(1) It is simple because Its PCR products were resolved by performing agarose gel electrophoresis. Compared to arbitrary markers such as RAPD, SCoT markers are highly reproducible due to the use of longer primers.

(2) Primers were designed according to the short conserved region surrounding the ATG translation start (or initiation) codon (or translational start site, TSS).

(3) it is a type of targeted molecular marker technique. with the ATG context as one part of a functional gene, markers generated from SCoT marker technique may be mostly correlated to functional genes and their corresponding traits.

Thanks sir,but sir whay ATG translation codon is more advantageous than the intersimple (ISSR), minisatellte (VNTR) or SSR regions?

It may be due to conservation of ATG translation start site and flanking sequences in plant genes. For details, you can see this reference....

Bertrand C. Y. Collard & David J. Mackill (2009) Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants. Plant Mol Biol Rep 27:86–93

Sir generaly the trend in diversity studies what i have seen is using a cumulative data set (RAPD+ISSR) but recently in a few reports like http://www.sciencedirect.com/science/article/pii/S0168945213000447 they are using only one marker that is SCoT.what can be the reason?

See the diversity information generated by the RAPD, SSR or ISSR is based on the non-coding regions of DNA, so it is not that useful in the context directly. But it is useful only when it is linked strongly to some trait. Whereas in SCoT markers as they reveal the genetic diversity at the level of genes thus have the possibility of finding new alleles among a given germplasm collection. So the information generated by this marker is far more crucial, as it is derived from either the gene itself or its immediate flanking sequences.

@Rajdeep thanks for your answer.It has helped me.

You are welcome....it's just discussion...so dialogue should always go on...

Cheers@Paromik

Has anybody ever confirmed these assumptions by empirical testing, e.g. by sequencing reaction products of SCoT experiments? Should be easy to do and quantify (gene vs. non-gene sequences) with next generation sequencing methods ...

It will be highly appreciated if our senior colleagues in the advanced world can help develop primers for the Under-utilized crops that are in abundance in tropical Africa.

Thus, African scientists would be able to carry out necessary improvement progams before these crops go into extingtion.

Paromik Bhattachayya, Rajdeep khangura and Berthold Heinze should please note.

The perfect answer is given rightly by Dr.Manoj Rai, which does not necessitates any further explanation.

scot primers are they universal primers like RAPD and ISSR or we have to design them specifically depending on our plant species...

The other gene targeted marker like CBDP (CAAT BOX DERIVED POLYMORPHISM) can be also used for genetic diversity analysis

It is because they are highly discriminatory in fingerprinting and biogical diversity study

To answer Dr. David Kolawole Ojo from Abeokuta,

actually what can be done with nearly any crop plant that is poorly characterized genetically is to determine chloroplast halpotypes with universal primers, followed by RFLP cutting of any products, and resolution of the bands in agarose. Such polymorphisms are more easy to interpret, and reproducible, than any methods based on (even guided) random priming, such as RAPD, ISSR, SCoT et cetera.

My ten-years-old database of such primers is still on the web at:

http://bfw.ac.at/rz/bfwcms2.web?dok=4977

described in this article:

https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-3-4

Example use:

https://www.researchgate.net/profile/Berthold_Heinze/publication/235762721_PCR-based_chloroplast_DNA_assay_for_the_identification_of_native_Populus_nigra_and_introduced_poplar_hybrids_in_Europe/links/0f317530b39736a677000000.pdf

There are more recent collections of 'universal' primers described e.g. in:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019954

http://www.funpecrp.com.br/gmr/year2015/vol14-4/pdf/gmr6493.pdf

https://www.researchgate.net/publication/225657696_Chloroplast-specific_universal_primers_and_their_uses_in_plant_studies

In principle, the same approach is possible for (mitochondrial and) nuclear genes. See e.g.

Strand, A. E., Leebensmack, J., and Milligan, B.G. (1997). Nuclear DNA-based markers for plant evolutionary biology. Molecular Ecology 6(113-118).

I am available for advice if you write to me privately.

best regards,

Berthold Heinze

Article PCR-based chloroplast DNA assay for the identification of na...

Article Chloroplast-specific universal primers and their uses in plant studies

What about the reaction condition of SCot primer, does it like other normal markers such as RAPD or ISSR? thanks for any answer

Thank you, Manoj K Rai your answer is very clear. What are the disadvantages of SCoT marker from your experience?

The SCoT markers are successfully employed in detecting genetic homogeneity by targeting ATG context and functional genes,