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Genetic  analysis of 56 samples of Jatropha curcas L. collected from Thailand and  other countries was performed using the methylation-sensitive amplification  polymorphism (MSAP) technique. Nine primer combinations were used to generate  MSAP fingerprints. When the data were interpreted as amplified fragment length  polymorphism (AFLP) markers, 471 markers were scored. All 56 samples were  classified into three major groups: γ-irradiated, non-toxic and toxic accessions. Genetic  similarity among the samples was extremely high, ranging from 0.95 to 1.00,  which indicated very low genetic diversity in this species. The MSAP fingerprint  was further analyzed for DNA methylation polymorphisms. The results revealed  differences in the DNA methylation level among the samples. However, the  samples collected from saline areas and some species hybrids showed specific  DNA methylation patterns. AFLP data were used, together with  methylation-sensitive AFLP (MS-AFLP) data, to construct a phylogenetic tree,  resulting in higher efficiency to distinguish the samples. This combined analysis  separated samples previously grouped in the AFLP analysis. This analysis also  distinguished some hybrids. Principal component analysis was also performed;  the results confirmed the separation in the phylogenetic tree. Some  polymorphic bands, involving both nucleotide and DNA methylation polymorphism,  that differed between toxic and non-toxic samples were identified, cloned and  sequenced. BLAST analysis of these fragments revealed differences in DNA  methylation in some known genes and nucleotide polymorphism in chloroplast DNA.  We conclude that MSAP is a powerful technique for the study of genetic  diversity for organisms that have a narrow genetic base.

Genetic diversity analysis of Jatropha curcas L. (Euphorbiaceae) based on methylation-sensitive amplification polymorphism