. QTL and Molecular Markers
QQ / MM x qq / mm Q Q q q M M m m P1 P2 Q q M m F1

4. Q q q q M m x 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

5. = 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
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
Likelihood
Ratio =
0.25

6. recombination frequency
Qq/Mm
Qq/mm
qq/Mm
qq/mm

7. How do we assess the strength of the evidence for linkage?
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:
LOD (r=0.1) N
Qq/Mm = x 10 = 2.6
Qq/mm = x 1 = Overall LOD
qq/Mm = x 1 =
qq/mm = x 8 = 2.1

9. Interval Mapping r A Q (marker) (putative QTL) r r1 r2 A Q B
Single Marker Method
(Sax 1923) r
A Q
(marker) (putative QTL)
Interval Mapping
(Lander and Botstein, 1986, 1989) r r1 r2
A Q B
(marker) (putative QTL) (marker)

10. Interval Mapping allows Independent Estimates of Location and Effect

11. QTL affecting tomato size or shape

12. How Many Genetic Differences Underlie Evolutionarily Important Traits?

13. M. cardinalis
M. lewisii
Genetics of Speciation: QTL mapping of Mimulus

14. Parentals
F1’s
QTL
Mapping
Test for correlations between flower
characters and genetic markers

15. QTL Mapping: Detecting Associations between genotype and phenotype

17. 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.