This document discusses quantitative trait loci (QTL) mapping. It defines QTLs as locations of genes that influence quantitative traits, which are traits measured on a continuous scale, like height. QTL mapping involves detecting statistical associations between genetic markers and quantitative traits in a segregating population to locate QTLs within the genome. Successful QTL mapping requires a population segregating for the trait, genotyping individuals for DNA markers, phenotyping individuals for the trait, and using statistical methods to test for associations between markers and traits. QTL mapping can be used for marker-assisted selection and to study the genetic basis of complex traits.

1. Genetic
mapping and
QTL detection

2. QTL Mapping
 Qualitative traits
 Quantitative traits
 Genes
 Locus/loci
 Epistasis
 Linkage groups
 Markers

3. Quantitative vs Qualitative traits

4. What is a quantitative trait?
Discontinuous variation Continuous variation

5. QTLs
 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.

6. 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).

7. 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

8. 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.

9. Two Point Cross Mapping

10. Three Point Cross Mapping
sc ec vg
sc+ ec+ vg+
X
8 combinations of genotypes are possible

11. Three Point Cross Mapping----2nd
example v cv ct
v+cv ct X
v cv ct
v cv ct
8 combinations of genotypes are possible

12. Grouping

13. Ordering

14. Basic issue of QTL analysis
Is there is a statistical relationship between alleles
at markers and plant phenotypes?
If the answer is positive, one tries to determine:
- the number of locus involved,
- their chromosomal location,
- their effects

15. What are the elements necessary
to detect QTLs?
 Availability of a population segregating for the trait(s)
of interest:
i. F2 population, recombinant inbred lines (DH or
SSD), back-cross, cross between heterozygous
plants, or other,
ii. Population size as large as possible.

16. Populations commonly used in QTL
mapping

17.  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

19. Single marker analysis Case of a
DH or SSD population

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

21. Some available software packages for QTL
mapping

23. How to describe the QTLs?
Putative QTLs detected for relative root length (RRL)

24. What is evaluated once a QTL
is detected?
 - 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)

25. 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 conservation