Basics of association_mapping

1. Basics of association
mapping
Ghulam Shabir

2. What is mapping?
• Determining the location of elements within a
genome, with respect to identifiable landmarks.
Types of mapping…
• genetic mapping
• physical mapping
• restriction mapping
• cytogenetic mapping
• comparative maping

3. Approaches to mapping
• Experimental crosses
– Backcrosses
– F2
– recombinant inbred line (RIL)
– double haploid (DH)
• Pedigree analysis
• Association studies (Linkage disequilibrium,
LD mapping)
1. With candidate genes (direct approach)
2. Localized association studies (chromosomal
region)
3. Whole-genome association studies

4. Two ways of Genetic mapping
1. Using the experimental populations (also
referred to as “biparental” mapping
populations) that is called QTL-mapping as
well as “genetic mapping” or “gene tagging.”
2. Using the diverse lines from the natural
populations or germplasm collections that is
called LD-mapping or “association
mapping.”

5. QTL Mapping
• statistical study of the alleles that occur in
a locus and the phenotypes (physical
forms or traits) that they produce.
The main goal of genetic mapping
• to detect neutrally inherited markers in
close proximity to the genes controlling the
complex quantitative traits.

6. Limitations of genetic mapping
• It requires the growth of three generations
before linkage analysis is possible.
• Very large segregating populations are needed
to achieve a high resolution map.
• The molecular markers may be specific
(polymorphic) to only one particular crossing
family.
• takes a long time
• requires considerable effort
• map has a relatively low resolution

7. Alternate approach (Association
mapping)
• successful in humans where large
mapping families do not exist
• In plants, little work has been done with
regard to LD mapping
• Linkage Disequilibrium or association
mapping is a novel approach in plants

8. Powerful genetic mapping tools
for crops:
• linkage disequilibrium (LD)-based
association study
• Advantages:
• as a high-resolution
• broader allele coverage
• cost effective gene tagging

9. Association mapping
• Association mapping or linkage
disequilibrium mapping is a method that
relies on linkage disequilibrium to study
the relationship between phenotypic
variation and genetic polymorphisms
(Breseghello and Sorrells, 2006).
• It involves the use of molecular markers to
find statistical associations between genes
(or markers) and traits.

10. Goal of association mapping
• to find a statistical association between
genetic markers and a quantitative trait.
• The basic objective of association
mapping (AM) studies is to detect
correlations between genotypes and
phenotypes in a sample of individuals,
based on linkage disequilibrium (LD)
(Zondervan and Cardon 2004).

11. Potential to identify
• a single polymorphism within a gene that
is responsible for the difference in
phenotype.
• many plant species have high levels of
diversity for which association approaches
are well suited to evaluate the numerous
alleles available.

12. Plant germplasm resources
worldwide
• Wild plant species
•
• Modern cultivars
•
• crop wild relatives
Ross-Ibarra et al 2007

14. Advantages of population-based association
study over traditional QTL-mapping
• Availability of broader genetic variations
with wider background for marker-trait
correlations (i.e., many alleles evaluated
simultaneously).
• likelihood for a higher resolution mapping
because of the utilization of majority
recombination events from a large number
of meiosis throughout the germplasm
development history.

15. Advantages of population-based association
study over traditional QTL-mapping (cont…)
• no need for the development of expensive
and tedious biparental populations that
makes approach timesaving and cost-
effective.

16. LINKAGE DISEQUILIBRIUM (LD)
Concept of LD
Linkage
• Although Mendel's Law of Independent
Assortment applies well to genes that are
on different chromosomes. It does not
apply well to two genes that are close to
each other on the same chromosome.
Such genes are said to be “linked” and
tend to segregate together in crosses.

17. Basic rules of linkage
• Loci on different chromosomes will not be co-inherited
i.e. locus A on chromosome 1 will not be co-
inherited with locus B on chromosome 2
• Loci on the same chromosome will be co-inherited
• The closer two loci are on the same chromosome the
greater the probability that they will be co-inherited
i.e the likelihood of recombination is small
Linkage analysis
• The mapping of a trait on the basis of its tendency to be
co-inherited with polymorphic markers

18. Two terms used in population
genetics.
• linkage equilibrium (LE)
• linkage disequilibrium (LD)

19. LINKAGE EQUILIBRIUM (LE)
• Linkage equilibrium occurs when the
genotype present at one locus is
independent of the genotype at a second
locus.

20. Hardy-Weinberg Equilibrium
• The Hardy-Weinberg law: allele frequencies in
a population will remain the same over time (in
equilibrium) if the following conditions are met:
• Equilibrium Assumptions
• The population follows the laws of mendelian
genetics
• The size of the population approaches infinity
• There is no gene mutation
• There is no natural selection
• There is no migration into or out of the
population
• Mating is totally random

21. LINKAGE DISEQUILIBRIUM (LD)
• non- random association of alleles at
separate loci located on the same
chromosome (Mackay and Powell, 2007).
Linkage disequilibrium occurs when
genotypes at the two loci are
not independent of another.

22. LINKAGE DISEQUILIBRIUM (LD)
cont……
• LD is not the same as linkage, although
tight linkage may generate high levels of
LD between alleles. Usually, there is
significant LD between more distant sites
or sites located in different chromosomes,
caused by some specific genetic

23. What is difference between Genetic
linkage and LD?
• Association between genetic
polymorphisms occurs when there is non-
random association of their alleles as a
result of their proximity on the same
chromosome; this is known as genetic
linkage.
• LD is non-random association of alleles at
two or more loci, not necessarily on the
same chromosome .

24. What is difference between Genetic
linkage and LD (Cont…)
1. Linkage focuses on a locus, Linkage-Disequilibrium
focused on an allele
2. Linkage is resulted from recombination events in the
last 2-3 generations, Linkage-Disequilibrium is
resulted from much earlier, ancestral recombination
events
3. Linkage measures co-segregation in a pedigree,
Linkage-Disequilibrium measures co-segregation in
a population (essentially a huge huge pedigree)

25. Factors contributing to the
increase of LD
• small population size
• inbreeding
• population subdivision
• low recombination rate
• population admixture
• epistasis.

26. Factors contributing to the
decrease of LD
• Out crossing
• high recombination rate
• high mutation rate
• gene conversion, etc.
(Kim et al., 2007)

27. LD will tend to decay
• with genetic distance between the loci
• genetically distant loci are more likely to
have recombined than tightly linked loci.
• More recombination lowers LD.

28. What is population structure?
• A population is said to be structured if
individuals do not mate at random (i.e., they
deviate from Hardy Weinburg equilibrium). For
example, individuals that are found in
geographical proximity may be more likely to
mate with one another than with individuals that
are geographically distant from each other.
Natural or artificial selection also contributes to
non-random mating among members of a
population

29. Steps in association mapping
1. selection of a group of individuals from a
natural population or germplasm collection with
wide coverage of genetic diversity;
2. recording or measuring the phenotypic
characteristics (yield, quality, tolerance, or
resistance) of selected population groups,
preferably, in different environments and
multiple replication/ trial design
3. genotyping a mapping population individuals
with available molecular markers;

30. Steps in association mapping
(cont…)
4. quantification of the extent of LD of a
chosen population genome using a
molecular marker data
5. assessment of the population structure
(the level of genetic differentiation
among groups within a sampled
population individuals) and kinship
(coefficient of relatedness between pairs
of each individuals within a sample)

31. Steps in association mapping
(cont…)
6. based on information gained through
quantification of LD and population
structure, correlation of phenotypic and
genotypic/haplotypic data with the
application of an appropriate statistical
approach that reveals “marker tags”
positioned within close proximity of
targeted trait of interest.

32. Major crop in which marker-trait
associations was recently investigated
• maize (Belo et al., 2008)
• wheat (Tommasini et al., 2007)
• barley (Rostoks et al., 2006)
• sorghum (Hamblin et al., 2004)
• rice (Garris et al., 2003)

33. Conclusion
• Association mapping will facilitate gene
mapping and identification of the
underlying causes of quantitative trait
variation in plants. Future studies of LD in
crop plants will also elucidate further the
structures of plant genomes and will also
facilitate the use of marker-assisted
selection (MAS) and map-based cloning of
genes for difficult traits.

34. Thanks