PS401- Lec. 3
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Transcript PS401- Lec. 3
Mapping Basics
MUPGRET Workshop
June 18, 2004
Randomly Intermated
P1 x
P2
F1
SELF
F2
1 2 3 4 5 6 7 ……
One seed from each used for next generation
Recombination.
After recombination self to create line.
Randomly Intermated.
Very high resolution.
Accumulates recombination events across
generations and fixes them.
Excellent for fine mapping
Only homozygous genotypes.
Population Size
Dependent on type of population
Generally 200-300 individuals
If doing trait analysis, the number of
individuals determines the maximum
number of QTL you can find.
Two samples from the same population will
produce different maps because they sample
different gametes.
Genetic Mapping Basics
Gene: a particular sequence of nucleotides
among a molecule of DNA which represents
a functional unit of inheritance. (Johannsen,
1909)
Locus: the position of a gene on a
chromosome or a genetic map. (Morgan,
Sturtevant, Muller, and Bridges, 1915)
More terminology
Linkage: the association in inheritance of
certain genes and their associated
phenotypes due to their being localized in
the same chromosome. (Morgan, 1910)
Linked: two genes showing less than 50%
recombination.
More terms
Recombination: Any process which gives
rise to cells or individuals (recombinants)
associating the alleles of two or more genes
in new ways. (Bridges and Morgan, 1923)
Recombinants are the end products of
exchange of alleles from parental types as a
result of crossing-over.
Terminology
Phenotype: the observable properties of an
organism, produced by the interaction
between the organism’s genotype and the
environment (Johannsen, 1909).
Genotype: the genetic constitution in
respect to the alleles at one or a few genetic
loci under observation. (Johannsen, 1909).
Recombination
Parental
Recombinant
Recombination and Mapping
Assume the frequency of crossing-over is
equal along the chromosome.
Two genes that are very close to one another
will have a lower likelihood of having a
cross-over between them than two genes
that are far apart.
Recombination and Mapping
So, we can determine the relative distance
between genes by counting the number of
recombinant genotypes for each pair of
genes.
– Lots of recombinants = far apart
– Fewer recombinants = close together
Two Point Analysis
Parental Types
Tall, Green
42
Recombinant Types
Tall, White
7
Short, White
39
Short, Green
12
=81%
=19%
Map Units
1 map unit is equal to 1% recombination.
Map units are also called centimorgans after
geneticist Thomas Hunt Morgan who won
the Nobel Prize for discovering how
chromosomes govern inheritance.
Challenge
How do we merge the information about
each pair of genes together into one
common framework?
How do we order the genes relative to one
another?
Three-Point Analysis
A
B
C
a
b
c
Single cross-over
Double cross-over
Double cross-overs and Map
Distance
If we only look at the outer markers A and C
on the previous slide, we will underestimate
the true distance between them because we
have not accounted for the double crossovers.
Three-Point Analysis
Distance = # Singles +2 * Doubles
Total
If cross-overs are equally likely along the
chromosome and closer genes have few
cross-overs, then the likelihood of two
cross-overs close to one another would be
small.
Double cross-overs
So mapping algorithms can order genes by
minimizing the number of double crossovers.
Maximum Likelihood Method
Gives an estimate of the distances and the
relative orders of the loci which would
maximize the probability that the observed
data would have occurred.
How Maximum Likelihood
Works
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MapMaker
Mapping program that uses maximum
likelihood method.
Initially calculates what is linked (< 50%
recombination).
MapMaker
Works one linkage group at a time.
Randomly picks two genes with the group
and calculates the distance between them.
Adds another gene from the group and
determines the correct placement by using
maximum likelihood to minimize the
double cross-overs.
MapMaker
Does this by calculating a LOD value for
the placement of the gene in each of the
intervals.
Accepts the placement with the highest
LOD value.
Can be used for molecular markers or for
trait data.
LOD
Log likelihood.
LOD = log 10 (Probability that the observed
data would have occurred /probability that
the gene is unlinked).