Table 1.

Comparison of different DNA markers used in biological sciences.

	RFLP	RAPD	AFLP	ISSR	SSR	SCAR	LAMP	DNA barcoding
Genomic abundance	High	Very high	Very high	Medium	medium	High	High	high
Genomic DNA required	2–5 μg	15–30 ng	200–300 ng	15–30 ng	30–50 ng	30–50 ng	10–20 ng	30–50 ng
inheritance	Co-dominant	Dominant	Dominant	Dominant	Co dominant	Co dominant	Co dominant	NA
Primers/probes used	Specific	Random	Specific to adapter sequence	Specific to repeats	Specific	specific	Specific	Specific
Type of polymorphism	Nucleotide base change that affect specificity of restriction endo-nucleases	Nucleotide base change at primer binding sequences	Nucleotide base changes that affect specificity of restriction endonucleases and presence/absence of nucleotide complementary to selective nucleotides	Nucleotide base change at primer binding sequences	Complete presence/absence of DNA fragment	Complete presence/absence of DNA fragment	Complete presence/absence of DNA fragment	Nucleotide changes in universal genes.
Reproducibility	Very high	Very low	High	Medium	Very high	Very high	Very high	Very high
Applicability in Plant authentication	Yes	Yes, but should not be used (It is genetic diversity marker)	Yes, but should not be used (It is a perfect genetic diversity marker)	Yes, but should not be used (It is genetic diversity marker)	Yes	Yes	Yes	Yes
Cloning/sequencing	Yes	No	No	No	Yes	Yes	Yes	Yes
Use of radioactivity	Yes, but not in PCR-RFLP	No	Yes	No	No	No (required in AFLP based SCAR)	No (required in AFLP based LAMP)	No
Detection of alleles	Yes	Generally no	Generally no	Generally no	Yes	Yes	Yes	Yes
Cost	High	low	High	Medium	medium	high	Medium	medium
Ease of use of automation	Not easy (PCR based AFLP is easy)	Very easy	difficult if radioactivity is used (Licor system is easy)	Easy	Very easy	Easy	Easy (However, primer designing sometimes becomes difficult)	Easy