QTL mapping for plant breeding and genetics course

1. 13/04/2012
Genetic mapping
and QTL detection

2. 13/04/2012
QTL Mapping
• Qualitative traits
• Quantitative traits
• Genes
• Locus/loci
• Epistasis
• Linkage groups
• Markers

3. 13/04/2012
Quantitative vs Qualitative traits
Quantitative Qualitative
Phenotypic
distribution
Continuous Discontinuous
Number of
genes
Polygenes Single or major
gene
Statistical
method
ANOVA 2 test
Environmental
effect
Highly affected Less affected

4. 13/04/2012
What is a quantitative trait ?
0
10
20
30
40
50
60
70
80
1 2 3 4 5 6 7 8 9 10
 Continuous variation:
0
10
20
30
40
50
60
1 2 3 4 5 6 7 8 9 10
 Discontinuous variation
A quantitative trait is
generally controlled by
several genes called
QTL (= quantitative
trait locus).
The observed
phenotype is the result
of the genotype, the
environment and the
genotype x environment
interactions.

5. 13/04/2012
QTL - Quantitative Trait Loci
A quantitative trait locus is the location of a gene (or
genes) that affects a trait that is measured on
aquantitative (linear) scale.
Examples of quantitative traits are plant height
(measured on a ruler) and grain yield (measured on a
balance).
These traits are typically affected by more than one
gene, and also by the environment. Thus, mapping QTL
is more complex than mapping a single gene that
affects a qualitative trait (such as flower colour).

6. 13/04/2012
Advantage of molecular
markers
on conventional genetics
Molecular markers allow
decomposition of quantitative
traits into their elementary
Mendelian components.
They permit,then, to localize
these QTLs in the genome
and identify markers tightly
linked to these genes in order
to manipulate them
individually.

7. 13/04/2012
F2
P2
F1
P1 x
large populations consisting of
thousands of plants
Resistant
Susceptible
MARKER-ASSISTED SELECTION (MAS)
MARKER-ASSISTED BREEDING
Method whereby phenotypic selection is based on DNA markers

8. 13/04/2012
QTL Mapping
QTLs are identified on the basis of statistical association
between the segregation of a phenotypic trait and the
segregation of genetic markers.
In principle, any class of markers can be used, but modern
breeding programs rely almost exclusively on maps built
with DNA markers (RFLPs, RAPDs, SSRs, SNPs) because:
they provide full genome coverage
they are robust, and
they are efficient.

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Two Point Cross Mapping

10. 13/04/2012
sc ec vg
sc+ ec+ vg+
sc ec vg
sc ec vg
x
sc----ec sc----vg ec----vg
Parental Par Rec. Par. Rec. Par. Rec
sc ec vg 233 233 233 233
sc+ ec+ vg+ 239 239 239 239
Recombinant
sc ec vg+ 241 241 241 241
sc+ ec+ vg 231 231 231 231
sc ec+ vg 12 12 12 12
sc+ ec vg+ 14 14 14 14
sc ec+ vg+ 14 14 14 14
sc+ ec vg 16 16 16 16
1000 944 56 498 502 502 498
Three Point Cross Mapping
8 combinations of genotypes are possible
5.6% 50.2% 49.8%

11. 13/04/2012
v----cv v----ct cv---ct
Parental Par Rec. Par. Rec. Par. Rec
v cv+ ct+ 400 400 400 400
v+ cv ct 409 409 409 409
Recombinant
v cv ct+ 31 31 31 31
v+ cv+ ct 28 28 28 28
v cv ct 61 61 61 61
v+ cv+ ct+ 65 65 65 65
v cv+ ct 2 2 2 2
v+ cv ct+ 4 4 4 4
1000 815 185 868 132 935 65
18.5% 13.2% 6.5%
v cv+ ct+
v+ cv ct
v cv ct
v cv ct
x
8 combinations of genotypes are possible
Three Point Cross Mapping----2nd example

12. 13/04/2012
Grouping

13. 13/04/2012
Ordering

14. 13/04/2012
Basic issue of QTL
analysis
Is there is a statistical relationship
between alleles at markers and plant
phenotypes?
Segregating population, marker x:
AA aa AA aa aa aa AA
Plant 1 Plant 2 Plant 3 Plant n
.....

15. 13/04/2012
If the answer is positive, one tries to determine:
- the number of locus involved,
- their chromosomal location,
- their effects

16. 13/04/2012
What are the
elements necessary to
detect QTLs?
1. Availability of a population segregating for
the trait(s) of interest:
 F2 population, recombinant inbred lines
(DH or SSD), back-cross, cross between
heterozygous plants, or other,
 Population size as large as possible.

17. 13/04/2012
Populations commonly used in QTL mapping
P1 x P2 F1
F2
F3
RIL
F1 x P1 (or P2)
BC1
F1
Anther
culture
DHL
(Recombinant inbred line)
(Backcross)
(Doubled haploid line)

18. 13/04/2012
2. Genotype of all individuals
constituting the segregating
population
+ For each individual of the
population, it is necessary to
know which allele it carries at a
set of markers regularly spaced
on the chromosomes
+ A good quality genetic map is
useful
+ 5 to 10 cM spacing
between markers
+ few missing data
RM146 RM101 RM341 RM257 RM236 RM30 OSR28
5 3 1 1 1 1 1 1
7 1 1 1 1 1 1 1
10 1 1 1 1 1 3 3
12 1 1 3 3 3 3 3
13 1 1 0 1 3 1 0
20 3 3 3 3 3 3 3
21 1 1 3 0 1 1 0
22 3 3 1 0 1 1 1
25 1 1 3 3 3 3 3
27 1 1 3 0 3 3 3
31 1 3 3 3 3 3 3
33 1 1 1 1 1 1 1
34 3 1 1 0 3 0 3
35 3 3 3 1 3 3 3
39 1 3 3 1 3 3 3
41 1 1 3 0 3 3 3
47 3 3 3 1 3 3 3
48 3 3 3 3 3 3 3

19. 13/04/2012
Single marker analysis
Case of a DH or SSD population
Line Allele at
marker 1
Plant
height
...Allele at
marker n
Plant
height
1 1 85 3 85
2 3 115 1 115
3 1 90 3 90
4 3 80 3 80
5 3 115 1 115
6 1 83 3 83
7 1 118 1 118
8 3 120 1 120
9 1 115 1 115
10 3 82 3 82
Mean group
with allele:
1 98.2 1 116.6
Mean group
with allele:
3 102.4 3 84.0
Likely QTL
No QTL
Test of
significance of
the mean
differences
between the
two groups:
through
analysis of
variance and F
test

20. 13/04/2012
New Strategies to map QTL
•Interval Mapping (Maximum likelihood)
•Interval Mapping (regression)
•Significance threshold by permutations
•Composite interval mapping
•Simplified composite interval mapping
•Multiple environments
•An integrated apprpoach

21. 13/04/2012
MAPMAKER/QTL Model Interval mapping
Population F2, BC, RIL, DHL
Computer platform PC window
Contact Eric Lander
(mapmaker@genome.wi.mit.edu)
QTL cartographer Model Composite interval mapping
Population F2, BC
Computer platform Mac, PC window
Contact Christopher Basten
(basten@essjp.stat.ncsu.edu)
MAPQTL Model Interval mapping
Population F2, BC, RIL, DHL, Heterozygous
F1
Computer platform Mac, PC
Contact Johan van Ooijen
(j.w.vanooijen@cpro.dlo.nl)
Map manager QTL Model Interval mapping using regression
Population F2, BC
Computer platform Mac, PC
Contact Kenneth Manly
(kmanly@mcbio.med.bufflo.edu)
Qgene Model Linear regression
Population F2, BC
Computer platform Mac
Contact James Nelson (jcn5@cornell.edu)
Some available software packages for QTL mapping

22. 13/04/2012

23. 13/04/2012
How to describe the QTLs
Putative QTLs detected for relative root length (RRL
Trait QTL Interval Chr Position
b
c
LOD
d
R
2
(%)
e
RRL QAlRr1.1 RG406-RZ252 1 6.0 2.4 9.0
QAlRr3.1 CDO1395-RG391 3 0.0 8.3 24.9
QAlRr7.1 RZ629-RG650 7 18.0 5.4 22.5
QalRr8.1 RG28-RM223 8 18.0 2.5 20.8
QAlRr9.1 RM201-WALI7 9 8.0 2.6 9.9
Best multiple QTL model
f
70.8

24. 13/04/2012
- QTL position with its confidence interval,
- its effect (in phenotypic units) for the
various genetic parameters (ex: additivity,
dominance)
- its direction (+/- sign of the effects)
- the phenotypic variance explained by the
QTL (= r2)
What is evaluated
once a QTL is detected ?

25. 13/04/2012
Applications of QTL Mapping
•Marker Assisted Selection
-Traits can easily be transferred into a wide
variety of population
- can reduce
breeding population sizes
continuous recurrent testing
time to develop superior variety
•Study of genetic diversity
•Germplasm characterization and coservation

26. 13/04/2012