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Table 1 Summary table of marker systems and groups

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]