Abstract: Methylation-sensitive amplification polymorphism（MSAP）analysis was performed in Ginkgo biloba var. epiphylla Mak.（epiphylla ginkgo）and Ginkgo biloba（ginkgo），at both the bud-burst stage and the leaf-expansion stage，to characterize the DNA methylation levels and patterns of CCGG sites. The results showed that 22 selected primer sets totally amplified 498 and 384 loci，respectively in bursting buds of epiphylla ginkgo and ginkgo. And among them，237（47.6%）and 165（42.4%）loci were found methylated. While at the leaf-expansion stage，40 selected primer sets totally produced 767，600 and 367 loci，respectively in epiphyllous-ovule leaf of epiphylla ginkgo（YZ2），normal leaf of epiphylla ginkgo（YC）and ginkgo（CK）. And among them，370（48.3%），244（40.5%）and 152（41.5%）loci were methylated. Further analysis revealed that more than half of the loci（52.1%，54.6%，64.2%）displayed changes in DNA methylation patterns in epiphylla ginkgo compared with ginkgo both at budding stages and leaf-expansion stages. Hypermethylation was found more frequent in both YZ1 and YZ2 than in CK，YC or CK. The greater variation of DNA methylation and more frequent hypermethylation occurred in epiphylla ginkgo suggested the unique DNA methylation profile of epiphylla ginkgo. These findings undoubtedly laid foundation for further discussing the origin and phylogeny of epiphylla ginkgo from the perspective of epigenetics.

Key words: Ginkgo biloba var. epiphylla, DNA methylation, methylation-sensitive amplification polymorphism（MSAP）, methylation patterns