Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis

Thomas K. Uthup, Rekha Karumamkandathil, Minimol Ravindran, Thakurdas Saha

Heterografting induced intraclonal epigenetic variations were detected among rubber plants. Interaction between genetically divergent root stock and scion tissues might have triggered these epigenetic changes which may eventually lead to intraclonal variability in rubber. DNA methylation in response to stress may be associated with the alteration in gene transcription leading to morphological changes in plants. Rubber tree is commercially propagated by bud grafting where the scion of a high yielding variety is grafted on to a genetically divergent root stock. Still, significant levels of intraclonal variations exist among them. Epigenetic changes associated with heterografting may be partly responsible for this conundrum. In the present study, an attempt was made to identify the impact of divergent root stock on the epigenome of scion in grafted rubber plants. Heterografts were developed by grafting eye buds from a single polyembryony derived seedling on to genetically divergent root stocks of unknown parentage. The plants were uniformly maintained and their DNA was subjected to MSAP analysis. Polymorphic DNA methylation bands corresponding to CG as well as the plant-specific CHG types of methylation were observed. Cloning of selected polymorphic regions and bisulfite sequencing confirmed the presence of methylation in the promoter and coding region of important genes including an LRR receptor kinase gene. Since divergent root stock is the major factor differentiating the grafted plants, the changes in DNA methylation patterns might have been triggered by the interaction between the two genetically different tissues of stock and scion. The study assumes importance in Hevea, because accumulation and maintenance of epigenetic changes in functional genes and promoters during subsequent cycles of vegetative propagation may contribute towards intraclonal variability eventually leading to altered phenotypes.