Abstract:In order to understand the genetic diversity of Piuns caribaea Morelet, the methylation diversity among 17 provenances to 3 varieties of P. caribaea was studied by using methylation sensitive amplification polymorphism (MSAP) technique. The results showed that a total of 425 bands were amplified by 56 pairs of primer combinations, 422 of them were polymorphic with a polymorphism rate of 99.25%. The major DNA methylation type in P. caribaea was hemi-methylation. The average methylation rate of P. caribaea var. caribaea, var. hondurensis and var. bahmaensis was 22.39%, 22.29% and 22.35%, respectively, which had no significant difference. The genetic diversity of DNA sequences (H=0.4376) was significantly higher than that of DNA methylation (H=0.3274). The Mantel test showed that there was no relation between genome genetic variation and methylation epigenetic variation (r=-0.171, P=0.16). The genetic cluster result was very different from that of methylation, although the two clustering results could not divided the three varieties of P. caribaea. So, it was suggested that P. caribaea had a high epigenetic diversity, which could provide excellent germplasm resources for genetic improvement of P. caribaea.