The epigenetic footprint of poleward range-expanding plants in apomictic dandelions

Molecular Ecology

Volumn 24, Issue 17, 2015, Pages 4406-4418

  Preite, V ^a,b   Snoek, L B ^a,b   Oplaat, C ^a   Biere, A ^a   Van Der Putten, W H ^a,b   Verhoeven, K J F ^a  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

apomictic dandelions; DNA methylation; epigenetic inheritance; MS AFLP; population epigenetics; range expansion

Indexed keywords

TARAXACUM OFFICINALE;

PLANT DNA;

ADAPTATION; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; DANDELION; DNA METHYLATION; DNA SEQUENCE; EUROPE; GENETIC EPIGENESIS; GENETIC VARIABILITY; GENETICS; POPULATION GENETICS;

ADAPTATION, PHYSIOLOGICAL; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; DNA METHYLATION; DNA, PLANT; EPIGENESIS, GENETIC; EUROPE; GENETIC VARIATION; GENETICS, POPULATION; SEQUENCE ANALYSIS, DNA; TARAXACUM;

EID: 84940780655     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13329     Document Type: Article

References (74)

1. Ahmad R, Liow PS, Spencer DF, Jasieniuk M, (2008) Molecular evidence for a single genetic clone of invasive Arundo donax in the United States. Aquatic Botany, 88, 113-120.
2. Angers B, Castonguay E, Massicotte R, (2010) Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Molecular Ecology, 19, 1283-1295.
3. Anway MD, Cupp AS, Uzumcu M, Skinner MK, (2005) Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science, 308, 1466-1469.
4. Asker S, Jerling L, (1992) Apomixis in Plants. CRC Press, Boca Raton, Florida.
5. Becker C, Hagmann J, Müller J, et al,. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature, 480, 245-249.
6. Bilichak A, Ilnystkyy Y, Hollunder J, Kovalchuk I, (2012) The progeny of Arabidopsis thaliana plants exposed to salt exhibit changes in DNA methylation, histone modifications and gene expression. PLoS ONE, 7, e30515.
7. Bonin A, Ehrich D, Manel S, (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology, 16, 3737-3758.
8. Bossdorf O, Zhang Y, (2011) A truly ecological epigenetics study. Molecular Ecology, 20, 1572-1574.
9. Bossdorf O, Richards CL, Pigliucci M, (2008) Epigenetics for ecologists. Ecology Letters, 11, 106-115.
10. Bossdorf O, Arcuri D, Richards CL, Pigliucci M, (2010) Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana. Evolutionary Ecology, 24, 541-553.
11. Cailliez F, (1983) The analytical solution of the additive constant problem. Psychometrika, 48, 305-310.
12. Castonguay E, Angers B, (2012) The key role of epigenetics in the persistence of asexual lineages. Genetics Research International, 2012, 1-9.
13. Cervera MT, Ruiz-Garcia L, Martinez-Zapater J, (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Molecular Genetics and Genomics, 268, 543-552.
14. Chao A, Shen T, (2003) Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environmental and Ecological Statistics, 10, 429-443.
15. Comes HP, Kadereit JW, (1998) The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science, 3, 432-438.
16. Cortijo S, Wardenaar R, Colomé-Tatché M, et al,. (2014) Mapping the epigenetic basis of complex traits. Science, 343, 1145-1148.
17. Cubas P, Vincent C, Coen E, (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature, 401, 157-161.
18. Davis MB, Shaw RG, (2001) Range shifts and adaptive responses to Quaternary climate change. Science, 292, 673-679.
19. Dowen RH, Pelizzola M, Schmitz RJ, et al,. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences USA, 109, E2183-E2191.
20. Fulneček J, Kovařík A, (2014) How to interpret Methylation Sensitive Amplified Polymorphism (MSAP) profiles? BMC Genetics, 15, 2.
21. Gao L, Geng Y, Li B, Chen J, 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 and Environment, 33, 1820-1827.
22. Henderson IR, Jacobsen SE, (2007) Epigenetic inheritance in plants. Nature, 447, 418-424.
23. Herrera CM, Bazaga P, (2010) Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytologist, 187, 867-876.
24. Herrera CM, Bazaga P, (2011) Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory. Molecular Ecology, 20, 1675-1688.
25. Herrera C, Pozo M, Bazaga P, (2011) Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast. Molecular Ecology, 21, 2602-2616.
26. Hirsch S, Baumberger R, Grossniklaus U, (2012) Epigenetic variation, inheritance, and selection in plant populations. Cold Spring Harbour Symposia on Quantitative Biology, 77, 97-104.
27. Hollingsworth ML, Bailey JP, (2000) Evidence for massive clonal growth in the invasive weed Fallopia japonica (Japanese Knotweed). Botanical Journal of the Linnean Society, 133, 463-472.
28. Jablonka E, Raz G, (2009) Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. The Quarterly Review of Biology, 84, 131-176.
29. Johannes F, Porcher E, Teixeira FK, et al,. (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genetics, 5, e1000530.
30. Kalisz S, Purugganan MD, (2004) Epialleles via DNA methylation: consequences for plant evolution. Trends in Ecology and Evolution, 19, 309-314.
31. Keyte AL, Percifield R, Liu B, Wendel JF, (2006) Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). Journal of Heredity, 97, 444-450.
32. Kirschner J, Štěpánek J, (2011) Typification of Leontodon taraxacum L. (= Taraxacum officinale FH Wigg.) and the generic name Taraxacum: a review and a new typification proposal. Taxon, 60, 216-220.
33. Latzel V, Klimešová J, (2010) Transgenerational plasticity in clonal plants. Evolutionary Ecology, 24, 1537-1543.
34. Li Y, Shan X, Liu X, 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). Ecological Research, 23, 927-930.
35. Lira-Medeiros CF, Parisod C, Fernandes RA, et al,. (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS ONE, 5, e10326.
36. Manly BFJ, (1991) Randomization and Monte Carlo Methods in Biology. Chapman and Hall, London.
37. Marfil CF, Asurmendi S, Masuelli RW, (2012) Changes in micro RNA expression in a wild tuber-bearing Solanum species induced by 5-Azacytidine treatment. Plant Cell Reports, 31, 1449-1461.
38. Massicotte R, Angers B, (2011) General-purpose genotype or how epigenetics extend the flexibility of a genotype. Genetics Research International, 2012, doi: 10.1155/2012/317175.
39. Massicotte R, Whitelaw E, Angers B, (2011) DNA methylation: a source of random variation in natural populations. Epigenetics, 6, 421-427.
40. Meirmans PG, Van Tienderen PH, (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794.
41. Meissner A, Gnirke A, Bell GW, et al,. (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Research, 33, 5868-5877.
42. Menken SBJ, Smit E, Nijs JCM, (1995) Genetical population structure in plants: gene flow between diploid sexual and triploid asexual dandelions (Taraxacum section Ruderalia). Evolution, 49, 1108-1118.
43. Mogie M, Ford H, (1988) Sexual and asexual Taraxacum species. Biological Journal of the Linnean Society, 35, 155-168.
44. Nicotra AB, Atkin OK, Bonser SP, et al,. (2010) Plant phenotypic plasticity in a changing climate. Trends in Plant Science, 15, 684-692.
45. Paszkowski J, Grossniklaus U, (2011) Selected aspects of transgenerational epigenetic inheritance and resetting in plants. Current Opinion in Plant Biology, 14, 195-203.
46. Paun O, Bateman RM, Fay MF, Hedrén M, Civeyrel L, Chase MW, (2010) Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae). Molecular Biology and Evolution, 27, 2465-2473.
47. Rapp RA, Wendel JF, (2005) Epigenetics and plant evolution. New Phytologist, 168, 81-91.
48. Reyna-Lopez G, Simpson J, Ruiz-Herrera J, (1997) Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Molecular and General Genetics, 253, 703-710.
49. Richards A, (1973) The origin of Taraxacum agamospecies. Botanical Journal of the Linnean Society, 66, 189-211.
50. Richards EJ, (2006) Inherited epigenetic variation-revisiting soft inheritance. Nature Reviews Genetics, 7, 395-401.
51. Richards EJ, (2008) Population epigenetics. Current Opinion in Genetics and Development, 18, 221-226.
52. Richards CL, Schrey AW, Pigliucci M, (2012) Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecology Letters, 15, 1016-1025.
53. Rogstad SH, (1992) Saturated NaCl-CTAB solution as a means of field preservation of leaves for DNA analyses. Taxon, 41, 701-708.
54. Sahu PP, Pandey G, Sharma N, et al,. (2013) Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Reports, 32, 1151-1159.
55. Salmon A, Clotault J, Jenczewski E, et al,. (2008) Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Science, 174, 61-70.
56. Schmitz RJ, Ecker JR, (2012) Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends in Plant Science, 17, 149-154.
57. Schmitz RJ, Schultz MD, Urich MA, et al,. (2013) Patterns of population epigenomic diversity. Nature, 495, 193-198.
58. Schrey AW, Coon CAC, Grispo MT, et al,. (2012) Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus) on two continents. Genetics Research International, 2012, Article ID 979751, 7.
59. Schrey AW, Alvarez M, Foust CM, et al,. (2013) Ecological epigenetics: beyond MS-AFLP. Integrative and Comparative Biology, 53, 340-350.
60. Schulz B, Eckstein RL, Durka W, (2013) Scoring and analysis of methylation-sensitive amplification polymorphisms for epigenetic population studies. Molecular Ecology Resources, 13, 642-653.
61. Schulz B, Eckstein RL, Durka W, (2014) Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb. Molecular Ecology, 23, 3523-3537.
62. Shea N, Pen I, Uller T, (2011) Three epigenetic information channels and their different roles in evolution. Journal of Evolutionary Biology, 24, 1178-1187.
63. Tas IC, Van Dijk PJ, (1999) Crosses between sexual and apomictic dandelions (Taraxacum). I. The inheritance of apomixis. Heredity, 83, 707-714.
64. Van der Hulst R, Mes T, Den Nijs J, Bachmann K, (2001) Amplified fragment length polymorphism (AFLP) markers reveal that population structure of triploid dandelions (Taraxacum officinale) exhibits both clonality and recombination. Molecular Ecology, 9, 1-8.
65. Verduijn MH, Van Dijk PJ, Van Damme JM, (2004) Distribution, phenology and demography of sympatric sexual and asexual dandelions (Taraxacum officinale sl): geographic parthenogenesis on a small scale. Biological Journal of the Linnean Society, 82, 205-218.
66. Verhoeven KJF, Biere A, (2013) Geographic parthenogenesis and plant-enemy interactions in the common dandelion. BMC Evolutionary Biology, 13, 23.
67. Verhoeven KJF, Preite V, (2014) Epigenetic variation in asexually reproducing organisms. Evolution, 68, 644-655.
68. Verhoeven KJF, Van Dijk PJ, Biere A, (2010a) Changes in genomic methylation patterns during the formation of triploid asexual dandelion lineages. Molecular Ecology, 19, 315-324.
69. Verhoeven KJF, Jansen JJ, van Dijk PJ, Biere A, (2010b) Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytologist, 185, 1108-1118.
70. Vijverberg K, Van der Hulst R, Lindhout P, Van Dijk P, (2004) A genetic linkage map of the diplosporous chromosomal region in Taraxacum officinale (common dandelion; Asteraceae). Theoretical and Applied Genetics, 108, 725-732.
71. Vos P, Hogers R, Bleeker M, et al,. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407-4414.
72. Xiong L, Xu C, Maroof MS, Zhang Q, (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Molecular and General Genetics, 261, 439-446.
73. Zhang M, Kimatu JN, Xu K, Liu B, (2010) DNA cytosine methylation in plant development. Journal of Genetics and Genomics, 37, 1-12.
74. Zhang YY, Fischer M, Colot V, Bossdorf O, (2013) Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytologist, 197, 314-322.