Dear colleagues,
We would like to discriminate between populations of a plant species at different geographical locations.
Yet, microsatellite markers (to distinguish them) are scarce.
Available genomic info is limited as well:
- The species only has a chloroplast genome sequenced.
- Only, there is a draft genome for its congeneric species.
As we are new to population genetics, Would you think we need to perform NGS whole genome sequencing - for the species at different geographical locations before we could achieve our goals?
or is there a smaller scale / easier way to do?
Please advise. Thanks :)
Hi Kay,
SSRs can quite often amplify across related species, so it might be worth trying a few if there are some available. You could use the cpDNA to look for SSRs as well. To design SSRs markers, you need to identify the repeat motifs. A perl script program (or similar) could identify SSRs. Then you can design primers from the flanking regions and then test these on several individuals. If you have a draft gemone for congeneric species, you could use a SSR identification tool such as MISA (http://pgrc.ipk-gatersleben.de/misa/) or similar - there are other such programs available. MISA is a perl script program that can identify repeats regions from sequence data and is reasonably easy to use. While whole genome NGS sequencing is more accessible these days with various new techniques available, it might be worth trying this out first. Alternatively, there are other methods rather than sequencing the whole genome, e.g RNA-Seq (sequencing the transcriptome). I'm sure there will be lots of advice from others on this topic. Good luck
hi dear Kay Wong
I think, in this case Genome walking is very useful.
You could also potentially use RAD-sequencing to do something similar to this. I think it is a pretty common "NGS" method for population-level studies.
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