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A few Basics about QTL Mapping

A few Basics about QTL Mapping

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Published by Vivay Salazar

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Published by: Vivay Salazar on Nov 18, 2010
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11/25/2012

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1
A few FAQs About QTL
Mapping
Guoyou Ye
E-mail: g.ye@cigar.org
Basics of QTL Mapping
What is QTL Mapping?
Map individual genetic factors on the quantitative traits,
to specific chromosomal segments in the genome.
The key questions in QTL mapping studies are:
How many QTL are there?
Where are they in the marker map?
How large an influence does each of them have on
the trait of interest?
Dataset of QTL Mapping
Mapping population
Linkage map (can be constructed
using your own marker genotype
data)
Marker genotype
Phenotypic data
Mapping Population
Biparental populations
F2
BC: backcross
DH, doubled haploids
RIL, recombination inbred lines
CSSL: chromosome segment substitution
lines
Natural population
Maximum Likelihood Method for
Estimating Recombination Rate
Recombination Rate
Recombinant gametes: are derived by
crossing over between the two parental
gametes received by an individual.
Recombination fraction: is the
probability that gamete transmitted by
an individual is recombinant.
Expected Marker Genotype Frequencies
BC1
BC2
DH
Counts
Expected Freq
M1M1M2M2
M1m1M2m2
M1M1M2M2
n1
f1=2
1(1
r)
M1M1M2m2
M1m1m2m2
m1m1M2M2
n2
f2=2
1r
M1m1M2M2
m1m1M2m2
m1m1M2M2
n3
f3=2
1r
M1m1M2m2
m1m1m2m2
m1m1m2m2
n4
f4=2
1(1
r)
Estimating Recombination Rate
Likelihood function
Logarithm operation of the likelihood function
Maximum likelihood estimate
Information: The negatives of the second derivatives
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Example
BC experiment
P1 and P2 are AABB and aabb, respectively
Number of plants of different genotypes in the
population
AABB162AABb40AaBB41
AaBb158
%
20
.
20
401
81
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Recombination Rate When Three
Markers Are Linked
Whenδ=0(Crossovers in the two intervals are
independent),
or
when δ= 1 (Complete interference, crossover at on
interval completely prevent crossover event in the other
interval)
23
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Mapping Function
Mapping distance
Unit of mapping distanceMorgan (Mor centi-Morgan (cM,
1M= 100 cM
Morgan is defined as that distance along which one crossing over is
expected to occur per gamete per generation
Mapping distance m is function of recombination rate
f is called mapping function
23
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m=

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