TABLE 2.
A summary of targeted and non-targeted functional DNA markers, their targets and used PCR strategies.
| Marker | Target | PCR strategy | Detection |
|---|---|---|---|
| SCOT | Start codon | Single primer-based amplification assay targeting the start codon | AGE |
| CDDP | Conserved DNA regions of specific genes | Single primer-based amplification assay targets conserved DNA priming sites with differential distribution across the genome | AGE |
| SRAP | Open Reading frame | It uses two primers with a distinct primer structure, a random filler sequence, an AT OR GC-rich core, and 3 selective nucleotides at the 3′end to enable the amplification of various regions of the genome | PAGE |
| TRAP | EST | It amplifies various genome regions using an arbitrary SRAP primer and an EST sequence-derived primer | PAGE |
| CoRAP | Conserved intron/EST | It uses two primers: a fixed primer from EST sequences, an arbitrary primer with a core sequence ‘CACGC,’ a plant-specific intron sequence | PAGE |
| PBA | Cytochrome P450-based analogue sequences | Universal primers targeting the P450 genes | AGE |
| TBP | Β-Tubulim | A single degenerate primer binds to the conserved introns of the β-tubulin. Polymorphism is based on varied intron length | AGE |
| ITAP | Intron/exon splice junctions | In two primers-based amplification assays, one primer is derived from SRAP, and the other targets the intron/exon splice junction | AGE |
| ISAP | SINES | Two primers-based amplification assays, designed with SINE elements to amplify the adjacent genomic regions | AGE |
| SCAR | Sequence-Specific clones | Two primer-based amplification assays, with the primers derived from single loci clones from unique RAPD, AFLP bands | AGE |
| SSAP | Transposable elements | Restriction digestion was followed by two primer amplifications, one LTR-specific and the other adapter-specific | PAGE |
| iSNAP | Small RNAs | Two primer amplification assays, where primers are designed within and at the flanking regions of small RNAs mapped on the genome | PAGE |
| PAAP | Promoters | Two primer-based amplification assays, with a plant-promoter-specific primer and an RAPD primer | PAGE |
AGE, agarose gel electrophoresis; PAGE, polyacrylamide gel electrophoresis.