Lecture 14 - Quantitative Variation and Heritability NEED TO COMPLETE

Question 1

complete 1-47

Question 2

What are some examples of pleiotropy

Answer 2

PKU mutation in humans
Vestigial allele vg in fruit fly
Frizzle allele in chickens

Question 3

What is pleiotropy

Answer 3

A single locus affects the expression of multiple traits

Question 4

What is linkage disequilibrium

Answer 4

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

Question 5

What occurs at linkage equilibrium

Answer 5

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)

Question 6

Coupling and repulsion

Answer 6

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Question 7

How is linkage disequilibrium calculated

Answer 7

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)

Question 8

How does recombination affect linkage disequilibrium

Answer 8

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

Question 9

What occurs if recombination occurs in an individual that is heterozygous at only one locus

Answer 9

no new haplotypes created

Question 10

What happens when recombination in a double heterozygote

Answer 10

New haplotypes are produced

Question 11

slide 61

Answer 11

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Question 12

When does epistasis occur

Answer 12

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

Question 13

What does genetic background mean

Answer 13

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

Question 14

domestication

Answer 14

add

Question 15

how do we identify genes/loci
causing this variation

Answer 15

Locating loci (not necessarily genes) that affect quantitative
characteristics:
– Mapping Quantitative Trait Loci (QTLs)
– Genome-wide association studies

Question 16

What is QTL and what does it do

Answer 16

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

Question 17

What does GWAS stand for and what does it do

Answer 17

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