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. 2020 Oct 22;11:5343. doi: 10.1038/s41467-020-19140-x

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a The phenotype of graft progeny (first generation) from Col-0/Col-0, as graft control, Col-0/msh1, with msh1 rootstock, and Col-0/dcl2,3,4,msh1, with a dcl2,3,4, msh1 quadruple mutant as rootstock. Seedling stage photo was taken at 21 days after planting (DAP). b Total leaf area (25 DAP), c days to bolting, and d seed weight (mg) for the first-generation graft progeny of Col-0/Col-0, Col-0/msh1 and Col-0/dcl2,3,4. b–d Bars represent means ± SE, n represents number of plants in each population. The Mann–Whitney U-test with two-sided alternative hypothesis were used to test the significance of the difference of mean in each comparison. e Total hyper- and hypomethylation DMP counts of first-generation graft progeny in Col-0/dcl2,3,4,msh1 vs. Col-0/msh1 comparison and in rootstocks of dcl2,3,4,msh1 vs. msh1 comparison. Each bar graph represents a single plant. CG, CHG, CHH context data are shown separately for each plant. DMPs were defined as hyper if the site methylation difference in comparisons of each individual to the average of reference plants is greater than 0 and defined as hypo if <0. f The relative frequency of DMPs over genic regions (blue shades), TE-related regions (red shades), and others (green shades) in first-generation graft progeny in the Col-0/dcl2,3,4,msh1 vs. Col-0/msh1 comparison and rootstocks in the dcl2,3,4,msh1 vs. msh1 comparison. The centroid of Col-0/dcl2,3,4,msh1 graft progeny was used as a reference for Col-0/msh1 analysis and dcl2,3,4,msh1 was used as reference for msh1 mutant analysis. Networks identified by Network Enrichment Analysis Test (NEAT) for the DMGs identified are shown for g Col-0/dcl2,3,4,msh1 vs. Col-0/msh1 and h dcl2,3,4 msh1 vs. msh1 comparisons. g, h p-values were computed using one-sided hypergeometric distribution test as implemented in NEAT (R package version 1.1.3). Significance codes: NS, no significance, *p < 0.05, **p < 0.01, ***p < 0.001. Source data underlying b–h are provided as a Source Data file.