Types of DNA markers
DNA markers are formed by different types of variation in the nucleotide sequence. The most important are substitutions (point mutations: substitution of one nucleotide by a different one), rearrangements (insertion or deletion of nucleotides, also called 'indels') or errors in replication, such as duplications.
These variations can be detected by different technical methods. Those printed in red are treated in more detail below; the rest are not part of the course, but you can come across them in older literature:
- Single nucleotide polymorphism (SNP)
- Sequence-Characterized Amplified Region (SCAR)
- Simple Sequence Repeats (SSRs) or 'microsatellites'
- Restriction fragment length polymorphism (RFLP)
- Random amplified polymorphic DNA (RAPD)
- Cleaved Amplified Polymorphic Sequence (CAPS)
- Amplified Fragment Length Polymorphism (AFLP)
- Inter-Simple Sequence Repeat (ISSR)
- Expressed Sequence Tags (EST)
- Sequence Tagged Site (STS)
- Diversity Arrays Technology (DArT)
Of these, SNPs and SSRs are currently the most used. Through the growing use of sequencing techniques, techniques that decipher the DNA genetic code, numerous SNPs can be discovered. Because of this and the availability of high-throughput scoring of many SNPs for many individuals at the same time, SNPs are currently very important as markers. SNPs have the additional advantage that they can be detected in the alleles of genes.
Because of the sequencing technologies becoming cheaper and more high-throughput all the time, the scoring of SNPs by using SNP arrays or bead based technologies, will be complemented or replaced by technologies generating, in segregating populations, for every individual in the population, smaller or longer sequence reads of segments of DNA containing more than a single SNP and that these reads are then used as multi-SNP sequence markers. These approaches are called genotyping-by-sequencing (GBS).