I am following a research paper which is published from our research group.I am enclosing the paper with the question. I want improvise the data analysis part of the work which I intend to do. Apart from just assessing the somaclonal variations what additional approach can be incorporated? Any constructive suggestion is most welcome.
Dear Paromik,
If you want to asses genetic stability within generations of clonally propagated plants using molecular marker, I would suggest you choose the co-dominant type markers (such as SSR or SNP markers) instead of dominant ones (ISSR or RAPD markers). However, you will need to select enough numbers and locations of loci to be able to detect changes in the plant gemome.
Just a short note, even if for certain generations based on a set of evaluated markers do not show any allele variation, it only means that they are stable for alleles of the evaluated loci. In the meantime, for other unevaluated loci, there may be allelic changes (variations) but they are undetected because the loci are not assessed.
Good luck...
Everybody can expect low genetic difference between the clonal plants, and it is better to use method that generate many markers like AFLP or TE-AFLP. RAPD would be good for task too, but number of primers must be really large, and all differentiating bands must be cloned and sequenced to develop specific primers.
For genetic fidelity testing one can use markers like SSR or ISSR ..but make sure that the sample size as well as the number of primers tested are sufficiently large. Always use parental DNA and totally unrelated or even DNA from other source as controls. The data will tell you two things.... Presence of any variant........and also true to the type plants (if you intended for that)........
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