Lecture 14 - Quantitative Variation and Heritability NEED TO COMPLETE Flashcards
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What are some examples of pleiotropy
PKU mutation in humans
Vestigial allele vg in fruit fly
Frizzle allele in chickens
What is pleiotropy
A single locus affects the expression of multiple traits
What is linkage disequilibrium
here is an association between alleles at
different loci (e.g., the A allele tends to be found with the B allele, the a allele
with the b allele)
* It does not require the loci to be physically linked (because it is a statistical
measure of association of alleles), but physical linkage can facilitate LD
* Therefore (importantly): LD ≠ physical linkage
What occurs at linkage equilibrium
At linkage equilibrium combinations of alleles at the A and B loci should be
randomly assorted (cannot predict allele at locus A from B and vice versa)
Coupling and repulsion
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How is linkage disequilibrium calculated
F(AB) = px + D
F(Ab) = py – D
F(aB) = qx – D
F(ab) = xy + D
D = F(AB)F(ab) – F(Ab)F(aB)
How does recombination affect linkage disequilibrium
Recombination removes linkage disequilibrium – i.e., breaks
up associations between alleles
Recombination is very effective at reducing LD
Therefore, LD is typically considered an unlikely explanation
for most genetic correlations
What occurs if recombination occurs in an individual that is heterozygous at only one locus
no new haplotypes created
What happens when recombination in a double heterozygote
New haplotypes are produced
slide 61
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When does epistasis occur
he effect of alleles at a
locus depends on alleles present at other loci
* Loci ‘interact’ in the statistical sense
– effects of each locus depends on the alleles present at
the other locus
* Appearance of interaction depends on the presence
of variation at each locus
What does genetic background mean
background can be another locus (e.g., effect of locus A
depends on alleles at locus B)
– or more generally the multilocus genotype
– e.g., effects of a mutation in mice might depend on which
strain the mutation occurs (or is created) in
domestication
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how do we identify genes/loci
causing this variation
Locating loci (not necessarily genes) that affect quantitative
characteristics:
– Mapping Quantitative Trait Loci (QTLs)
– Genome-wide association studies
What is QTL and what does it do
A Quantitative Trait Locus (QTL) is a location in the genome that causes
different values of the trait in question
* A QTL does not have to be caused by differences in the coding region
of a gene
– e.g., alleles can be caused by differences in some regulatory element
– So, they often do not reflect changes to the protein produced by a gene (i.e.,
are often not caused by amino acid changes)
* Indeed, QTL are very often not associated with differences in proteins,
but rather, differences in gene expression
What does GWAS stand for and what does it do
A Genome-Wide Assocation Study (GWAS) identifies loci associated
with trait variation, usually in natural populations
– Originally done by testing whether groups with different phenotypes have
different frequencies of alleles at a locus
– More often done by looking at the statistical association with the
frequency of an allele in individuals and their trait value
* Most often done (in large studies) using genotyping array data, but
can also be done using any type of marker data
