I am doing some SSR work on soybean, my understanding is that as a tetraploid, soybean can have either one of the four alternative alleles in one locus for SSR (Simple sequence repeat) markers? (I am not sure about this but think that's the case). my other question is, if I amplify an SSR locus and run it on a 3 % agarose gel for example and I see only one band on the gel, can I sequence this or would it be a waste of resources and time?
Thanks in advance for all the answers
It depends on the size of the SSR repeats. As a rule of thumb, you can resolve a 10% difference in product sizes on a standard agarose gel. For example, 10 bp difference if the larger product is 100 bp, 20 bp difference if the larger product is 200 bp, etc. If you don't know the size of the repeats, you can use a DNA ladder to get a better size estimate. Honestly, sequencing is so cheap I would just try sequencing what you have. If there is more than one SSR allele, then you will see it in your sequencing data.
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