Ø Baurens FC, Nicolleau J, Legavre T, Verdeil JL, Monteuuis O (2004) Genomic DNA Methylation

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

 Baurens FC, Nicolleau J, Legavre T, Verdeil JL, Monteuuis O (2004) Genomic DNA methylation of juvenile and mature Acacia mangium micropropagated in vitro with reference to leaf morphology as a phase change marker. Tree Physiol 24:401-407  Bobadilla Landey R, Cenci A, Georget F, Bertrand B, Camayo G, Dechamp E, Herrera JC, Santoni S, Lashermes P, Simpson J, Etienne H (2013) High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate. PLoS ONE 8:e56372  Cicatelli A, Todeschini V, Lingua G, Biondi S, Torrigiani P, Castiglioneet S (2014) Epigenetic control of heavy metal stress response in mycorrhizal versus non-mycorrhizal poplar plants. Environ Sci Pollut R 21:1723-1737  Correia B, Valledor L, Meijón M, Rodriguez JR, Dias MC, Santos C, Canal MJ, Rodriguez R, Pinto G (2013) Is the interplay between epigenetic markers related to the acclimation of cork oak plants to high temperatures? PLoS ONE 8:e53543  Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107:8689-8694  Gao M, Huang Q, Chu Y, Ding C, Zhang B, Su X (2014) Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides. BMC Genetics 15:S8  Jaligot E, Beulé T, Baurens FC, Billotte N, Rival A (2004) Search for methylation-sensitive amplification polymorphisms associated with the “mantled” variant phenotype in oil palm (Elaeis guineensis Jacq.). Genome 47:224-228  Kanchanaketu T, Sangduen N, Toojinda T, Hongtrakul V (2012) Genetic diversity analysis of Jatropha curcas L.(Euphorbiaceae) based on methylation-sensitive amplification polymorphism. Genet Mol Res 11:944-955  Klimaszewska K, Noceda C, Pelletier G, Label P, Rodriguez R, Lelu-Walter MA (2009) Biological characterization of young and aged embryogenic cultures of Pinus pinaster (Ait.). In Vitro Cellular and Developmental Biology – Plant 45: 20-33  Klimaszewska K, Overton C, Stewart D, Rutledge RG (2011) Initiation of somatic embryos and regeneration of plants from primordial shoots of 10-year-old somatic white spruce and expression profiles of 11 genes followed during the tissue culture process. Planta 233: 635-647  Lafon-Placette C, Faivre-Rampant P, Delaunay A, Street N, Brignolas F, Maury S (2013) Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state. New Phytol 197:416-430  Li A, Hu B-Q, Xue Z-Y, Chen L, Wang W-X, Song W-Q, Chen C-B, Wang C-G (2011) DNA methylation in genomes of several annual herbaceous and woody perennial plants of varying ploidy as detected by MSAP. Plant Mol Biol Rep 29:784-793  Liang D, Zhang Z, Wu H, Huang C, Shuai P, Ye C-Y, Tang S, Wang Y, Yang L, Wang J, Yin W, Xia W (2014) Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress. BMC Genetics 15:S9  Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Gomes Ferreira PC (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS ONE 5:e10326  Ma K, Song Y, Yang X, Zhang Z, Zhang D (2013) Variation in genomic methylation in natural populations of chinese white poplar. PLoS ONE 8:e63977  Rico L, Ogaya R, Barbeta A, Peñuelas J (2014) Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change. Plant Biol 16:419-427  Rodríguez López CM, Wetten AC, Wilkinson MJ (2010) Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants. New Phytol 186:856-868  Sáez-Laguna E, Guevara M-Á, Díaz L-M, Sanchez-Gomez D, Collada C, Aranda I, Cervera M-T (2014) Epigenetic variability in the genetically uniform forest tree species Pinus pinea L. PLoS ONE 9:e103145  Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA, 2012. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 196:713-725  Song Y, Ma K, Bo W, Zhang Z, Zhan D (2012) Sex-specific DNA methylation and gene expression in andromonoecious poplar. Plant Cell Rep 31:1393-1405  Valledor L, Meijón M, Hasbún R, Cañala MJ, Rodríguez R (2010) Variations in DNA methylation, acetylated histone H4, and methylated histone H3 during Pinus radiata needle maturation in relation to the loss of in vitro organogenic capability. J Plant Physiol 167:351-357  Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH (2013) Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biol 13:92  Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH (2012) Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics 13:27  Zhu R, Shevchenko O, Ma C, Maury S, Freitag M, Strauss SH (2013) Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology. Planta 237:1483-1493