I'm working on polyploid crop with intraspecific ploidy variation. Our crop do not have a reference genome. I need to
find SNP's associated with traits and for that intend to use ddRAD sequencing. I have few questions:
1) Regarding the choice of restriction enzyme,there is a paper dealing with optimized ddRAD protocol in angiosperms. Can we just go with this reported restriction enzyme combination as we don't have reference genome to do insilico digestion analysis.
2) How to decide the number of crop varieties that need to be sampled to find SNP's ?
Hi Aswathi,
There are a few things you could try before finalizing the set of restriction enzymes:
a. You can try in-silico digestion on a closely related species genome.
b. You can also try and digest DNA of your species using various combinations of enzymes, and then check the size distribution (using tapestation or bioanalyser).
I recommend doing both the above steps before finalizing the enzyme combination. Of course, you can take help from what enzyme combinations are frequently used in the literature on related species and test for your species.
Try REDigest for the in silico analysis
https://github.com/abhijeetsingh1704/REDigest
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