Epigenetic bases of grafting-induced vigour in eggplant

Abstract

27In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This 28 is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Despite its 29 wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain 30 largely unknown. Given that epigenetics plays a crucial role during distance signalling in plants, we studied 31 the genome-wide changes induced by DNA methylation in eggplant (Solanum melongena) plants grafted onto 32 two interspecific rootstocks used to increase scion vigour. As a control, we compared any epigenetic effect 33 found in such grafts to patterns detected in self-grafted plants. We found that vigour was associated with a 34 specific change in scion gene expression and a genome-wide hypomethylation in CHH context. Interestingly, 35 this hypomethylation correlated with the down-regulation of younger and potentially more active LTR 36 retrotransposons (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated to both 37 physiological and molecular phenotypes in grafted plants. We propose that rootstocks can promote vigour by 38 reducing DNA methylation in the scion genome, following similar principles found in some heterotic hybrids. 39 40

Grafting with Different Rootstocks Induced DNA Methylation Alterations in Pecan [Carya illinoinensis (Wangenh.) K. Koch]

“…According to the obtained results in the present study, although the methylation levels in CG were highest throughout genome, the methylation changes in CHG and CHH were more frequent. The similar results were also reported previously [15,30,42]. Apart from the significant decrease in CHH methylation found in grafted eggplants [15], CHH methylation was reported to change significantly and the CHH-DMRs account for most of the DMRs during the developmental processes of soybean seeds [30].…”

“…The similar results were also reported previously [15,30,42]. Apart from the significant decrease in CHH methylation found in grafted eggplants [15], CHH methylation was reported to change significantly and the CHH-DMRs account for most of the DMRs during the developmental processes of soybean seeds [30]. Domb et al also found that specific elimination of CG methylation did not dysregulate genes or transposons, and, in contrast, exclusive removal of non-CG methylation massively up-regulated genes and transposons [42].…”

“…trees obtained methylation levels ranging from 16.42% to 19.80% in the scions on different rootstocks [14]. Hetero-grafting experiments on eggplant also revealed that CHH methylation levels significantly decreased by 3.37% and 2.58% in eggplant scions grafted on S. torvum and 'Emperador RZ' rootstocks, respectively, compared to those of the self-grafted plants [15]. The detailed data provided in these studies reflected the overall methylation changes induced by rootstocks.…”

“…Several studies using methylation-sensitive amplified polymorphism (MSAP) technique suggested that rootstocks can induce different extent of DNA methylation changes in amplified sites of scions [12][13][14], and the sites with different methylation patterns were sequenced to analyze their potential functions [12,14]. By grafting eggplant (Solanum melongena L.) on Solanum torvum Swartz rootstock or tomato F1 commercial hybrid Emperador RZ rootstock, Cerruti et al investigated the epigenetic bases of the grafting-induced vigor and found that CHH (C= cytosine; H = adenine, thymine, or cytosine) methylation levels decreased significantly in eggplant scions on the two rootstocks compared to that of self-grafted plants, which was associated with enhanced vigor in hetero-grafted eggplant scions [15]. Although these studies provided some clues on the involvement of DNA methylation in grafting process [12][13][14][15], the mechanisms on mediation of DNA methylation in rootstock-induced vigor changes in scions remain largely unknown, and systematic studies are urgently needed regarding this issue.…”

Long distance signalling and epigenetic changes in crop grafting

“…The translocation of siRNAs across the grafting junction has also been explored in several crops, including eggplant, pumpkin (Cucurbita pepo), cucumber, potato, Nicotiana benthamiana, grapevine (Vitis vinifera) and several bean (Fabaceae) species (Tournier et al, 2006;Bai et al, 2011;Zhang et al, 2014;Cerruti et al, 2021;Davoudi et al, 2022;Rubio et al, 2022;Zhang et al, 2022). In addition, several miRNAs in potato have been demonstrated to be graft-transmissible, including miR156, miR339, miR395 and miR172 (Pant et al, 2008;Buhtz et al, 2010;Kasai et al, 2010).…”