Table 6-5.3(a).1 Comparative study of the five most commonly used DNA markers for genetic mapping in plants

Feature and description	RFLP	RAPD	AFLP	SSR	SNP
Genomic abundance	High	High	High	Moderate to High	Very High
Genomic coverage	Low copy coding region	Whole genome	Whole genome	Whole genome	Whole genome
Expression/inheritance	Co-dominant	Dominant	Dominant /Co-dominant	Co-dominant	Co-dominant
Number of loci	Small (<1,000)	Small (<1,000)	Moderate (1,000s)	High (1,000s – 10,000s)	Very high (>100,000)
Level of polymorphism	Moderate	High	High	High	High
Type of polymorphism	Single base changes, indels	Single base changes, indels	Single base changes, indels	Changes in length of repeats	Single base changes, indels
Type of probe/primers	Low copy DNA or cDNA clones	10 bp random nucleotides	Specific sequence	Specific sequence	Allele-specific PCR primers
Cloning and/or sequencing	Yes	No	No	Yes	Yes
PCR-based	Usually no	Yes	Yes	Yes	Yes
Radioactive detection	Usually yes	No	Yes or No	Usually no	No
Reproducibility/ reliability	High	Low	High	High	High
Effective multiplex ratio	Low	Moderate	High	High	Moderate to High
Marker index	Low	Moderate	Moderate to High	High	Moderate
Genotyping throughput	Low	Low	High	High	High
Amount of DNA required	Large (5 – 50 μg)	Small (0.01–0.1 μg)	Moderate (0.5–1.0μg)	Small (0.05–0.12 μg)	Small (≥0.05μg)
Quality of DNA required	High	Moderate	Moderate to High	High	High
Technically demanding	High	Low	Moderate	Low	Low
Time demanding	High	Low	Moderate	Low	Low
Ease of use	Not easy	Easy	Moderate	Easy	Easy
Ease of automation	Low	Moderate	Moderate to High	High	High
Development/start-up cost	Moderate to High	Low	Moderate	Moderate to High	High
Cost per analysis	High	Low	Moderate	Low	Low
Number of polymorphic loci per analysis	1.0 – 3.0	1.5 – 5.0	20 – 100	1.0 – 3.0	1.0
Primary application	Genetics	Diversity	Diversity and genetics	All purposes	All purposes

Table6-5.3(a).1 Comparison between most widely used DNA marker; Adapted from Collard et al. (2005), Semagn et al. (2006a), Xu (2010), and others also given in “Plant Breeding from Laboratories to Fields”, Chapter 3(Molecular Markers and Marker-Assisted Breeding in Plants) Page 52 & 53.