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F2 population x 2
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F2 population
x
Progeny testing
x
QTL
QTL
QTL
QTLE
ffect
of g
enot
ype
Location of recombination
QTL
QTL
QTL
QTLE
ffect
of g
enot
ype
Location of recombination
position (cM)44 46 48 50 52 54 56 58
Effe
ct o
f gen
otyp
e
-0.2
-0.1
0.0
0.1
0.2
0.3
0.4
0.5
position (cM)
44 46 48 50 52 54 56 58
Effe
ct o
f gen
otyp
e
-0.2
-0.1
0.0
0.1
0.2
0.3
0.4
0.5
Progeny testing
x
Oliver et al. 2005PLoS Biol 3(5): e135
Single QTL
Christians et al. 2006 Genetics 173: 1547–1553
Multiple QTL
Alternative approaches
• Recombinant inbred lines (RIL)
Recombinant inbred lines (by sibling mating)
From www.complextrait.org/Powerpoint/ctc2004/karl_broman.ppt
Recombinant inbred lines(by selfing)
From www.complextrait.org/Powerpoint/ctc2004/karl_broman.ppt
Recombinant inbred lines
• Only have to genotype each line once• Can phenotype multiple individuals per
genotype• Can measure multiple phenotypes• Different environments• A number of RILs already available, e.g.,
WebQTL http://www.genenetwork.org/home.html
The “Collaborative Cross”
From www.complextrait.org/Powerpoint/ctc2004/karl_broman.ppt
Genome of an 8-way RI
From www.complextrait.org/Powerpoint/ctc2004/karl_broman.ppt
Alternative approaches• Recombinant inbred lines• Collaborative cross• Heterogeneous stocks – like collaborative
cross, but not inbred• Microarrays combined with QTL• Expression QTL
Expression QTL• How often is regulation cis vs. trans?, e.g.,
Ronald et al. 2005 PLoS Genet 1(2): e25.• Mapping “cluster regulators”
Yvert et al. 2003, Nature Genetics 35: 57-64
• How often is regulation cis vs. trans?• Mapping “cluster regulators”/ networks
Chesler et al. 2005, Nature Genetics 37: 233-242
• Mapping expression networks and behaviour
Chesler et al. 2005, Nature Genetics 37: 233-242
Alternative approaches• Recombinant inbred lines• Collaborative cross• Heterogeneous stocks – like collaborative
cross, but not inbred• Microarrays combined with QTL• Expression QTL• In silico methods
In silico methods• Use already-available phenotypes from
many inbred lines• Associate with marker data, e.g., Pletcher
et al. (2004 PLoS Biol 2(12): e393) typed many new SNPs
• Associate with haplotypes, not individual marker genotypes
Strain Marker A Marker B Marker C Marker D Marker E Marker F
1 A T A G A T
2 G T A G G G
3 C T A G C A
4 T T G C T C
5 A A G C T T
In silico methods• Use already-available phenotypes from
many inbred lines• Associate with marker data, e.g., Pletcher
et al. (2004 PLoS Biol 2(12): e393) typed many new SNPs
• Associate with haplotypes, not individual marker genotypes
Strain Marker A Marker B Marker C Marker D Marker E Marker F
1 A T A G A T
2 G T A G G G
3 C T A G C A
4 T T G C T C
5 A A G C T T
In silico methods• Use already-available phenotypes from
many inbred lines• Associate with marker data, e.g., Pletcher
et al. (2004 PLoS Biol 2(12): e393) typed many new SNPs
• Associate with haplotypes, not individual marker genotypes
• In addition, can look for concordance of QTL location between different crosses, different species (!) (Burgess-Herbert 2008; Genetics 180: 2227–2235)