Transcript Meiotic mapping of whole genomes

BIO341
Meiotic mapping of whole genomes
(methods for simultaneously
evaluating linkage relationships
among large numbers of loci)
First, some review of a standard linkage test
In a pairwise comparison of loci, we test observed genotype ratios for goodness
of fit to the 1:1:1:1 ratio expected under the null hypothesis of random
assortment.
For example a cross following two marker loci in a haploid organism:
AB x ab
AB
ab
Ab
aB
observed
10
12
9
13
expected
11
11
11
11
(obs-exp)2/ exp
0.09
0.09
0.36
0.36
Total chi squared=0.90
three degrees of freedom
Cannot reject null hypothesis
another example:
AB
ab
Ab
aB
observed
25
29
5
7
expected
16.5
16.5
16.5
16.5
(obs-exp)2/ exp
4.37
9.47
8.02
5.47
Total chi squared=27.33
Three degrees of freedom
P<0.005
Reject null hypothesis
Once groups of linked loci are identified, various methods can be used to find
the most likely true order of the loci on the chromosome. More about ordering
loci later.
There is, however, another means of finding linkage among markers that can
be used to assess linkage even small numbers of progeny.
For each genotype in the progeny of a genetic cross, we can calculate an "odds
ratio," which is the ratio of the odds that the observed genotype could have
arisen via one model (two loci in question are linked at the observed, or at an
arbitrary, percent recombination) divided by the odds that the same data could
have arisen via the other model (two loci are not linked).
The combined odds ratio is obtained by multiplying all of the individual odds
ratios.
An easier way to make this calculation, is to take the logarithm of each
individual odds ratio, called a LOD score, and sum all individual LOD scores
to find the overall LOD for each pair of loci.
If LOD is over 3.0 (which means a combined odds ratio of greater than 1,000),
we generally accept linkage. The following is an example of how odds ratios
would be calculated for DIPLOID, F2 progeny:
P1
X1/X1, Y1/Y1
F1
X
X2/X2, Y2/Y2 (homozygous at first,
and at second, locus)
X1/X2, Y1/Y2
(heterozygous at both loci)
Now let's look at the gametes giving rise to the F2
generation
GAMETE 2
G
A
M
E
T
E
1
F2
X1 Y1
X1 Y2
X2 Y1
X2 Y2
X1 Y1
0.203/
0.063
0.023/
0.063
0.023/
0.063
0.203/
0.063
X1 Y2
0.023/
0.063
0.003/
0.063
0.003/
0.063
0.023/
0.063
X2 Y1
0.023/
0.063
0.003/
0.063
0.003/
0.063
0.023/
0.063
X2 Y2
0.203/
0.063
0.023/
0.063
0.023/
0.063
0.203/
0.063
Top of fraction: likelihood with recombination at 10%
Bottom of fraction: likelihood with recombination at 50%
Here is an example from the computer program MAPMAKER (by L. Proctor et
al., 1990):
For each locus, F2 genotypes are coded as:
A =1 1
B =2 2
H =1 2 or 2 1
C =not 1 1
D =not 2 2
- = missing
The current sequence is
-> load-data "Tutorial Raw Data"
Computing new 190 pairwise distances...
loaded file 'Tutorial Raw Data' as F2 data
(120 individuals, 20 markers)
USING F2 INTERCROSS DATA
-> sequence 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
The current sequence is :
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
->
Raw Data: 120 individuals, 20 loci, symbols: 'ABCDH-'
> group Linkage criteria: maximum theta: 0.40, m inimum LOD score: 3.00
Suspected linkage groups:
----Group 1 = 1 2 3 7 8 11 12 15
Group 2 = 4 5 6 9 10 16 17 18
Group 3 = 13 14 20
Group 4 = 19
From:
Principles of
Genetics.
1997. Snustad
et al.
From: Principles of
Genetics. 1997.
Snustad et al.
Linkage analysis of Elliptocytosis and Rh factor
From: Principles of Genetics. 1997.
Snustad et al.
Summary
• LOD score analysis of linkage compares two possibilities: two
loci are (a) linked at some specified recombination frequency
and (b) are unlinked (rec. =50%). LOD = log10(probability of
a genotype under a/ probability of the same genotype under
b)
• Each progeny individual makes a positive or negative
contribution to LOD.
• LOD scores of progeny from different families or crosses
can be combined.
• A LOD score total of 3.0 or greater is generally considered
strong evidence of linkage.
• Recombination frequency itself can be estimated by
calculating LOD for different recombination values. The
recombination frequency resulting in the maximum LOD
score is treated as the most likely.