CAPS Cleaved Amplified Polymorphic Sequence

1. CAPSCleaved Amplified Polymorphic Sequence

2. 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.

3. 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.

4. CAPS PCR on specific DNA region using specific primers Digestion of PCR products by restriction enzymes Electrophoresis (agrose gel) of digested PCR products

5. CAPS on chloroplast/mitochondrial DNA regions

6. CAPS PCR products of the trnS-trnM region (cpDNA) restricted by TaqI 580 bp 290 bp 180 bp 580 bp 180 bp 290 bp 290 bp 180 bp

7. CAPS PCR products of the trnM-rbcL region (cpDNA) restricted by BclI 3000 bp 2000 bp 1000 bp 3000 bp 2000 bp 1000 bp

8. CAPS PCR products of the rpl16 intron (cpDNA) restricted by EcoRI 500 bp 490 bp 420 bp 200 bp 80 bp 500 bp 490 bp 200 bp 80 bp 420 bp 490 bp 200 bp

9. CAPS on nuclear DNA regions

10. CAPS A nuclear DNA region was amplified by PCR and then digested by HincII. F1 progenies C A M AM C Segregation patterns of F1 progenies. C : Control A : Acacia auriculformis M : Acacia mangium AM : Acacia auriculformis x A. mangium

11. CAPS • DNA variation due to: • presence/absence of restriction site • insertion/deletion • co-dominant marker if applied on nuclear genome.