Hi all,
We're working with the plant genus Diascia. There's no reference genome, and there isn't data on the overall genome size. We want to use ddRAD for population genetic analysis (~15 populations of 30 individuals each) but we're not sure how to choose the fragment size/enzyme pair. Not much seems to have been done for population genetics with ddRAD in plants and so we have had trouble finding much useful precedent in the literature (most pop gen has been with fish and most plant ddRAD focuses on association mapping or linkage - maybe we've missed a key article?). From what we have gathered, it seems that for the best coverage and reliability of base calling, we would want around the 100-300 bp range for our fragment size. Any suggestions or guidance would be very welcome! Thank you!
We're working with the plant genus Diascia. There's no reference genome, and there isn't data on the overall genome size. We want to use ddRAD for population genetic analysis (~15 populations of 30 individuals each) but we're not sure how to choose the fragment size/enzyme pair. Not much seems to have been done for population genetics with ddRAD in plants and so we have had trouble finding much useful precedent in the literature (most pop gen has been with fish and most plant ddRAD focuses on association mapping or linkage - maybe we've missed a key article?). From what we have gathered, it seems that for the best coverage and reliability of base calling, we would want around the 100-300 bp range for our fragment size. Any suggestions or guidance would be very welcome! Thank you!
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