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How do you go from QTL to gene?
Fine mapping
• Progeny testing
• Collaborative cross
• Heterogeneous stocks
• Other outbred populations
From
www.complextrait.org/Powerpoint/
ctc2004/karl_broman.ppt
x
How do you go from QTL to gene?
Fine mapping
• Limited resolution?
• Incomplete annotation of genes in region
• Regulatory sequence within region
(separate from genes)
How do you prove a gene is
responsible for the effect of a QTL?
“The nature and identification of quantitative
trait loci: a community’s view” by Members
of the Complex Trait Consortium. Nature
Reviews Genetics (2003) 4: 911-916.
Standards will vary between taxa?
How do you prove a gene is
responsible for the effect of a QTL?
Most conclusive: allele replacement by
knock-in
Or knock-outs, rescued by alternate
alleles?
How do you prove a gene is
responsible for the effect of a QTL?
Circumstantial evidence
• Polymorphisms in coding or regulatory regions
• Gene function
• Expression differences
• Homology
• Knock-out studies
• Mutational analysis
• In vitro functional studies
• Transgenesis with bacterial artificial
chromosomes (BAC)
• Quantitative complementation test
Complementation test
heterozygous for QTL segment
heterozygous for gene X knock out
Complementation test
If gene X is the gene
responsible for the effect of the
QTL, the genotypes at the QTG
will be
If gene X is not the gene
responsible for the effect of the
QTL, the genotypes at the QTG
will be
Assumptions!
white /
KO
dark /
KO
The phenotypic
difference between
these two
genotypes
white /
white
>
will be
greater
than
dark /
white
white /
white
dark /
white
the phenotypic
difference between
these two
genotypes.
white /
white
dark /
white
=
The phenotypic will be
the phenotypic
equal to difference between
difference
between these two
these two genotypes
genotypes
Example of gene identification (?):
Klein et al. 2004; Science 303: 229-232
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Mapped QTL affecting BMD in mice to a 31 MB region.
Analysed gene expression by microarray.
Only one gene within region was differentially expressed.
Confirmed with RT PCR.
Gene was in a pathway known to inhibit bone formation.
Expression of bone formation markers was altered in cell
cultures from the two genotypes.
• Overexpression of the gene in cell culture affected
markers of bone formation.
• Phenotype of knock-out mouse was consistent with
difference in expression between QTL genotypes (high
expression -> low BMD).
• Pharmacological inhibitors of the gene’s product affected
BMD in a manner consistent with the QTL genotypes/
knock-outs (improved BMD in rodent models of
osteoporosis).