There are some data about intra-cultivar SNP variability for potato, especially for old varieties (Theor Appl Genet (2015) 128:2387–2401 DOI 10.1007/s00122-015-2593-y). Is it possible to find variation within potato cultivars by SSR analysis?
Yes, possible
just screening out SSR markers as many as you can, identify the polymorphic marker that can distinguished cultivars of potato.
generally, compound SSRs are more polymorphic, try it first.
Yes, you can find variations among cultivars using SSR.
Several significant disadvantages exist with SNP markers, because they are not as polymorphic as other markers and more SNPs are required to reach equivalent powers of discrimination or random match probabilities. Butler et al. (2007) suggested that the power of 13–15 SSR loci (as are commonly in use today) is comparable with at least 40–60 SNPs.
Hope it helps!
1. To follow up Clizia's comment, in this paper (see below), it also indicates that "the resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis."
Paper title: Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties
2. Other paper also suggests the same (see attachment #2):
"However, Yu et al. (2009) suggested over 10 times more SNPs than SSRs should be used to estimated relative kinship and Inghelandt et al. (2010) proposed between 7 and 11 times should be used to infer population structure in maize association analysis."
3. But, I am not sure how powerful it is by using SSR on intra-cultivar genetic variability analysis.
@Yuan-Yeu, I must explain the reason of my question: we had a dispute about practical application of SSR|SNP markers for potato cultivars identification. The first opinion was: potato is a somatically multiplied plant, thus, SSR|SNP will be uniform within one cultivar.
The second opinion: new potato cultivars must be uniform in SSR|SNP if molecular passport was used for the cultivar registration. But, in old cultivars, somatic mutations can cause a certain variation of SSR|SNP markers, even if the morphological traits stay uniform. In such case, potato seeds propagated in different regions may have different frequency of major SSR|SNP genotypes within the same cultivar.
@ Alex,
1. Yes, I totally agree with you. That's why on the #3 point in my earlier post, I mentioned that I am not sure about using them in 'INTRA-cultivar', especially for those clonally-propagated crops. The materials used to compare in the examples (papers) given above were between 'different cultivars', not 'intra-cultivar (or within a cultivar)'.
2. I am attaching a paper for you (see below). Although it is not from a clonally-propagated crop, it is a comparison of SSR and SNP markers using in a study of 'clonal lineages' of a self-fertilizing fish. It may offer some insights for you.
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