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We  analyzed genetic diversity and population genetic structure of four artificial  populations of wild barley (Hordeum brevisubulatum); 96 plants collected  from the Songnen Prairie in northeastern China were analyzed using amplified  fragment length polymorphism (AFLP), specific-sequence amplified polymorphism  (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices  of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype  frequency, cluster analysis, PCA analysis and AMOVA analysis generated from  MSAP, AFLP and SSAP markers had the same trend. We found a high level of  correlation in the artificial populations between MSAP, SSAP and AFLP markers  by the Mantel test (r &gt; 0.8). This is incongruent with previous findings  showing that there is virtually no correlation between DNA methylation  polymorphism and classical genetic variation; the high level of genetic  polymorphism could be a result of epigenetic regulation. We compared our  results with data from natural populations. The population diversity of the  artificial populations was lower. However, different from what was found using  AFLP and SSAP, based on MSAP results the methylation polymorphism of the  artificial populations was not significantly reduced. This leads us to suggest  that the DNA methylation pattern change in H. brevisubulatum populations  is not only related to DNA sequence variation, but is also regulated by other  controlling systems.

Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP