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In vegetatively propagated plants, branches of periclinal chimera give rise to bud mutants, or `sports', which have been used to breed new cultivars. Here, we have examined DNA methylation profiles in the cells of the L1 and L2+3 layers from single plants of vegetatively propagated carnations. The band patterns of methylation-sensitive amplified fragment polymorphism (M-AFLP) of the genomic DNAs in the L1 and L2+3 layers of the carnation cultivar, `White Sim', vegetatively propagated over the past 50 years, were completely different. The bud mutant, `White Mind', obtained from `White Sim' about 25 years ago, also had very different M-AFLP patterns to the parental `White Sim' line. The cultivar, `Red', which was separated from `Satisfaction' as a bud mutant two years ago, showed similar patterns to `Satisfaction' in each corresponding layer. However, we were able to detect minor, but significantly different M-AFLP patterns between the cultivars, `Red' and `Satisfaction'. The number of bands that differed between these cultivars was larger in the L2+3 layers than in the L1 layers. The results indicate that the DNA methylation profiles differ between each cell layer derived from distinct cell lineages of vegetatively propagated plants, and that changes in these profiles occur frequently and accumulate in the cells of the L2+3 layers, rather than in the L1 layer. [ABSTRACT FROM AUTHOR]