Table 1 Comparison of most widely used DNA marker system 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 (< 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 |