where your restriction conditions satisfying? you could change for another pair of enzymes! which pair of isoschizomers have you used?

If you have just digested your untreated DNA samples with two different isochizomers then I don't think there'll be a gros difference in their patterns in an agarose unless there is massive methylation at repetitive DNA (which is probed for by the REs). Usually any RE digest of total genomic DNA will appear as a smear on agarose gels. I think once  you digest with different enzymes, then you need to probe a southern blot of the same with a repetitive DNA probe or a candidate multicopy region, which will then show up as differential patterns (essentially RFLP), To make it easy, you can also do RAPD PCRs using the digested DNA as template to look at length polymorphisms - which reads out as differential pattern in the two PCRs carried out with the same primer sets. (inbox me if you need to understand details of RFLP or RAPD). There are multiple methods using updated technologies to answer the same question, but i have only listed to easy ones here. One can move into genome wide approaches as well. 

@ Herve Levesque I have used MsP I and Hpa II...@ Subhojit Sen  is it possible to do RAPD PCR with the restricted total DNA?

suggestions to be tested : you can probe your restricted DNA with a total DNA probe (for example after sonication or cleavage with a 4 bases specific recognition site RE or RE cocktail) ; several RE known to be sensitive to methylation, especially C methylation, could be tested and compared to other insensitive even though not isoschizomers ; mean fragment length - midpoint of the smear mentionned by Subhojit Sen - could served as a criterion for comparison and a mean to evaluate average methylation

Hi Maya,

Before going into using bisulfite conversion and whole genome sequencing, which can be expensive and very difficult to analyse with in a polyploid species as sugarcane, I would recommend trying a fingerprinting approach. Since you have restricted your DNA with HpaII and MspI I would recommend using and MSAP (methylation sensitive amplified polymorphism) approach. Just keep one thing in mind, MspI, although sometimes described as methylation insensitive, is methylation sensitive. Its methylation sensitivity is different than that of HpaII. Finally, because sugarcane genome is quite big you will probably have to use a large number of selective bases during PCR amplification after restriction. I would suggest to start with 4 selective bases for HpaII/MspI and 4 for EcoRI. Please let me know if you need any more help