Inter-Species Grafting Caused Extensive and Heritable Alterations of DNA Methylation in Solanaceae Plants

Abstract

BackgroundGrafting has been extensively used to enhance the performance of horticultural crops. Since Charles Darwin coined the term “graft hybrid” meaning that asexual combination of different plant species may generate products that are genetically distinct, highly discrepant opinions exist supporting or against the concept. Recent studies have documented that grafting enables exchanges of both RNA and DNA molecules between the grafting partners, thus providing a molecular basis for grafting-induced genetic variation. DNA methylation is known as prone to alterations as a result of perturbation of internal and external conditions. Given characteristics of grafting, it is interesting to test whether the process may cause an alteration of this epigenetic marker in the grafted organismal products.Methodology/Principal FindingsWe analyzed relative global DNA methylation levels and locus-specific methylation patterns by the MSAP marker and locus-specific bisulfite-sequencing in the seed plants (wild-type controls), self- and hetero-grafted scions/rootstocks, selfed progenies of scions and their seed-plant controls, involving three Solanaceae species. We quantified expression of putative genes involved in establishing and/or maintaining DNA methylation by q-(RT)-PCR. We found that (1) hetero-grafting caused extensive alteration of DNA methylation patterns in a locus-specific manner, especially in scions, although relative methylation levels remain largely unaltered; (2) the altered methylation patterns in the hetero-grafting-derived scions could be inherited to sexual progenies with some sites showing further alterations or revisions; (3) hetero-grafting caused dynamic changes in steady-state transcript abundance of genes encoding for a set of enzymes functionally relevant to DNA methylation.Conclusions/SignificanceOur results demonstrate that inter-species grafting in plants could produce extensive and heritable alterations in DNA methylation. We suggest that these readily altered, yet heritable, epigenetic modifications due to interspecies hetero-grafting may shed one facet of insight into the molecular underpinnings for the still contentious concept of graft hybrid.

Mobile small RNAs regulate genome-wide DNA methylation

“…They could consider potential modification of gene expression patterns in sink tissues via sRNA transmission from source tissues. The mobile sRNAs can alter DNA methylation in germ-line tissue (37), so that DNA methylation patterns altered by grafting may be heritable by progeny plants (37,60).…”

Development of cassava periclinal chimera may boost production

“…Recently, epigenetic alterations causing heritable complex traits such as plant height have been reported (Johannes et al, 2009). Epigenetic alterations, on specific locus, were also noted in plants, where two species coexisted on the same individual, being attributed to the interaction between species (Wu et al 2013). This phenomenon was cited as a possible molecular basis for phenotype changes as noted in grafts, called graft hybridization, and heterosis (Tsaftaris et al, 2008;Johannes et al, 2009;Wu et al, 2013).…”

ALTERATIONS OF DNA METHYLATION IN DIVERSE GRAFTED HYBRID TOMATOES (Solanum lycopersicum L.)

“…Therefore, in recent years, the technologies and theories concerning plant grafts have gained more and more importance. Grafting can not only give rise to phenotypic variations, but also create inheritable variations (Keiko et al, 2007;Li et al, 2013;Wu et al, 2013), and variation in cellular environments. .…”

“…The degree of methylation after the grafting of disease-sensitive cultivar "MM" (which is low light stress tolerant too) to diseaseresistant cultivar "1221" altered, the former as scion began to change and approached approximately middle of the expression of two check cultivars, which might result in gene expression changes in tomato cultivars and affect the alteration of phenotypic traits. A recent study reported that hetero-grafting altered DNA methylation patterns extensively in a locus-specific manner, especially in scions, although relative methylation levels remain largely unaltered (Wu et al, 2013). Further, the altered methylation patterns in the hetero-grafting-derived scions could be inherited to sexual progenies with some sites showing further alterations or revisions and caused dynamic changes in steady-state transcript abundance of genes encoding for a set of enzymes functionally relevant to DNA methylation.…”