Table 1.

Comparison of widely using molecular marker systems for plant genome analyses.

	Isozyme	RFLP	RAPD	AFLP	SSR	SNP
Abundance	Low	Medium	Very high	Very high	High	Very high
Types of polymorphism	Amino acid change in polypeptide	Single base change, insertion, deletion, inversion	Single base change, insertion, deletion, inversion	Single base change, insertion, deletion, inversion	Repeat length variation	Single base change
DNA quality	-	High	Medium	High	Medium	Medium
DNA sequence information	-	Not required	Not required	Not required	Required	Required
Level of polymorphism	Low	Medium	High	High	High	High
Inheritance	Co-dominance	Co-dominance	Dominance	Dominance	Co-dominance	Co-dominance
Reproducibility	Medium	High	Low	Medium	High	High
Technical complexity	Medium	High	Low	Medium	Low	Medium
Developmental cost	Medium	High	Low	Low	High in start	High
Species Transferribility	High	Medium	High	High	Medium	Low
Automation	Low	Low	Medium	Medium	High	High

Note: Data on the RFLP, RAPD, AFLP and SSR were modified from Semagn et al. [48].