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Table 1 Comparison of most widely used DNA marker system in plants

From: Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes

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 (< 1000) Small (< 1000) Moderate (1000s) High (1000s–10,000s) Very high (> 100,000)
Level of polymorphism Moderate High High High High
Type of polymorphism Single base change, indel Single base change, indel Single base change, indel Changes in length repeat Single base change, indel
Cloning and/or sequencing Yes No No Yes Yes
Type of probes/primers Low-copy DNA or cDNA clones 10 bs random nucleotides Specific sequence Specific sequence Allele-specific PCR primer
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
Amount of DNA required Large (5–50 μg) Small (0.01–0.1 μg) Moderate (0.5–1.0 μg) Small (0.05–0.12 μg) Small (> 0.05 μg)
Genotyping throughput Low Low High High High
Cost Moderate to high Low Moderate Moderate to high High
Marker index Low Moderate Moderate Moderate to high Moderate
Time demanding High Low Moderate Low Low
Number of polymorphic per loci 1.0–3.0 1.5–5.0 20.100 1.0–3.0 1.0
Primary application Genetic Diversity Diversity and genetic All purposes All purposes