Our experience in SSR genotyping of large apple germplasms indicate that the within-cultivar variation is quite low (it only depends on mutations of the number of repeats over different clones of a given cvr for a given SSR, which is not so high ...).

Conversely, the number of errors in cultivar denomination is quite high: it frequently come from errors in grafting/multiplication, or errors in pomological identification (inferences on the cvr name based on pomological observations).

Are you sure about the true-to-typeness of the genotypes/clones considered to belong to a single cvr ? 

(for TTT see Evans et al. Mol Breed 2006 : http://www.goffredo.ch/pseudo/HiDRAS_TTT.pdf

Charles-Eric

Speaking on AMOVA in crop plants this can happen very often and several article exist showing higher molecular variance within the cultivar than among the cultivars. I think it can happen if the cultivars are pro-genies of the same parents or if they are some time selection from the seed propagated plant material (most likely selfed). Attached is a good study on peach.

I agree with all of you.  There are many reasons for this diversity including the genomic mobile elements

Article Environmental Stress Activation of Plant LTR-Retrotransposons

Thank you Arun Prabhu Sir.Can you please tell me your mail so that can discuss further. This will be very helpful for me in my PhD

Yes, occur molecular variation among cultivars of apple. But within the cultivar will be rare because the molecular variation depends on the mutation rate and time of release of the cultivar. The techniques: SSR, AFLP and RAPD are not suitable for studies of RNA or enzymes (environment)

Our experience in SSR genotyping of large apple germplasms indicate that the within-cultivar variation is quite low (it only depends on mutations of the number of repeats over different clones of a given cvr for a given SSR, which is not so high ...).

Conversely, the number of errors in cultivar denomination is quite high: it frequently come from errors in grafting/multiplication, or errors in pomological identification (inferences on the cvr name based on pomological observations).

Are you sure about the true-to-typeness of the genotypes/clones considered to belong to a single cvr ? 

(for TTT see Evans et al. Mol Breed 2006 : http://www.goffredo.ch/pseudo/HiDRAS_TTT.pdf

Charles-Eric

Charles Eric sir

Thank you for sending me your valuable research paper. I have collected samples from different commercial private orchards. I am little bit confused about the true to type concept in the case of apple, as farmers report that they have grafted scions of the same cultivar.They identify the cultivars according to pomological obseravations.

Fully agree with prof. Durel. In our experience, it was very difficult to find consistent differences among clonal variants of a few varieties, such as the 'Gala' or 'Fuji' series. By SSRs (screen with a few tens) we found complete homogeneity at the intra-variety level. Then we used S-SAP (transponible elements-based markers), and the polymorphic amplicons we found one season were scarcely reproduced with samples of the same genotypes collected the following season (unpublished results).

Theoretically, you should expect no within-cvr polymorphism as apple cvrs are fixed.

If different samples for a given cvr name come from different orchards, they should all be 'true-to-type', i.e. they should all share the same SSR profil as a reference sample (from a germplasm collection for example). As indicated by Dr. Hinrischen, within-cvr variations are extremely rare for SSR.

Perhaps, the variations you observe come mainly from ISSR which markers can be more variable and difficult to score (?).

If SSR profils are variable for different samples (of different orchards) from a given cvr, either there is an error in the grafting process or there is an error in the leave sampling, DNA extraction, DNA amplification process (which can not be excluded even in very cautiously performed experiments ; we had some in the lab, rather rare fortunately !).

Best,

CE

It is possible

If  the clones are taken from different  sources or scions, we will get variation with in species

Yes it is possible to get variation. I have found within accession variations with Cp SSRs which could be correlated with the country of Origin/collection

Yes,  I agree.  There are many ecotypes variations you can capture using different types of Molecular markers (e.g SSR, IRAP, REMAP, ....)