Biotechnology for Crop Improvement. Molecular Plant Breeding-Marker Assisted Breeding/Selection. Comparison between three main and commonly discussed marker systems- RFLP, RAPD and AFLP. Basic Understanding for Simple Sequence Repeats, SCAR and CAPS. Strategies to overcome food shortages using molecular plant breeding approaches, Application of various molecular marker systems and examples. Reference List. Presenter: Brenda Chong

1. Molecular Plant Breeding:
Marker Assisted Breeding/Selection

2. Types of Markers
• Morphological markers :- phenotypic characters
including pigmentation and dwarfism.
• Biochemical markers :- proteins, can be distinguished by
electrophoresis by their sizes and charges.
• Molecular markers :- very specific for different species.
e.g., AFLP, RFLP, RAPD, SSR/micro satellites etc.
• Flanking markers :- reduce “linkage drag”.
(Undesirable DNA associated with the gene of interest
from the non-recurrent parent)

3. Molecular Marker Systems
Comparison
RFLP RAPD AFLP
1. Digestion with RE
2. Separation using gel
electrophoresis
3. Transfer of DNA to membrane
4. Hybridization with labeled probe
5. Visualization
1. PCR amplification
2. Separation using gel
electrophoresis
3. Visualization with
Ethidium Bromide
(EtBr) stain
1. Digestion with 2 different RE
2. Ligation with oligonucleotide
adapters
3. Selective amplification
4. Separation using gel
electrophoresis
5. Visualization
Co-dominant markers Dominant markers Dominant markers
No primer is needed Random primer Selective primer
Large quantity of purified DNA Small quantity of DNA Large quantity of purified DNA
Highly reproducible Low reproducibility Highly reproducible
• Time consuming and labourious
• Complex procedure
• Profiling is dependent
on the reaction
conditions (PCR).
• Time consuming and labourious
• High levels of variation (mutation)
• Abundance of data

4. Molecular Marker Systems
(SSR, SCAR, CAPS)
• Requires sequence data
• Develop primers
• Co-dominant markers
SSR
• Can detect multiple alleles
• Anchored primers: Addition of nucleotides to the
dsDNA, allow addition of complementary primer.
(Upstream/downstream of tandem repeats)
• Enhance selection process
• Unanchored primers: Primers are designed based
on the tandem repeats.
SCAR
• From RAPD, select single polymorphism.
PCR
amplification
DNA
Digestion
Separation
Visualization

5. Overcoming food shortages
• DNA Fingerprinting – Identify plant cultivars
• Gene Mapping – Improve self-pollinated and cross-
pollinated species.

6. Overcoming
1. RAPD and AFLP – dominant markers for phylogenetic
study of closely related species.
2. RFLP and Sequence Characterized Amplified Region
(SCAR) – co-dominant marker, allows discrimination
between plant species and genotypes.
3. Flanking markers or Simple Sequence Repeats (SSR) –
population genetics study, determination of functional
diversity and germplasm collection analysis.
4. PCR based SCAR and CAPS markers – assist selection
process for high and low oil germplasm in oat breeding
programs (Orr and Molnar, 2007).

7. References
• Simmonds, N. & Smartt, J. (1999). Principles of Crop
Improvement. 2nd ed., pp. 300-303. Tokyo:
Blackwell Science.
• Brown, J. & Caligari, P. (2008). An Introduction to
Plant Breeding (1st ed., pp. 172-176). Blackwell
Science.
• Orr, W. and Molnar, S. (2007). Development and
Mapping of PCR-Based SCAR and CAPS Markers
Linked to Oil QTLs in Oat. Crop Science, 47(2),
p.848.