As I got to know multi locus markers are the Markers represent various loci along the genome. e.g. RAPD, AFLP
Thing that I don't understand is why RFLP is not an multi locus markers? RFLP is categorize under single locus markers.
But as far as I understood AFLP and RFLP looks similar unless primer used.
I'd appreciate if some one clarify the concept and exact difference between between single locus and multi locus markers
Dear Akila,
May be the difference between microsatellites and RFLP would clarify the difference in terminology used. Microsatellites, for example, take advantage of the abundant and ubiquitously distributed simple sequence repeats (SSRs) in the eukaryotic genome. The variation in repeat number can be visualized as differences in the length of PCR-amplified products. Analysis of SSRs requires prior characterization of sequences flanking the repeats to allow the design of primers, to each locus, for PCR amplification. SSRs are codominant markers and can reveal multiple alleles at a single locus. On the other hand, Restriction Fragment Length Polymorphism (RFLP) is a difference in homologous DNA sequences that can be detected by the presence of fragments of different lengths after digestion of the DNA samples in question with specific restriction endonucleases. RFLP, as a molecular marker, is specific to a single clone/restriction enzyme combination.
To illustrate your inquiries:
If you do RAPD marker - you use single primer to get PCR amplified product(s). The product(s) may be the results of annealing the same single primer in a number of different locations in the genome. From the annealing sites, one obtains amplification of the target locations. The different sizes of amplified products are therefore representing the different locations of the genome. If we define "different locations" in the genome as "loci" then by using single primer - one actually can investigate a number of "different locations" aka "different loci" of the genome at once using RAPD marker. Therefore, RAPD and any marker generating a number of DNA fragments using a single (i.e. ISSR markers) or a pair of primers (i.e. AFLP) in one PCR reaction, even from individual samples. The DNA fragments represent different locations of the genome; therefore, they are called "multi-loci" markers.
On the other hand, if you do RFLP - you use a fragment of the genome as DNA probe. This means that you investigate only the location in the genome that have sequence identity similar to the probe you use ( single location). Subsequently, any variation you generated using the probe represent different alleles in the investigated locus (i.e. one similar to the probe). Since what you investigate is a variation of alleles in one locus - you call RFLP marker as the single locus marker. RFLP and other similar markers (SSR, SSCP) are also known as multi-allele marker, since you will probably generate different alleles from one locus investigated in a population scales.
I hope these can answer to your questions. Good luck...
Dear Prof. Sudarsono, Thank you very much for spending your valuable time on well explanation. It's very good illustration.
Dear Dr. Temim, Thank you for your valuable answer.
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