Random Amplified Polymorphic DNA (RAPD): RAPD uses a short arbitrary primer that serves as both, forward and reverse primer, to amplify random DNA segments without requiring prior DNA sequencing.
Restriction Fragment Length Polymorphism (RFLP): RFLP involves using restriction enzymes to cut DNA at specific sites, resulting in fragments of varying lengths.
Single Nucleotide Polymorphism (SNP): SNPs are single base pair variations in the DNA sequence, detected using SNP chips.
Amplified Fragment Length Polymorphism (AFLP): AFLP combines PCR and restriction digestion to amplify selected DNA fragments.
Sequence Characterized Amplified Region (SCAR): SCAR uses PCR with longer primers to produce highly reproducible markers.
Cleaved Amplified Polymorphic Sequence (CAPS): CAPS involves PCR amplification followed by restriction digestion to reveal polymorphisms.
Microsatellites or Simple Sequence Length Polymorphisms (SSLPs): Microsatellites or simple sequence repeated (SSR) loci are PCR-based markers that required previous knowledge of gene sequence.
Expressed Sequence Tags (EST): Expressed sequence tags are molecular markers synthesized by partial sequencing of random cDNA clones and used as tags for identification of genes.
Inter Simple Sequence Repeat (ISSR): ISSR uses PCR to amplify DNA segments between microsatellite repeat using a single primer with microsatellite core regions.