CAPS
Cleaved Amplified Polymorphic Sequence
CAPS
- CAPS (cleaved amplified polymorphic sequence)
is also known as PCR-RFLPs (polymerase chain
reaction-restriction fragment length
polymorphisms).
- it was developed after the emerge of PCR
technique.
- it was originally conceived as a technique to
detect base changes in DNA sequences and
therefore acts as a tool in the diagnosis of genetic
diseases.
- it was soon recognized that the technology would
have much wider applications in genetic diversity
studies.
CAPS
- CAPS is one of the many methods to detect
sequence variation within a DNA fragment amplified
by PCR.
- it is an alternative to direct sequencing for
detecting sequence variation.
- it is rather a simple and inexpensive technique.
- it requires a small amounts of relatively crude
genomic DNA.
CAPS
PCR on specific DNA region using
specific primers
Digestion of PCR products by
restriction enzymes
Electrophoresis (agrose gel) of
digested PCR products
CAPS on chloroplast/mitochondrial
DNA regions
CAPS
PCR products of the trnS-trnM region (cpDNA) restricted by TaqI
580 bp
290 bp
180 bp
580 bp
290 bp
180 bp
290 bp
180 bp
CAPS
PCR products of the trnM-rbcL region (cpDNA) restricted by BclI
3000 bp
2000 bp
1000 bp
3000 bp
2000 bp
1000 bp
CAPS
PCR products of the rpl16 intron (cpDNA) restricted by EcoRI
500 bp
490 bp
420 bp
200 bp
80 bp
500 bp
80 bp
420 bp
490 bp
200 bp
490 bp
200 bp
CAPS on nuclear DNA regions
CAPS
A nuclear DNA region was amplified by PCR and then digested by
HincII.
C
A M
F1 progenies
AM
Segregation patterns of F1 progenies.
C : Control
A : Acacia auriculformis
M : Acacia mangium
AM : Acacia auriculformis x A. mangium
C
CAPS
- DNA variation due to:
- presence/absence of restriction site
- insertion/deletion
- co-dominant marker if applied on nuclear
genome.