Shaped by the environment - Adaptation in plants: Meeting report based on the presentations at the FEBS Workshop 'Adaptation Potential in Plants' 2009 (Vienna, Austria)

FEBS Journal

Volumn 276, Issue 17, 2009, Pages 4705-4714

  Siomos, Maria F ^a  

^a GREGOR MENDEL INSTITUTE OF MOLECULAR PLANT BIOLOGY   (Austria)

Author keywords

Adaptation; Arabidopsis; Climate change; Darwin; Ecology; Environment; Evolution; Genomic variability; Speciation; Stress

Indexed keywords

ECOLOGY; ENVIRONMENTAL STRESS; EPIGENETICS; EVOLUTIONARY ADAPTATION; GENETIC VARIABILITY; GENOMICS; NONHUMAN; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; WILD TYPE;

ADAPTATION, PHYSIOLOGICAL; BIOLOGICAL EVOLUTION; ECOSYSTEM; ENVIRONMENT; GENOME, PLANT; PLANT PHYSIOLOGICAL PHENOMENA; SIGNAL TRANSDUCTION;

ARABIDOPSIS;

EID: 68849097903     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2009.07170.x     Document Type: Review

References (68)

1. Darwin C (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, 1st edn. John Murray, London.
2. Dobzhansky T (1973) Nothing in biology makes sense, except in the light of evolution. Am Biol Teacher 35, 125 129.
3. Mendel G (1866) Versuche über Pflanzenhybriden. Verhandlungen des naturforschenden Vereines in Brünn, Abhandlungen 1865 (4 3 47.
4. Watson JD Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171, 737 738.
5. Rando OJ Verstrepen KJ (2007) Timescales of genetic and epigenetic inheritance. Cell 128, 655 668.
6. LeClerc JE, Li B, Payne WL Cebula TA (1996) High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274, 1208 1211.
7. Matic I, Radman M, Taddei F, Picard B, Doit C, Bingen E, Denamur E Elion J (1997) Highly variable mutation rates in commensal and pathogenic Escherichia coli. Science 277, 1833 1834.
8. Bjedov I, Tenaillon O, Gerard B, Souza V, Denamur E, Radman M, Taddei F Matic I (2003) Stress-induced mutagenesis in bacteria. Science 300, 1404 1409.
9. Denamur E, Bonacorsi S, Giraud A, Duriez P, Hilali F, Amorin C, Bingen E, Andremont A, Picard B, Taddei F et al. (2002) High frequency of mutator strains among human uropathogenic Escherichia coli isolates. J Bacteriol 184, 605 609.
10. Parker JE, Coleman MJ, Szabo V, Frost LN, Schmidt R, van der Biezen EA, Moores T, Dean C, Daniels MJ Jones JD (1997) The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the toll and interleukin-1 receptors with N and L6. Plant Cell 9, 879 894.
11. Noel L, Moores TL, van Der Biezen EA, Parniske M, Daniels MJ, Parker JE Jones JD (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11, 2099 2112.
12. Richards EJ (2006) Inherited epigenetic variation - revisiting soft inheritance. Nat Rev Genet 7, 395 401.
13. Brzeski J Jerzmanowski A (2003) Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J Biol Chem 278, 823 828.
14. Knizewski L, Ginalski K Jerzmanowski A (2008) Snf2 proteins in plants: gene silencing and beyond. Trends Plant Sci 13, 557 565.
15. Mathieu O, Reinders J, Caikovski M, Smathajitt C Paszkowski J (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130, 851 862.
16. Reinders J, Wulff BB, Mirouze M, Mari-Ordonez A, Dapp M, Rozhon W, Bucher E, Theiler G Paszkowski J (2009) Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 23, 939 950.
17. Mosher RA, Schwach F, Studholme D Baulcombe DC (2008) PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA 105, 3145 3150.
18. Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ Baulcombe DC (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460, 283 286.
19. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24, 133 141.
20. Mackay TFC (2009) Q&A: genetic analysis of quantitative traits. J Biol 8, 23, doi :.
21. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203 218. (Pubitemid 351972300)
22. Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317, 338 342.
23. Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D Nordborg M (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39, 1151 1155.
24. Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N Weigel D (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18, 2024 2033.
25. Clauss MJ Koch MA (2006) Poorly known relatives of Arabidopsis thaliana. Trends Plant Sci 11, 449 459.
26. Consortium TIH (2005) A haplotype map of the human genome. Nature 437, 1299 1320.
27. Nordborg M Weigel D (2008) Next-generation genetics in plants. Nature 456, 720 723.
28. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C et al. (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1, e60, doi :.
29. Michaels SD Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11, 949 956.
30. Sheldon CC, Burn JE, Perez PP, Metzger J, Edwards JA, Peacock WJ Dennis ES (1999) The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11, 445 458.
31. Johanson U, West J, Lister C, Michaels S, Amasino R Dean C (2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290, 344 347.
32. Shindo C, Lister C, Crevillen P, Nordborg M Dean C (2006) Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response. Genes Dev 20, 3079 3083.
33. Schranz ME, Manzaneda AJ, Windsor AJ, Clauss MJ Mitchell-Olds T (2009) Ecological genomics of Boechera stricta: identification of a QTL controlling the allocation of methionine- vs branched-chain amino acid-derived glucosinolates and levels of insect herbivory. Heredity 102, 465 474.
34. Cubas P, Vincent C Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157 161.
35. Linnaeus C (1753) Species Plantarum. Laurentii Salvii, Stockholm.
36. Linnaeus C (1758) Systema Naturae, 10th edn. Laurentii Salvii, Stockholm.
37. Mayr E (1942) Systematics and the Origin of Species. Columbia University Press, New York, NY.
38. de Queiroz K (2005) Ernst Mayr and the modern concept of species. Proc Natl Acad Sci USA 102 Suppl 1, 6600 6607.
39. Bomblies K Weigel D (2007) Arabidopsis: a model genus for speciation. Curr Opin Genet Dev 17, 500 504.
40. Josefsson C, Dilkes B Comai L (2006) Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol 16, 1322 1328.
41. Dilkes BP, Spielman M, Weizbauer R, Watson B, Burkart-Waco D, Scott RJ Comai L (2008) The maternally expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis. PLoS Biol 6, 2707 2720.
42. Bomblies K, Lempe J, Epple P, Warthmann N, Lanz C, Dangl JL Weigel D (2007) Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol 5, e236, doi :.
43. Paun O, Forest F, Fay MF Chase MW (2009) Hybrid speciation in angiosperms: parental divergence drives ploidy. New Phytol 182, 507 518.
44. Lolle SJ, Victor JL, Young JM Pruitt RE (2005) Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis. Nature 434, 505 509.
45. Krolikowski KA, Victor JL, Wagler TN, Lolle SJ Pruitt RE (2003) Isolation and characterization of the Arabidopsis organ fusion gene HOTHEAD. Plant J 35, 501 511.
46. Lolle SJ, Hsu W Pruitt RE (1998) Genetic analysis of organ fusion in Arabidopsis thaliana. Genetics 149, 607 619.
47. Mercier R, Jolivet S, Vignard J, Durand S, Drouaud J, Pelletier G Nogue F (2008) Outcrossing as an explanation of the apparent unconventional genetic behavior of Arabidopsis thaliana hth mutants. Genetics 180, 2295 2297.
48. Peng P, Chan SW, Shah GA Jacobsen SE (2006) Plant genetics: increased outcrossing in hothead mutants. Nature 443, E8 discussion E8-9.
49. Easterling WE, Aggarwal PK, Batima P, Brander KM, Erda L, Howden SM, Kirilenko A, Morton J, Soussana J-F, Schmidhuber J et al. (2007) Food, Fibre and Forest Products. Climate Change 2007: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge, UK.
50. Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG Thomashow MF (2005) Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41, 195 211.
51. Fowler SG, Cook D Thomashow MF (2005) Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol 137, 961 968.
52. Doherty CJ, Van Buskirk HA, Myers SJ Thomashow MF (2009) Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. Plant Cell 21, 972 984.
53. Zarka DG, Vogel JT, Cook D Thomashow MF (2003) Cold induction of Arabidopsis CBF genes involves multiple ICE (inducer of CBF expression) promoter elements and a cold-regulatory circuit that is desensitized by low temperature. Plant Physiol 133, 910 918.
54. Vierling E (1991) The roles of heat-shock proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 42, 579 620.
55. Larkindale J Vierling E (2008) Core genome responses involved in acclimation to high temperature. Plant Physiol 146, 748 761.
56. Hong SW Vierling E (2000) Mutants of Arabidopsis thaliana defective in the acquisition of tolerance to high temperature stress. Proc Natl Acad Sci USA 97, 4392 4397.
57. Morcuende R, Bari R, Gibon Y, Zheng W, Pant BD, Blasing O, Usadel B, Czechowski T, Udvardi MK, Stitt M et al. (2007) Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant Cell Environ 30, 85 112.
58. Gyula P, Schafer E Nagy F (2003) Light perception and signalling in higher plants. Curr Opin Plant Biol 6, 446 452. (Pubitemid 37195746)
59. Kevei E, Schafer E Nagy F (2007) Light-regulated nucleo-cytoplasmic partitioning of phytochromes. J Exp Bot 58, 3113 3124.
60. Pfeiffer A, Kunkel T, Hiltbrunner A, Neuhaus G, Wolf I, Speth V, Adam E, Nagy F Schafer E (2009) A cell-free system for light-dependent nuclear import of phytochrome. Plant J 57, 680 689.
61. Carabelli M, Possenti M, Sessa G, Ciolfi A, Sassi M, Morelli G Ruberti I (2007) Canopy shade causes a rapid and transient arrest in leaf development through auxin-induced cytokinin oxidase activity. Genes Dev 21, 1863 1868.
62. Steindler C, Matteucci A, Sessa G, Weimar T, Ohgishi M, Aoyama T, Morelli G Ruberti I (1999) Shade avoidance responses are mediated by the ATHB-2 HD-zip protein, a negative regulator of gene expression. Development 126, 4235 4245.
63. Sessa G, Carabelli M, Sassi M, Ciolfi A, Possenti M, Mittempergher F, Becker J, Morelli G Ruberti I (2005) A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. Genes Dev 19, 2811 2815.
64. Petrasek J, Mravec J, Bouchard R, Blakeslee JJ, Abas M, Seifertova D, Wisniewska J, Tadele Z, Kubes M, Covanova M et al. (2006) PIN proteins perform a rate-limiting function in cellular auxin efflux. Science 312, 914 918.
65. Zazimalova E, Krecek P, Skupa P, Hoyerova K Petrasek J (2007) Polar transport of the plant hormone auxin - the role of PIN-FORMED (PIN) proteins. Cell Mol Life Sci 64, 1621 1637.
66. Bogre L, Magyar Z Lopez-Juez E (2008) New clues to organ size control in plants. Genome Biol 9, 226, doi :.
67. Menges M, Doczi R, Okresz L, Morandini P, Mizzi L, Soloviev M, Murray JA Bogre L (2008) Comprehensive gene expression atlas for the Arabidopsis MAP kinase signalling pathways. New Phytol 179, 643 662.
68. Molinier J, Lechner E, Dumbliauskas E Genschik P (2008) Regulation and role of Arabidopsis CUL4-DDB1A-DDB2 in maintaining genome integrity upon UV stress. PLoS Genet 4, e1000093