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Table 2 Comparison of various aspects of gene-targeted and functional marker techniques

From: Advances in plant gene-targeted and functional markers: a review

  Conserved DNA and gene family based markers (CDMs)   Transposable element based markers (TEMs)  
  CDDP PBA TBP ITP IRAP/REMAP ISAP iPBS SSAP
Abundance Medium, may depend on targeted genes High Medium Low, may depend on targeted genes High High High High
Reproducibility High High High High Medium High High High
Polymorphism Medium High High Medium Medium Medium High High
Prior sequence information Yes No No Yes Yes Yes No Yes
Visualization Agarose gel electrophoresis Agarose gel electrophoresis Agarose gel electrophoresis or silver stained PAGE Agarose gel electrophoresis sometimes with high resolution Agarose gel electrophoresis Agarose gel electrophoresis Agarose gel electrophoresis Silver stained PAGE
Specificity Not reported High High High High High High High
Size of bands 200-1,500 bp 100-1,500 bp 500-2,000 bp 50-800 bp 100-5,000 bp (up to 10 kbp) 250-2,500 bp 100-5,000 bp 50-500 bp
Homoplasy High High Low Low Medium Not reported Low Low
Reaction artifacts         
i. Uniparental bands Not reported Not reported No No No Not reported No No
ii. Heteroduplexes Not reported, but may occur Not reported, but may occur Not reported, but may occur Yes No No No No
iii. Nested priming Not reported Not reported, but may occur No No May occur Not reported Not reported May occur
iv. Other Amplicons may be generated from pseudogene loci Inconsistencies in bands associated with TE activity No No Inconsistencies in bands associated with TE activity