| [1] | Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168: 81–91.
|
| [2] | Richards EJ (2006) Inherited epigenetic variation – revisiting soft inheritance. Nature Rev Genet 7: 395–401.
|
| [3] | Bossdorf O, Richards CL, Pigliucci M (2008) Epigenetics for ecologists. Ecol Letters 11: 106–115.
|
| [4] | Richards CL, Bossdorf O, Pigliucci M (2010) What role does heritable epigenetic variation play in phenotypic evolution? Bioscience 60: 232–237.
|
| [5] | Kakutani T (2002) Epi-alleles in plants: inheritance of epigenetic information over generations. Plant Cell Physiol 43: 1106–1111.
|
| [6] | Jablonka E, Raz G (2009) Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Quart Rev Biol 84: 131–176.
|
| [7] | Finnegan EJ, Genger RK, Kovac K, Peacock WJ, Dennis ES (1998) DNA methylation and the promotion of flowering by vernalization. Proc Natl Acad Sci USA 95: 5824–5829.
|
| [8] | Cubas P, Vincent C, Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157–161.
|
| [9] | Manning K, Tor M, Poole M, Hong Y, Thompson AJ, et al. (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nature Genet 38: 948–952.
|
| [10] | Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, et al.. (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genetics 5: ,e1000530.
|
| [11] | Noyer JL, Causse S, Tomekpe K, Bouet A, Baurens FC (2005) A new image of plantain diversity assessed by SSR, AFLP and MSAP markers. Genetica 124: 61–69.
|
| [12] | Vaughn MW, Tanurdzic M, Lippman Z, Jiang H, Carrasquillo R, et al. (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology 5: 1617–1629.
|
| [13] | Fang J, Song C, Zheng Y, Qiao Y, Zhang Z, et al. (2008) Variation in cytosine methylation in Clementine mandarin cultivars. J Hort Sci Biotechnol 83: 833–839.
|
| [14] | Herrera CM, Bazaga P (2010) Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytol 187: 867–876.
|
| [15] | Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, et al. (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One 5: e10326.
|
| [16] | Paun O, Bateman RM, Fay MF, Hedren M, Civeyrel L, et al. (2010) Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae). Mol Biol Evol 27: 2465–2473.
|
| [17] | Richards CL, Schrey AW, Pigliucci M (2012) Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecol Letters 15: 1016–1025.
|
| [18] | Herrera CM, Bazaga P (2011) Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory. Mol Ecol 20: 1675–1688.
|
| [19] | Herrera CM, Bazaga P (2013) Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and nonprickly leaves in heterophyllous Ilex aquifolium (Aquifoliaceae) trees. Bot J Linn Soc 171: 441–452.
|
| [20] | Richards EJ (2008) Population epigenetics. Curr Opin Genetics Dev 18: 221–226.
|
| [21] | Richards EJ (2011) Natural epigenetic variation in plant species: a view from the field. Curr Opin Plant Biol 14: 204–209.
|
| [22] | Jablonka E, Lamb MJ (1995) Epigenetic inheritance and evolution. Oxford:Oxford University Press. 346 p.
|
| [23] | Jablonka E (2013) Epigenetic inheritance and plasticity: the responsive germline. Progr Biophysics Mol Biol 111: 99–107.
|
| [24] | Salmon A, Clotault J, Jenczewski E, Chable V, Manzanares-Dauleux MJ (2008) Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Sci 174: 61–70.
|
| [25] | Scoville AG, Barnett LL, Bodbyl-Roels S, Kelly JK, Hileman LC (2011) Differential regulation of a MYB transcription factor is correlated with transgenerational epigenetic inheritance of trichome density in Mimulus guttatus. New Phytol 191: 251–263.
|
| [26] | Verhoeven KJF, Jansen JJ, van Dijk PJ, Biere A (2010) Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytol 185: 1108–1118.
|
| [27] | Novero AU, Mabras MB, Esteban HJ (2012) Epigenetic inheritance of spine formation in sago palm (Metroxylon sagu Roettb). Plant Omics J 5: 559–566.
|
| [28] | Becker C, Weigel D (2012) Epigenetic variation: origin and transgenerational inheritance. Curr Opin Plant Biol 15: 562–567.
|
| [29] | Li YD, Shan XH, Liu XM, Hu LJ, Guo WL, et al. (2008) Utility of the methylation-sensitive amplified polymorphism (MSAP) marker for detection of DNA methylation polymorphism and epigenetic population structure in a wild barley species (Hordeum brevisubulatum). Ecol Res 23: 927–930.
|
| [30] | Gao LX, Geng YP, Li B, Chen JK, Yang J (2010) Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation. Plant Cell Environ 33: 1820–1827.
|
| [31] | Flatscher R, Frajman B, Sch？nswetter P, Paun O (2012) Environmental heterogeneity and phenotypic divergence: can heritable epigenetic variation aid speciation? Gen Res Int 2012: 9 doi:10.1155/2012/698421.
|
| [32] | Berger F, Twell D (2011) Germline specification and function in plants. Ann Rev Plant Biol 62: 461–484.
|
| [33] | Takeda S, Paszkowski J (2006) DNA methylation and epigenetic inheritance during plant gametogenesis. Chromosoma 115: 27–35.
|
| [34] | Migicovsky Z, Kovalchuk I (2012) Epigenetic modifications during angiosperm gametogenesis. Frontiers Plant Gen Genom 3: 20 doi:10.3389/fpls.2012.00020.
|
| [35] | Gutierrez-Marcos JF, Dickinson HG (2012) Epigenetic reprogramming in plant reproductive lineages. Plant Cell Physiol 53: 817–823.
|
| [36] | Mathew B (1989) Hellebores. St. John's Woking, Surrey: Alpine and Garden Society. 180 p.
|
| [37] | Werner K, Ebel F (1994) Zur Lebensgeschichte der Gattung Helleborus L. (Ranunculaceae). Flora 189: 97–130.
|
| [38] | Guitián J, Medrano M, Herrera CM, Sánchez-Lafuente AM (2003) Variation in the structural gender in the hermaphrodite Helleborus foetidus (Ranunculaceae): within- and among-population patterns. Plant Syst Evol 241: 139–151.
|
| [39] | Herrera CM, Bazaga P (2008) Population-genomic approach reveals adaptive floral divergence in discrete populations of a hawk moth-pollinated violet. Mol Ecol 17: 5378–5390.
|
| [40] | Caballero A, Quesada H, Rolán-Alvarez E (2008) Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 179: 539–554.
|
| [41] | Pérez-Figueroa A (2013) msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data. Mol Ecol Res 13: 522–527.
|
| [42] | R Development Core Team (2010) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Available: http://www.R-project.org. Accessed 2013 Jun 30.
|
| [43] | Xiong LZ, Xu CG, Maroof MAS, Zhang QF (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genetics 261: 439–446.
|
| [44] | Ashikawa I (2001) Surveying CpG methylation at 5′-CCGG in the genomes of rice cultivars. Plant Mol Biol 45: 31–39.
|
| [45] | Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.
|
| [46] | Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440–9445.
|
| [47] | Paradis E (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26: 419–420.
|
| [48] | Bonin A, Ehrich D, Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Mol Ecol 16: 3737–3758.
|
| [49] | Legendre P, Legendre L (1998) Numerical ecology. 2nd edition. Amsterdam:Elsevier. 853 p.
|
| [50] | Venables WN, Ripley BD (2002) Modern applied statistics with S. 4th edition. New York:Springer. 495 p.
|
| [51] | SAS Institute (2006) The GLIMMIX Procedure, June 2006. Cary, NCUSA:SAS Institute. Available: http://support.sas.com/rnd/app/papers/gl？immix.pdf. Accessed 2013 Jun 30.
|
| [52] | Castiglioni P, Ajmone-Marsan P, van Wijk R, Motto M (1999) AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution. Theor Appl Gen 99: 425–431.
|
| [53] | Chagné D, Lalanne C, Madur D, Kumar S, Frigério JM, et al. (2002) A high density genetic map of maritime pine based on AFLPs. Ann Forest Sci 59: 627–636.
|
| [54] | Hartigan JA, Hartigan PM (1985) The dip test of unimodality. Ann Stat 13: 70–84.
|
| [55] | Fraley C, Raftery AE, Murphy TB, Scrucca L (2012) mclust Version 4 for R: normal mixture modeling for model-based clustering, classification, and density estimation. Technical Report no. 597. Seattle, WAUSA: Department of Statistics, University of Washington. 57 p.
|
| [56] | Chinnusamy V, Zhu JK (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12: 133–139.
|
| [57] | Feil R, Fraga MF (2012) Epigenetics and the environment: emerging patterns and implications. Nature Rev Genet 13: 97–109.
|
| [58] | Molinier J, Ries G, Zipfel C, Hohn B (2006) Transgeneration memory of stress in plants. Nature 442: 1046–1049.
|
| [59] | Crawford RMM (2008) Plants at the margin. Ecological limits and climate change. Cambridge: Cambridge University Press. 478 p.
|
| [60] | Dickinson HG, Grant-Downton R (2009) Bridging the generation gap: flowering plant gametophytes and animal germlines reveal unexpected similarities. Biol Rev 84: 589–615.
|
| [61] | Klekowski EJ (1988) Mutation, developmental selection, and plant evolution. New York: Columbia University Press. 373 p.
|
| [62] | Herrera CM (2009) Multiplicity in unity. Plant subindividual variation and interactions with animals. Chicago: University of Chicago Press. 437 p.
|
| [63] | Echlin P (1972) Ultrastructure and ontogeny of pollen in Helleborus foetidus L. IV. Pollen grain maturation. J Cell Sci 11: 111–129.
|
| [64] | Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461–472.
|
| [65] | Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Rev Genet 11: 204–220.
|
| [66] | Janousek B, Matsunaga S, Kejnovsky E, Ziuvova J, Vyskot B (2002) DNA methylation analysis of a male reproductive organ specific gene (MROS1) during pollen development. Genome 45: 930–938.
|
| [67] | Oakeley EJ, Jost JP (1996) Non-symmetrical cytosine methylation in tobacco pollen DNA. Plant Mol Biol 31: 927–930.
|
| [68] | Feil R, Berger F (2007) Convergent evolution of genomic imprinting in plants and mammals. Trends Genetics 23: 192–199.
|
| [69] | Becker C, Hagmann J, Muller J, Koenig D, Stegle O, et al. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480: 245–249.
|
| [70] | Zhang YY, Fischer M, Colot V, Bossdorf O (2013) Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytol 197: 314–322.
|
| [71] | Saze H, Scheid OM, Paszkowski J (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nature Genet 34: 65–69.
|
