Cytosine Methylation and Diversity in Gossypium hirsutum
Previous studies have examined genetic diversity within the tetraploid, G. hirsutum, using allozyme data and RFLPs, and we would like to know if the epigenetic diversity mirrors this genetic diversity to any extent. To get at the epigenetic diversity of this species, we are using a modified version of the AFLP technique to survey cytosine methylation in the genomes of various G. hirsutum accessions. In addition, we plan to isolate polymorphic bands to determine what sequences are methylated.
Methylation sensitive AFLP involves digesting genomic DNA in parallel with two isoschizomers, HpaII and MspI, in our case. Both restriction enzymes cut at CCGG sites but are differentially sensitive to methylation at the internal cytosine. Differences in banding pattern between the parallel HpaII and MspI digests allow us to detect methylation at the internal cytosine.