Effect of DNA methylation on molecular diversity of watermelon heirlooms and stability of methylation specific polymorphisms across the genealogies

American watermelon heirlooms are phenotypically diverse in terms of their growth habits, fruit traits and responses to biotic and abiotic stress. Wide ranging DNA marker tools resolved narrow molecular diversity among these collections. The current research explored additional insights such as extent of diversity at the methylation level among the watermelon cultivars. DNA profiles were generated using Methylation-sensitive AFLP assay for 47 watermelon heirlooms. Results indicated that methylation specific diversity (43%) in US watermelon heirlooms is higher than the diversity (19.8%) estimated by several investigators using conventional DNA markers. In tree topologies of Neighbor-Joining (NJ) phenograms, the clustering pattern of principal component analyses of separate data sets obtained from the methylation specific isoschizomers MspI and HpaII resolved the diversity associated with methylation. Methylation-induced clustering was further verified using model-based population structure analysis. Our study clearly revealed the extent of methylations that are shared between parental heirlooms and progeny heirlooms, when tracked in known genealogies and breeding histories of heirlooms. Methylation sites that were not carried over and de novo methylations in the progeny heirlooms were fewer, when compared to the methylations that are stable.