SCAR
Sequence Characterized Amplified Regions (SCARs) uses the sequence of polymorphic fragments of DNA, such as sequenced fragments that are picked-up from mRNA. The primers that are used for SCAR are not chosen randomly but they are especially developed to amplify a unique site in the genome. The primers are about 15-30 nucleotides. Such long primers will fit only one specific DNA sequence in the organism, and are very unlikely to fit by chance some non-target DNA sequence in the genome. Because of their length that corresponds to a sequence in the genome, DNA fragments are reliably amplified and reproducibly generated independent of the lab that runs those markers.
The procedure is as follows:
- A DNA fragment is chosen, such as a cDNA fragment of a gene of interest
- The DNA fragment is cloned and sequenced
- Long primers are designed, based on the sequence information for each end, usually with the use of a computer program.
Dominant or co-dominant. The polymorphism displayed by SCAR markers may consist of amplification of DNA in one parent and failure in the other parent. Such a polymorphism leads to a dominant SCAR marker. A second possibility may be that in both parents an amplified DNA fragment is obtained, but of different size. In that case we have obtained a co-dominant marker. Finally, in both parents an equally long DNA fragment may appear from the PCR. Then a further possibility to find and exploit polymorphism might be to sequence the obtained fragments and compare the sequences between the parents. For example, sequencing may reveal polymorphism in the 200th base-pair (one nucleotide change). This constitutes a SNP, and may be exploited as explained earlier (see SNP markers).
Summary
→ SCAR markers can either be dominant or codominant
→ SCAR primers are specifically designed based on the sequence of a known DNA fragment
→ SCAR markers are highly reproducible