CAPSCAPSCleaved Amplified Polymorphic SequenceCleaved Amplified Polymorphic Sequence

CAPSCAPS

- 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.

CAPSCAPS- 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.

CAPSCAPS

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 CAPS on chloroplast/mitochondrial DNA regionsDNA regions

CAPSCAPS

580 bp

290 bp

180 bp

580 bp 180 bp

180 bp290 bp290 bp

PCR products of the trnS-trnM region (cpDNA) restricted by TaqI

CAPSCAPS

3000 bp

2000 bp

1000 bp

3000 bp

1000 bp2000 bp

PCR products of the trnM-rbcL region (cpDNA) restricted by BclI

CAPSCAPS

490 bp

420 bp

200 bp

200 bp

200 bp420 bp

PCR products of the rpl16 intron (cpDNA) restricted by EcoRI

80 bp

500 bp

500 bp 490 bp

490 bp80 bp

CAPS on nuclear DNA regionsCAPS on nuclear DNA regions

CAPSCAPSA nuclear DNA region was amplified by PCR and then digested by HincII.

Segregation patterns of F1 progenies.

F1 progenies C A M AM C

C : Control

A : Acacia auriculformis

M : Acacia mangium

AM : Acacia auriculformis x A. mangium

CAPSCAPS

- DNA variation due to:

- presence/absence of restriction site

- insertion/deletion

- co-dominant marker if applied on nuclear genome.