Hi Raj,

Each DNA based molecular marker has its own significance in genetic diversity studies. Based on accessibility of the various markers you optimize the parameters and use them for your study. Also refer published articles.

Article Analysis of population structure and genetic diversity in an...

Article Analysis of genetic variation in sorghum (Sorghum bicolor (L...

Good luck.

https://doi.org/10.1080/13102818.2017.1400401

I guess it's a good article

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885095/

https://www.sciencedirect.com/science/article/pii/S235240731500030X

https://www.jstor.org/stable/4181463?seq=1#page_scan_tab_contents

Dear Raj,

Please keep in mind that each marker has its own nature, which might not be suitable for all applications, but generally speaking, markers can be either used for inter or intra specific variation assessment. The RAPD and ISSR of markers you have mentioned are mostly used for within (intra) species variation, the RAPD is to be excluded (due to serious technical problems) and I strongly advice against it for solving taxonomical issues. While SNPs markers detected by using fingerprinting techniques (e.g. AFLP) or Sanger sequencing are the most recommended, due to several reasons, one of which is the ability to apply several phylogenentic approches, and estimate several evolutionary and population parameters, which definitly are the key to resolve most of the taxnomical issues.

In a short answer, using DNA sequencing, will save you effort and money, and the outputs for your taxnomical problem is highly probable to be solved than applying the other markers you mentioned.

Several literature can be found, but beware, genetic variation within a population (intra) is one thing while between species (inter) is another thing!

Best wishes!

Thank you for all your reply

ISSR is robust and reliable marker compared to RAPD. CBOL recommends matK and rbcL loci for plant taxonomic analysis. ITS full length or ITS2 sequences is commonly used.I suggest use DNA marker if your analyzing diversity and variations within a localized area of sampling (within India or specific to particular area) or if have taxonomic problem concerning to one or two species .If your trying solved the taxonomic problem of genus or genera wherein you have several species DNA barcode is recommended. I agree with @Mahmoud Magdy Elmosallamy sequence based analysis is more reliable, will save you effort and time.

Thank You @ Shrisha Naik

Interesting responses!

Issr can be used reliable and inexpensive markers. SCot markers are more advanced and recent dominant markers. But always use two different markers systems so that one result can be validated by others and results produced would be more reliable. U can use SSR also along chloroplast specific markers. See this paper for reference.