Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis

Abstract

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.

Small RNA populations reflect the complex dialogue established between heterograft partners in grapevine

“…Similarly, endogenous repeated sequences located in the scion were shown to induce DNA methylation in the rootstock by generating mobile siRNAs of 24nts (reviewed in [ 52 ]). As far as perennials are concerned, although DNA methylation reprogramming has been evidenced after heterograft of rubber tree [ 53 ] and citrus under drought stress [ 54 ], direct evidence that these methylation changes are associated with mobile siRNA is missing. Similarly changes in DNA methylation associated with heterograft were recently reported in citrus plants using a genome wide approach.…”

Epigenetic Changes and Transcriptional Reprogramming Upon Woody Plant Grafting for Crop Sustainability in a Changing Environment

“…In another study conducted for Hevea brasilensis methylation differences were detected between buds from a single own rooted polyembryony-derived seedling grafted to genetically divergent rootstock (Uthup et al, 2018). MSAP and bisulfite sequencing techniques revealed significant alterations in DNA methylation profiles between heterografts and the levels of those epigenetic rearrangements was found to depend on the degree of incompatibility between the rootstock and the scion.…”

“…Recently such graft-induced epigenetic alterations were reported also in woody species. DNA methylation profiles in Hevea brasiliensis (rubber tree) heterografts were significantly altered depending on rootstock and rootstock-scion genotype combinations (Uthup et al, 2018) and DNA methylation polymorphisms were found between juvenile seedlings, grafts, and adult trees, in apple (Perrin et al, 2020). All the aforementioned studies indicate that grafting can trigger changes in epigenetic factors such as DNA methylation and small RNAs, potentially impacting important traits of agronomical relevance.…”

Grafting: a potential method to reveal the differential accumulation mechanism of secondary metabolites

“…2b ). For example, grafted rubber ( Hevea brasiliensis ) scions exhibited epigenetic changes after grafting to genetically distinct rootstocks [ 61 ]. As another case, when the Valencia (VO) citrus scion variety was grafted on the two rootstocks Rangpur lime (RL) and Sunki Maravilha (SM), the two combinations presented polymorphic alterations of epigenetic marks for this crop [ 62 ].…”