Factors critical to successful QTL mapping

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Factors critical to successful QTL mapping

• Good molecular map
• Good phenotyping
• Rigorous statistical/ genetic analysis
• Validation of QTL

(1 to 3 absolutely critical for genetic analysis
1 to 4 are all critical for implementation in
breeding)
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Why is good phenotyping important?Response to
selection and heritability
R i sP h2
3
Response to selection
h2 100
h2 50
h2 0
Original population
frequency
Trait value
Selected population
small s2G
moderate s2G
large s2G
As such, heritability is best thought of as the
correlation of phenotype with genotype
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Response to selection and heritability
R i sP h2
Narrow-sense heritability
Single observation h2 s2G s2GE / (s2G
s2GE s2Residual)
Multiple observations h2 s2G / (s2G
s2GE/ne s2Residual/nenr )
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Mapping population size limits accuracy of QTL
mapping (simulated data)

• QTL h2 n Power Bias (?G2)
• 10 .30 100 9 559
• 10 .95 100 39 197
• 10 .30 500 57 144
• 40 .95 500 46 165
• (Beavis, 1998)

(more markers do not solve this problem!)
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(Real data!!)
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Location of QTL

• Perfect marker (SNP) Rht-B1b for plant height
• Marker/gene located at 51.8cM along chromosome
• Analysis of plant height data in
  Cranbrook/Halberd
• 8 environments (h2SP 0.41 to 0.78)
• Depending on environment, QTL located at 47 to
  58cm along chromosome 4B
• One-step, multi-environment analysis (h2LM 0.91
  0.04)
• QTL located at 52cM along chromosome 4B

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So?

• Heritability limits QTL detection independent of
  map quality
• Heritability is a test of the potential genetic
  variance that can be accounted for
• So, why dont journals require heritability be
  published?

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QTLNetwork version 2.0
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Breeding progress for yield at CIMMYT reflected
in higher stomatal conductance
Fischer et al., 1998
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Leaf section
Stomatal cavity
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Stomatal conductance also impacts of
transpiration efficiency and adaptation to drought
12CO2 diffuses more rapidly through stomatal
pores 12CO2 preferentially fixed by Rubisco
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Leaf porosity measured using viscous flow
porometer
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Stomatal conductance - Cranbrook/Halberd
Plant height
Anthesis date
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Stomatal conductance Sunco/Tasman
Plant height
Anthesis date