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

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

	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

ISSN: 1746-4811