Functional Markers in plants

Dr. S.V. Amitha Mithra

NRCPB
 Introduction
Generally markers are classified on the basis of their technical aspects – how do
they generate polymorphism and how much polymorphism do they generate, how
to handle them etc.

It is possible to generate thousands of random DNA markers which are

phenotypically neutral in any species which can be used in genetic diversity,
mapping , F1 testing, MAS, background selection etc.

When such markers are used for marker assisted selection, they may have some
limitations owing to genetic recombination.

Functional markers in contrast are developed from polymorphic sites within genes
that causally affect target trait variation i.e based on functional characterization of
the polymorphisms. Hence they are more meaningful in plant breeding.

The structural and functional genomic projects operational/ completed in many

crop species are the backbone for development of functional markers.

Anderson and Lubberstedt (2003) Trends in plant Science vol 8. number 11

 Comparison of marker types
Marker Origin of Fn of Method for Marker Quality *of
type DNA polymorphic functional develop marker
sequence site sequence motif ment
characterization costs

Random Unknown Not known - Low Low

DNA
marker
Gene Gene Not known - Low Medium
targeted
marker
Indirect Gene Functional Association studies Medium High
functional motif
marker
Direct Gene Functional Isogenic lines High High
functional motif
marker

*By quality, the risk of recombination and functional characterization are represented.
 Functional characterization of genes

1. Cloning and characterization

2. Homology or synteny relationships (comparative mapping or sequence
homology) – putative function
3. Insertional mutagenesis approaches
4. (Differential) Expression profiling techniques – transcriptomic
approaches – too much information – not one to one relationship
5. RNAi
6. Use of NILs (by TILLING or mapping or cloning approaches using HR –
NILs are obtained by both repeated BCing or TILLING (mutagenesis) or
HR based cloning )
7. Association mapping studies (indirect evidence)
In functionally characterized genes, allelic polymorphism is searched for and its
association with the trait established (by AM or NIL mapping) before developing
functional markers.
 Features of Functional markers

Once known and established, they are the most reliable circumventing the
recombination issue.

Do not require additional calibration across mapping populations.

Useful for most efficient fixation of alleles in populations (more efficient foreground
selection).

Can be directly used in natural as well as breeding populations.

Combining useful FMs in a cross for crop improvement

More accurate description of diversity in plant breeding and biodiversity studies by

FMs or their combinations.

Once primers are developed for FM they can be used for targeted search in
Germplasm collections
 Limitations

 Autogamous vs. Allogamous species – resolution and isogenic line

development

 Allele mining – how many alleles or genotypes?

 Functional motifs – how many?

 Interaction effects

 Direct marker development cost

 Using all FMs in a single cross