How do I analyze Population epigenetics using Methylation profiles?

11 December 2014 1 9K Report

Hi,

I am using methylation data from 6 varieties of common beans and I am looking for detecting differentiation between populations, or other population genetics approaches...

I have been using the R package methyKit (one of the only one dealing with more than one population) and I could do cluster analysis, PCA, calculate DMCs and DMRs, etc...

Is there a way to extract more information? For instance, using DMC or DMR as markers to make a map? Unfortunately I don't have the parents of these varieties...

Thanks!

Nicholas Wagner

From what I know from human epigenetics I would guess that you will have to assess the intra-variety variation (so the variation that occurs within each of the six bean varieties) before assessing the inter-variety variation of methylation (i.e. the comparison of methylation between the varieties).

Assessing the methylation level of one bean variety from just one single bean seems a bit risky. But I am not en expert on comparison of methylation data from different species, so I am really curious to hear what they have to say!

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