June 18, 2004
P1 x P2
1 2 3 4 5 6 7 ……
One seed from each used for next generation
After recombination self to create line.
Very high resolution.
Accumulates recombination events across
generations and fixes them.
Excellent for fine mapping
Only homozygous genotypes.
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
Genetic Mapping Basics
Gene: a particular sequence of nucleotides
among a molecule of DNA which
represents a functional unit of inheritance.
Locus: the position of a gene on a
chromosome or a genetic map. (Morgan,
Sturtevant, Muller, and Bridges, 1915)
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: 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.
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 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
– Lots of recombinants = far apart
– Fewer recombinants = close together
Two Point Analysis
Parental Types Recombinant Types
Tall, Green Tall, White
Short, White Short, Green
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.
How do we merge the information about
each pair of genes together into one
How do we order the genes relative to one
A B C
a b c
Double cross-overs and Map
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 cross-
Distance = # Singles +2 * Doubles
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
So mapping algorithms can order genes by
minimizing the number of double cross-
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
Mapping program that uses maximum
Initially calculates what is linked (< 50%
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
Does this by calculating a LOD value for
the placement of the gene in each of the
Accepts the placement with the highest
Can be used for molecular markers or for
LOD = log 10 (Probability that the observed
data would have occurred /probability that
the gene is unlinked).