From: Advances in plant gene-targeted and functional markers: a review
Group | Marker system | Principle in a nutshell |  References |
---|---|---|---|
(1) Conserved DNA and gene family based markers (CDMs) | (1.1) CDDP | Conserved plant genes are targeted with short universal or degenerate primers to reveal length polymorphism. Use of primer combinations is also possible. | Collard and Mackill [57] |
 | (1.2) PBA | Universal primers target the exon-intron junction sites of cytochrome (cyt) P450 mono-oxygenases. Polymorphism is revealed based on the random distribution of gene family members. | Yamanaka et al. [58] |
 | (1.3) TBP | Single degenerate primer pairs anneal to the conserved parts of the β-tubulin exons and amplify intercalated introns from different tubulin isotypes. | Bardini et al. [59]; Breviario et al. [60]; Galasso et al. [61] |
 | (1.4) ITP | Intron regions of choice are amplified by exon flanking primers revealing polymorphism. | Weining and Langridge [62] |
(2) Transposable element based markers (TEMs) | (2.1) IRAP | Amplification of internal sequences between two retrotransposon repeats with primers annealing to LTR motifs. | Kalendar et al.[63] |
 | (2.2) REMAP | An LTR specific primer and an ISSR primer are used to detect polymorphism. | Kalendar et al. [63] |
 | (2.3) ISAP | Primers designed in various positions within SINE elements are used to amplify adjacent genomic regions. | Seibt et al. [64] |
 | (2.4) iPBS | Primers anneal to PBS regions of head-to-head oriented LTR retrotransposons. The amplified products contain LTR regions and intervening genomic regions. | Kalendar et al. [65] |
 | (2.5) SSAP | DNA is digested with restriction enzymes. Adapters are ligated to restriction sites, and amplification is performed with LTR specific and adapter specific primers containing selective nucleotides. | Waugh et al. [66] |
(3) Resistance-gene based markers (RGMs) | (3.1) RGAP | Resistance-gene based analogue fingerprints are generated with degenerate specific primers or primer pairs, designed to match conserved regions of R-genes. | Leister et al. [67] |
 | (3.2) NBS-profiling | Genomic DNA is digested with restriction enzymes after the ligation of adapters. Specific fingerprints are generated from resistance gene regions with adapter specific and R-gene specific primers. | Linden et al. [68] |
(4) RNA-based markers (RBMs) | (4.1) iSNAP | Primers are designed from small RNAs and flanking regions to generate polymorphic banding patterns. | Gui et al. [69] |
 | (4.2) cDNA-AFLP | An AFLP analysis is carried out using cDNA as a starting pool, with several modifications existing for fine-tuning. | Bachem et al. [70] |
 | (4.3) cDNA-RFLP | cDNA is used for probes in RFLP analysis. | Bryan et al. [71] |
 | (4.4) EST-SSR | EST databases are mined in silico to locate SSRs and design primers to match genetic microsatellites. | Kantety et al. [72] |
(5) Targeted fingerprinting markers (TFMs) | (5.1) DALP | The common M13 sequencing primer is paired with a forward primer containing the −40 USP core and 3’ selective nucleotides to generate fingerprints. | Desmarais et al. [73] |
 | (5.2) PAAP | Degenerate regions annealing to plant promoter regions are added to short oligonucleotides to detect polymorphism. | Pang et al. [74] |
 | (5.3) SRAP | Primers contain a random 5’ filter, a core sequence (AATT or CCGG) and three variable nucleotides at their 3’. Amplification follows a two step procedure where first mismatches are allowed at a lower temperature to generate a starting pool for subsequent higher temperature amplification. | Li and Quiros [75] |
 | (5.4) TRAP | An arbitrary SRAP primer is paired with a fixed primer designed from ESTs. | Hu and Vick [76] |
 | (5.5) CoRAP | Arbitrary primers are designed from ESTs as in TRAP, but the fixed primer contains a different core (CACGC), as in SRAP. This sequence is often found in plant introns. | Wang et al. [77] |
 | (5.6) SCoT | ATG start codons are incorporated into random primers to generate polymorphic fragments from the genome. Primers can be used alone or in combination. | Collard and Mackill [78] |