Researchers highlight the correlation between grafting vigour and DNA de-methylation in eggplant

Plant grafting is the process of joining tissues from two plants, the upper scion and the lower rootstock, and is since more than 2000 years used as horticultural technique for the cultivation of fruit trees. Nowadays grafting is widely employed by horticulturists in Solanaceous species with the goal to provide resistance or tolerance to biotic and abiotic stresses, such as soil-borne pathogens, salinity, and drought. They can also improve scion vigour and change plant architecture, mineral element composition, fruit quality and yield.  However, the molecular mechanisms that underlie rootstock-mediated control of scion phenotypes remain largely unknown.

DNA methylation is one of the most common epigenetic processes that alter gene expression without changing the DNA sequence. In higher plants, it involves the addition of a methyl group to 5^th carbon of a cytosine by DNA methyltransferase (5-mc) at CG, CHG or CHH sites. Grafting involves the bidirectional long-distance transport of macromolecules, which are able to induce epigenetic variation and physiological changes. Previous studies have provided evidence locus‐specific DNA methylation in interspecies grafting in the Solanaceae, and it has been hypothesized that DNA methylation is the driving mechanism that generates phenotypic diversity through grafting.

Recently, a group of researchers led by Dr. Cinzia Comino of the University of Torino, Italy and Dr. Marco Catoni of the University of Birmingham, UK tested this hypothesis and reported that the enhanced vigour induced by heterografting in eggplant was associated with genome-wide hypomethylation in the CHH context. This study was published in Horticulture Research.

Whole genome bisulfite sequencing (WGBS) was used to generate the first eggplant genome methylation profile at single-cytosine resolution. Methylation profiles in hetero-grafted plants with enhanced vigour showed a significant genome-wide reduction in CHH methylation, which was more prominent at transposable elements (TEs) than at coding genes.

Genome-wide RNA expression was then profiled to investigate the association between the observed epigenetic variation and gene expression. Interestingly, researchers observed upregulation of DNA methyltrasferases associated to CHG and CG methylation, rather than CHH context, and they    concluded that the observed CHH hypomethylation is likely the effect of indirect compensatory effects on epigenetic landscape induced by a rootstock.   

“It is probable that most of the epigenetic changes are not directly associated with the regulation of gene expression, but rather hint towards grafting-induced mechanisms targeting only particular genes”, the researchers said.

They also developed the functional annotation pipeline LTRpred and used it to de novo re-annotate long terminal repeat retrotransposable elements (LTR-TEs). A correlation between hypomethylation and the downregulation of younger and potentially more active LTR-TEs was observed.

In brief, this study emphasized the role of epigenetic regulation (especially reduced CHH methylation) in the control of vigour in grafted Solanaceae species. These findings mark a critical milestone, as described by the researchers: “Our work provides the first DNA methylome of eggplant and sheds new light on the molecular mechanisms underlying the effects of rootstock on the scion…We conclude that the use of grafting represents a promising alternative to traditional breeding to manipulate plant epigenomes and improve plant production.”