This is a lecture for Bio4025, a graduate class at Washington University in St. Louis. Some slides are derived from Julin Maloof (University of California, Davis), some of which were altered.
2. What is a QTL?
• QTL
– Quantitative Trait Locus
– A genetic locus that contributes to quantitative
variation in a trait
• What is a quantitative trait? What contributes
to the concept of “trait?”
– Genes?
– Environment?
– Cross/allele/species background?
– The researcher?
3. Is hypocotyl length a quantitative
trait? No?
Qualitative: can classify
as tall or shortWT phyB
4. Is hypocotyl length a quantitative
trait? Yes?
Segregation Ler x Cvi RIL
Quantitative: must
measure (quantify)
differences
5. What causes quantitative segregation?
• Signal to noise (allelic effect versus
unexplained variance, environment, error)
• Multiple genes segregating, smaller effects
(polygenic traits)
6. What causes quantitative segregation?
• Signal to noise (allelic effect versus
unexplained variance, environment, error)
• Multiple genes segregating, smaller effects
(polygenic traits)
allele effect = 3 allele effect = 2
8. Why study development with QTL?
• Micro-evolution
– what makes two strains/populations/species
different?
– (Teosinte/Maize; Mimmulus; etc)
• Plant Breeding
– Fruit shattering
– Flowering
– etc.
• Human Disease
• Different spectrum of loci than available through
forward genetics
11. Marker “A” is linked to a hypocotyl QTL Marker “C” is unlinked
• Simplified version:
– Phenotype all individuals
– Genotype all individuals
– Look for correlation
QTL mapping: Single marker
regression
12. -Repeat, analyzing correlation to trait for 100s of
makers
-Limitations:
-Confounding: can not separate QTL effect (size)
and location of the QTL (relative to the marker).
-Does not account for effect of other contributing
loci/markers
QTL mapping: Single marker
regression
13. y = m*x + b
hyp = m*gtB + mean + error
is m not equal to 0? If so, then we have a QTL
QTL mapping: Single marker
regression
14. y = m*x + b
hyp = m*gtB + mean + error
is m not equal to 0? If so, then we have a QTL
QTL mapping: Single marker
regression
16. QTL mapping: recombination
increases variance
• The QTL “Q” may be some distance from
marker “B”
• Parent genotypes: B-Q and b-q
• Progeny genotypes: B-Q, b-q, B-q, b-Q
• genotype at QTL: Q or q
• Solution:
– Interval mapping
17. Simple Interval Mapping
(SIM; Lander and Botstein)
• Evaluate intervals between markers rather than
markers themselves
• Conceptually:
– Parents: B-Q-D and b-q-d
– Progeny:
• B-Q-D and b-q-d
• b-q-D b-Q-D B-Q-d B-q-d
• very rare: B-q-D b-Q-d
– Use B-D and b-d to estimate allelic effect size of QTL
– Use recombinants to estimate whether QTL is closer to B or
D
– LOD score: Likelihood of linkage. Log10 of ratio of likelihood
of linkage / likelihood unlinked
18. Simple Interval Mapping
(SIM; Lander and Botstein)
• Evaluate intervals between markers rather than markers
themselves
• In reality
– The position of the QTL in the interval is evaluated by maximum likelihood.
– At each position in the interval an iterative algorithm is used to determine
the most likely model given the data.
– The likelihood of a model with the QTL is compared to the null model (no
QTL).
– These two likelihoods are compared to give a LOD score
• LOD score = log10(Likelihood with QTL/Likelihood no QTL)
– what does a LOD score of 2 indicate?
29. y = m*x + b
hyp = m*gtB +mean + error
is m not equal to 0? If so, then we have a QTL
QTL mapping: Single marker
regression
J. MaloofPhotos: Charlie Rick, TGRC
Solanum pennellii
(Peruvian desert)
Solanum lycopersicum
(cultivated)
Desert tomato
Cactus
Single marker regression, sort of:
Tomato introgression lines
30. Single marker regression, sort of:
Tomato introgression lines
X
Backcross,
marker-assisted
selection
Self
…
Look for
phenotypic
differences
S. lycopersicum
(domesticated)
S. pennellii
(desert)
45. • Measure visitation rates in F2 population
• Look for correlation between floral QTL and
visitation
• One QTL increases carotenoids -> decreases
bee visitation 80%
• Another QTL increases nectar 3-fold, double
hummingbird visits (indpendent of color)
Which Traits affect pollinator visitation?
46. Genetics of Reproductive Isolation
• 12 Traits…47 QTL
• 9/12 Traits had “major” QTL
• Therefore, major QTL can play a role in
speciation.
– Contrasts with a very polygenic, additive small effect
loci view of evolution
50. Frary et al. Science 2000
Crop Breeding
S. pimpinellifolium S. lycopersicum
Transgenic for
S. pennellii fw2.2
candidate
51. Fruit Weight
• Cross wild to domesticated
• 11 fruit mass QTL
• fw2.2 largest effect, modifying fruit size up to
30%
• Create NIL and backcross
• Large allele in domesticated partially recessive
• Transgenics with wild allele have smaller fruit
• Structural homology to ras oncogene
52.
53. Developmental effect of fw2.2?
• What makes 2 alleles different?
• Expression: temporal expression different
• Phenotypic effect: Reduced cell division in
carpels
54. Real QTL effects are often “wimpy”
--ie, polygenic, small
effects
--Contrasts with tb1 and
pollinator shifts
55. Drastic differences in fruit and leaf phenotypes
between wild and domesticated tomato species
56. How do we measure leaf shape?
Elliptical Fourier Shape Descriptors
57. How do we measure leaf shape?
Elliptical Fourier Shape Descriptors
-2 SD +2 SD Overlay
PC1
44.4%
S.penn
(desert)
S.lyco
(dom.)
58. How do we measure shape?
Elliptical Fourier Shape Descriptors
-2 SD +2 SD Overlay
PC1
44.4%
PC2
13.0%
59. How do we measure shape?
Elliptical Fourier Shape Descriptors
-2 SD +2 SD Overlay
PC1
44.4%
PC2
13.0%
PC3
6.9%
PC4
6.6%
PC5
4.1%
65. The Punctate phenotype:
An example of bulk-segregant approaches
with next-generation sequencing
S. pennellii, low magnification S. penn., high magnification
66. The Punctate locus lies on chromosome 10
S. lycopersicumIL10-3, chrom. 10
73. On the Pn interval are four related MYBs,
one of which is is Anthocyanin 1 (ANT1)
“MYB250” ANT1 “MYB270” Heavy metal-associated
domain gene
“MYB290”
S. lycopersicum:
Aashish Ranjan
74.
75. This et al. TAG 2007
Foumier-Level et al. Genetics 2009
. . . but berry color in grape is also caused
by a set of tandemly duplicated MYBs!
MYBA2 MYBA1
V. vinifera:
MYBA3
83. Gene expression as phenotype: eQTL, cis- and trans-
relationships, and transcriptional networks
IL4-3:
I
II
III
IV
VVI
VII
VIII
IX
X
XI
XII
S. pennellii (desert)
S. lycopersicum (domesticated)
84. Gene expression as phenotype: eQTL, cis- and trans-
relationships, and transcriptional networks
S. pennellii (desert)
S. lycopersicum (domesticated)
IL4-3:
IV
Differentially expressed:
IL4-3 <-> S. lycopersicum
cis- regulation
85. Gene expression as phenotype: eQTL, cis- and trans-
relationships, and transcriptional networks
S. pennellii (desert)
S. lycopersicum (domesticated)
IL4-3:
IV
Differentially expressed:
IL4-3 <-> S. lycopersicum
cis- regulation
trans-regulation
