ANALYSIS OF DNA REFERENCES FAMILY EXPERIMENTAL DESIGN MAIN CONCLUSION METHYLATION s(see below)

SALICACEAE 3 Populus triploids with their diploids and/or tetraploids parents * MSAP DNA methylation is nonlinearly related to the ploidy level Li et al. 2011 greenhouse

3 andromonoecious Populus DNA methylation sites have the potential to regulate the tomentosa clones * nursery * flower MSAP Song et al. 2012 genes’ transcript levels development

9 populations of 432 individuals of Genome methylation presented tissue-specific Populus tomentosa with distinct MSAP Ma et al. 2013 characteristics origins * outdoor

1 Populus alba clone * metal-polluted DNA methylation would adapt gene expression in site or not * inoculation with fungi G. MSAP Cicatelli et al. 2014 response to biotic and abiotic stress mosseae or G. intraradices or not

10 subpopulations Populus trichocarpa with distinct origins * MeDIP-SEQ DNA in recombination hotspots is less methylated Slavov et al. 2012 greenhouse

DNA methylation is tissue specific and gene-body DNA 1 Populus trichocarpa clone * outdoor MeDIP-SEQ methylation has a more repressive effect on transcription Vining et al. 2012 than promoter methylation 1 Populus trichocarpa clone * in vitro MeDIP-SEQ DNA methylation varies in a highly gene- and Vining et al. 2013 chromosome-differential manner during in vitro differentiation and regeneration. Hypermethylation of gene bodies may serve a protective role against activation of abundant transposable elements Methylated DNase 1 hypersensitive sites covered 1.9 % of the poplar geome but contains 74 % of genes models. 1 Populus trichocarpa clone * Lafon-Placette et al. MeDIP-SEQ Euchromatin gene body DNA methylation depends on greenhouse 2013 structural gene characteristics (gene size, redundancy and tissue-specific expression) 2 intraspecific Populus deltoides The methylation patterns of the parents both partially and parental lines and their reciprocal MeDIP-SEQ dynamically passed onto their hybrids and F1 hybrids has Gao et al. 2014 hybrids * greenhouse and outside a non-additive methylation level

First report for a DNA methylation modified-tree. The 1 Populus tremula x alba clone * Genomic decrease of DNA phenotypic consequences of reduced DDM1 activity and PtDDM1-RNAi transgenic lines * in methylation using RNAi Zhu et al. 2013 DNA methylation appears to increase with cumulative vitro and greenhouse strategy plant propagation and growth

If patterns of methylation are very similar in flowering 1 Populus trichocarpa clone * WGBS-SEQ plants, CHG methylation levels in transposons and repeats Feng et al. 2010 greenhouse were much higher in poplar

DNA methylation in response to stress regulates genes by 1 Populus trichocarpa clone * WGBS-SEQ methylating TEs in promoters and gene body of Liang et al. 2014 greenhouse * water stress and control transcription factors

1 Pinus pinaster clone * in vitro DNA methylation variations during aging of embryogenic Klimaszewska et al. somatic embryogenesis * 5- MSAP cultures and in response to 5-azacytidine treatment 2009 azacytidine treatment

25 individuals Pinus radiata * outdors DNA methylation variations during needle maturation in PINACEAE MSAP Valledor et al. 2010 and in vitro relation to the loss of in vitro organogenic capability

Variable epigenetic markers discriminate individuals and 5 Pinus pinea natural populations with MSAP differentiates two well represented populations contrary to Saez-Laguna et al. 2014 20 individuals * climatic chamber genetic variation 1 Acacia mangium willd clone * in Differences in DNA methylation exist between juvenile MSAP Baurens et al. 2004 vitro aging and mature plant materials

1 Quercus suber clone * outdoor and DNA methylation variations under a high temperature FAGACEAE MSAP Correia et al. 2013 greenhouse * 4 distinct temperatures stress

1 natural population of Quercus ilex * MSAP DNA methylation variations under drought Rico et al. 2014 outdoor * drought or control

1 Elaeis guineensis Jacq. clone * in DNA methylation polymorphism discriminates between ARECACEAE vitro normal and mantled somatic MSAP the two phenotypes (normal and mantled) only when they Jaligot et al. 2004 embryos were from the same genetic origin

COMBRETACE 2 populations Laguncularia racemosa Higher DNA methylation differentiation than genetic one MSAP Lira-Medeiros et al. 2010 AE * outdoors salt marsh and riverside between adapted populations to distinct environment

STERCULIACE 114 regenerants of one Theobroma Short periods of callus growth induce variations of DNA Rodriguez Lopez et al. MSAP AE cacao clone * in vitro methylation during regeneration process 2010

56 Jatropha curcas individuals from EUPHORBIA DNA methylation polymorphism is observed between Kanchanaketu et al. distinct origins * gamma-irradiation or MSAP CEAE indivuduals and in response to gamma-irradiation 2012 not

145 individuals of 2 hybrids Coffea Very low level of DNA methylation variation from Bobadilla Landey et al. RUBIACEAE MSAP arabica * in vitro somatic embryos to regenerated plants 2013 References

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