Now a days RAPD markers are not considered to be very good markers as they are reported to lack consistency i.e, the results may not be reproduced in different laboratories with different set of conditions. However if there is amplification of a particular RAPD band (marker) consistently appearing in PCR amplified DNA of individuals with specific trait, then those bands can be eluted, purified, sequenced and develop new set of forward and reverse primers of the sequence. These are SCAR markers and should consistently amplify the trait associated bands. The SCAR markers are better markers and sustain their efficacy in all conditions.

recently many types of molecular markers could be used as markers assisted selection related to unique trait, i.e. SSR, SNP and others, but if you want simple and low cost, you must RAPD then make a SCAR marker for target band

Dear Dr khaled, I totaly agree with Petikam that RAPD technique is very week and not recommended as Molecular markers. Simply because it is not reproducible. I have studied the efficiency of RAPD as a Molecular markers in comparison with other techniques and the results shows that it's not recommended. I think retrotransposons based Molecular markers is very efficient and more informative.

Article Retrotransposon-based molecular markers for assessment of ge...

In this paper I made in 2008 to compare between the three techniques

Data Comparative Assessment of Genetic Diversity in Tomato Cultiv...

In this paper I tried to enhance the RAPD capacities by using three compatible RAPD primers in the same reaction. It was very good for presenting the genetic diversity but again, NOT Molecular markers. I hope those papers can conclude my point of view

Conference Paper Diversity assessments among Mango (Mangifera indica L.) cult...

Dear Dr Ahmed: I agree with you that RAPDs are not reproducible, but we can make it more using the hybrid technique called R-ISSR, that we made combinations between RAPD and ISSR primers and it was very successful as molecular marker

You can review this paper

Conference Paper Marker- Assisted Selection Associated with Sugar Content in ...

I did use the R-ISSR before but I still don't think it is a solid technique for "Molecular markers". However, we can use it for screening for Molecular diversity. I will be glad to talk in the future and do more cooperation in this regard.

With my best wishes

I am looking for this cooperation and hope to meet you soon

Regards

Niraj,

I would say about two groups of molecular markers: 1) arbitrary (AP-, RAPD-, DAF, ISSR-, REP-, ITE-PCR) generated with unknown sequence, and 2) sequence-associated (SSR, SCAR, STS, SNP). Main difference between the arbitrary-primer markers can be in reproducibility of bands that depends on primers length and PCR conditions. Primer similarity to tandem repeats (ISSR) or to genetic mobile elements (ITE) plays less important role than it could be expected.

20 years ago we applied RAPD with 12-nucleotide primers at Ta=40oC and had very reproducible band amplification. Arbitrary-primered bands sequencing gave unexpected results - only small part (10-25%) of fragments had high homology of flanking regions to the applied primers (out of 400 sequenced fragments). The bands of the same length (+-5%) often had different sequence. Our data suggested that RAPD was best for identification of somatic mutations or intra-cultivar variation, ITE-PCR – intercultivar or inter-landrace diversity, ISSR – for subspecies difference.

So, you can apply Arbitrary-primered PCR to get fragments linked to phenotype traits, but you must sequence them and use sequence-associated markers (STS, SCAR) to confirm the association and for practical selection.

Alex: i agree with your suggest, we could use RAPD, ISSR and/or R-ISSR to obtain fragments linked to traits and use sequence-associated markers (like SCAR) to confirm it

Thanks

Thanks Alex for your comprehensive answer