Transcript Molecular Mapping - Plant Root Genomics Consortium Project

Molecular Mapping
Terminology
Gene: a particular sequence of
nucleotides along 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)
Terminology
Allele: one of two or more alternate
forms of a gene occupying the same
locus on a particular chromosome or
linkage structure and differing from
other alleles of that locus at one or
more sites. (Johannsen, 1909).
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.
Terminology
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 product 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)
Terminology
Genotype: the genetic constitution in
respect to the alleles at one or a few
genetic loci under observation.
(Johannsen, 1909)
AA
Aa
aa
Parental Type
A
a
B
b
A
B
a
b
Recombinant
A
b
a
B
Two Point Analysis
Parental types


Tall, Green
42
Short, White
39
= 81 %
Recombinant types


Tall, White
7
Short, Green
12
=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 cross-overs.
Three-point analysis
Distance =
# Singles + 2 ( # Doubles)
Total
Double cross-overs
If cross-overs are equally likely along
the chromosome and closer genes have
few cross-overs, then the likelihood of
two crossovers close to one another
would be small.
Double cross-overs
If cross-overs are equally likely along the
chromosome and closer genes have
few cross-overs, then the likelihood of
two crossovers close to one another
would be small.
So, mapping algorithms can order genes
by minimizing the number of double
cross-overs.
Mapping Maize at UMC

Genetic mapping is based on DNA
fingerprint data of offspring from two
parents which differ in their
appearance.

Similar fingerprint data for two gene
indicates they are physically close together
on a chromosome.
Scoring your gel


Each parent A and B have different size
DNA fragments.
Progeny are either:




A (homozygous parent A)
H (heterozygous)
B (homozygous parent B)
Can also use a – if missing or not clear.
Molecular mapping
Digest DNA
Electrophorese
Hybridize
with probe
Southern
blot
+
Scoring data
A
B
H
H
A
B
A
H
Recombination and Mapping
Assume that the frequency of crossingover 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 very 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
Few recombinants = close together
How Maximum Likelihood
Works
BHBBAHBHHBHHBHB
HHBBABBHHBBBBAB
BHBBABHAHHBHBAB
BHBBABBAHHBHBAB
BHBBHBHAHHBHBAB
umc157
umc76
asg45
zb4
csu3
BHBBAHBHHBHHBHB
BHBBABHAHHBHBAB
HHBBABBHHBBBBAB
BHBBABBAHHBHBAB
BHBBHBHAHHBHBAB
umc157
asg45
umc76
zb4
csu3
SSR gel scoring
ABAABAAAAABABBBBBABABBAB
BAABAAABAAAAGBABAABBBBAA
ABBGAABABABAABABBAAABBAB
ABBBBAABBAAAABBBGBABABAB