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Genetic Mechanisms Enhancing Plant Biodiversity

  • Evangelia SinapidouEmail author
  • Ioannis S. Tokatlidis
Chapter
Part of the Sustainable Agriculture Reviews book series (SARV, volume 7)

Abstract

Biodiversity is essential for an evolving ecosystem and as a resource for further development of natural products by breeding. At present agriculture is under pressure by the demand for increased crop production and the public anticipation for sustainable cultivation practices. Undeniably, the prerequisite for adaptation of an organism to changing environmental conditions is genetic variability. The answer to the concern that the persistent accumulation of desirable alleles in a few cultivars could erode genetic variability and ultimately impede further improvement, comes from the fields of genetic and epigenetic studies that have revealed a range of mechanisms which result in remarkable variability even in narrow gene pools.

We review small and large scale mutations and transposable element activity that create genetic variability, as well as epigenetic mechanisms that could give rise to variation not necessarily depending on DNA sequence alterations. Major points include the naturally occurring mutation rate that might explain the difficulty in controlling weeds with single-target herbicides, in addition to the advances in plant breeding through intentional mutation. Moreover, allele expression biases are presented in polyploid species, as well as the implication of transposable element activity in intra-species variation.

Another major point refers to the reduced expression levels of a locus that correlates with DNA methylation, a process that has further been associated with phenomena such as paramutation, parental imprinting, and heterosis. Intriguingly, transposable element activity in cases like during environmental stress, has been implied to be controlled by DNA methylation and demethylation systems causing genome restructure, together with the fact that methylated nucleotides are themselves hot-spots for mutations.

Other major points involve histones, proteins responsible for DNA packaging and organization, that are involved in gene activation and silencing, for example during stress conditions or at different developmental stages. Lastly, some RNA molecules are implicated both in endogenous gene regulation and the control of invading genetic entities, which is particularly important when using biotechnological methods for the development of novel crops through the introduction of transgenes. Overall, epigenetic changes seem to happen more frequently and be reversible, whereas spontaneous DNA mutations are often random and more stable.

In conclusion, plant biodiversity can serve as a resource for sustainable agriculture. It is important for plant breeders to take advantage of the range of modern tools and knowledge of plant genomes, so that breeding is less a ‘hit and miss’ process, but a more precise strategy, where successful selection for crop improvement is increasingly supported by understanding the genetic variation underlying the phenotype.

Keywords

DNA methylation Epigenetic mechanisms Genetic variation Histone modifications Mutation Plant breeding RNA molecules Sustainable agriculture Transposable elements 

References

  1. Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100:4649–4654. doi:10.1073/pnas.0630618100PubMedGoogle Scholar
  2. Adams KL, Percifield R, Wendel JF (2004) Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168:2217–2226. doi:10.1534/genetics.104.033522PubMedGoogle Scholar
  3. Agius F, Kapoor A, Zhu JK (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 103:11796–11801. doi:10.1073/pnas.0603563103PubMedGoogle Scholar
  4. Ahloowalia BS, Maluszynski M, Nichterlein K (2004) Global impact of mutation-derived varieties. Euphytica 135:187–204. doi:10.1023/B:EUPH.0000014914.85465.4fGoogle Scholar
  5. Akimoto K, Katakami H, Kim HJ, Ogawa E, Sano CM, Wada Y, Sano H (2007) Epigenetic inheritance in rice plants. Ann Bot 100:205–217. doi:10.1093/aob/mcm110PubMedGoogle Scholar
  6. Alvarez-Venegas R, Pien S, Sadder M, Witmer X, Grossniklaus U, Arramova Z (2003) ATX-1 an Arabidopsis homologue of trithorax activates flower homeotic genes. Curr Biol 13:627–637. doi:10.1016/S0960-9822(03)00243-4PubMedGoogle Scholar
  7. Aufsatz W, Mette MF, Van Der Winden J, Matzke M, Matzke AJ (2002) HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 21:6832–6841. doi:10.1093/emboj/cdf663PubMedGoogle Scholar
  8. Baroux C, Spillane C, Grossniklaus U (2002) Evolutionary origins of the endosperm in flowering plants. Genome Biol 3:1026.1–1026.5. doi:10.1186/gb-2002-3-9-reviews1026Google Scholar
  9. Bartel DP (2004) MicroRNAs. Cell 116:281–297. doi:10.1016/S0092-8674(04)00045-5PubMedGoogle Scholar
  10. Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58. doi:10.1080/07352680590910410Google Scholar
  11. Bastow R, Mylne J, Lister C, Lippman Z, Martiennsen R, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167. doi:10.1038/nature02269PubMedGoogle Scholar
  12. Baumbusch LO, Thorstensen T, Kraus V, Fischer A, Numann K, Assalkhou R, Schulz I, Reuter G, Aalen RB (2001) The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionary conserved classes. Nucleic Acids Res 29:4319–4333. doi:10.1093/nar/29.21.4319PubMedGoogle Scholar
  13. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621–627. doi:10.1016/j.gde.2005.09.010PubMedGoogle Scholar
  14. Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132. doi:10.1093/aob/mci008PubMedGoogle Scholar
  15. Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363–366. doi:10.1038/35053110PubMedGoogle Scholar
  16. Bhasin M, Reinherz EL, Reche PA (2006) Recognition and classification of histones using support vector machine. J Comput Biol 13:102–112. doi:10.1089/cmb.2006.13.102 DOI:dx.doi.orgPubMedGoogle Scholar
  17. Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679–1691. doi:10.1105/tpc.021410PubMedGoogle Scholar
  18. Budar F, Thia-Toong L, Van Montagu M, Hernalsteens J-P (1986) Agrobacterium-mediated gene transfer results mainly in transgenic plants transmitting T-DNA as a single Mendelian factor. Genetics 114:303–313, PMID: 17246346, PMCID: PMC1202937Google Scholar
  19. Capy P, Gasperi G, Biemont C, Bazin C (2000) Stress and transposable elements: co-evolution or useful parasites? Heredity 85:101–106. doi:10.1046/j.1365-2540.2000.00751.xPubMedGoogle Scholar
  20. Castiglione MR, Cremonini R, Frediani M (2002) DNA methylation patterns on plant chromosomes. Caryologica 55:275–282. doi:10.1007/s00709-010-0116-xGoogle Scholar
  21. Chandler V, Stam M (2004) Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 5:532–544. doi:10.1038/nrg1378PubMedGoogle Scholar
  22. Chen X, Liu X, Wu D, Shu QY (2006) Recent progress of rice mutation breeding and germplasm enhancement in China. Plant Mutat Rep 1:4–6Google Scholar
  23. Chinnusamy V, Zhu J-K (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12:1–7. doi:10.1016/j.pbi.2008.12.006Google Scholar
  24. Choi CS, Sano H (2007) Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics 277:589–600. doi:10.1007/s00438-007-0209-1PubMedGoogle Scholar
  25. Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110:33–42. doi:10.1016/S0092-8674(02)00807-3PubMedGoogle Scholar
  26. Cosgrove MS, Boeke JD, Wolberger C (2004) Regulated nucleosome mobility and the histone code. Nat Struct Mol Biol 11:1037–1043. doi:10.1038/nsmb851 DOI:dx.doi.orgPubMedGoogle Scholar
  27. Cubas P, Vincent C, Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401:157–161. doi:10.1038/43657PubMedGoogle Scholar
  28. Cullis CA (2005) Mechanisms and control of rapid genomic change in flax. Ann Bot 95:201–206. doi:10.1093/aob/mci013PubMedGoogle Scholar
  29. Davuluri GR, Tuinen A, Mustilli AC, Manfredonia A, Newman R, Burgess D, Brummell DA, King SR, Palys J, Uhlig J, Pennings HMJ, Bowler C (2004) Manipulation of DET1 expression in tomato results in photomorphogenic phenotypes caused by post-transcriptional gene silencing. Plant J 40:344–354. doi:10.1111/j.1365-313X.2004.02218.xPubMedGoogle Scholar
  30. Davuluri GR, vanTuinen A, Fraser PD, Manfredonia A, Newman R, Burgess D, Brummell DA, King SR, Palys J, Uhlig J, Bramley PM, Pennings HM, Bowler C (2005) Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat Biotechnol 23:890–895. doi:10.1038/nbt1108PubMedGoogle Scholar
  31. De Chiara TM, Robertson EJ, Efstratiadis A (1991) Parental imprinting of the mouse insulin-like growth factor II gene. Cell 64:849–859. doi:10.1016/0092-8674(91)90513-XGoogle Scholar
  32. Dou Y, Milne TA, Tackett AJ, Smith ER, Fukuda A, Wysocka J, Ailis DC, Chait BT, Hess JL, Roeder R (2005) Physical association and coordinate function of H3K4 methylotransferase MLL1 and the H4K16 acetylotransferase MOF. Cell 121:873–885. doi:10.1016/j.cell.2005.04.031PubMedGoogle Scholar
  33. Dudley JW, Lambert RJ (2004) 100 generations of selection for oil and protein in corn. Plant Breed Rev 24:79–110Google Scholar
  34. Eady CC, Kamoi T, Kato M, Porter NG, Davis S, Shaw M, Kamoi A, Imai S (2008) Silencing onion lachrymatory factor synthase causes a significant change in the sulfur secondary metabolite profile. Plant Physiol 147:2096–2106. doi:10.1104/pp. 108.123273PubMedGoogle Scholar
  35. Elbasir SM, Lendeckel W, Tuschl T (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15:188–200. doi:10.1101/gad.862301Google Scholar
  36. Elliot FC (1958) Plant breeding and cytogenetics. McGraw Hill Book Company, Inc., New YorkGoogle Scholar
  37. Fasoula DA (1990) Correlations between auto-, allo- and nill-competition and their implications in plant breeding. Euphytica 50:57–62. doi:10.1007/BF00023161Google Scholar
  38. Fasoula VA, Boerma HR (2005) Divergent selection at ultra-low plant density for seed protein and oil content within soybean cultivars. Field Crops Res 91:217–229. doi:10.1016/j.fcr.2004.07.018 DOI:dx.doi.orgGoogle Scholar
  39. Fasoula VA, Boerma HR (2007) Intra-cultivar variation for seed weight and other agronomic traits within three elite soybean cultivars. Crop Sci 47:367–373. doi:10.2135/cropsci2005.09.0334Google Scholar
  40. Fasoula VA, Fasoula DA (2002) Principles underlying genetic improvement for high and stable crop yield potential. Field Crop Res 75:191–209. doi:10.1016/S0378-4290(02)00026-6 DOI:dx.doi.orgGoogle Scholar
  41. Fasoulas AC (2000) Building up resistance to Verticillium wilt in cotton through honeycomb breeding. In: Gillham FM (ed) New frontiers in cotton research. Proceedings of the 2nd world cotton research conference, 6–12 Sept 1998, Athens, pp 120–124Google Scholar
  42. Felsenfeld G, Groudine M (2003) Controlling the double helix. Nature 421:448–453. doi:10.1038/nature01411DOI:dx.doi.orgPubMedGoogle Scholar
  43. Fermin G, Tennant P, Gonsalves C, Lee D, Gonsalves D (2004) Comparative development and impact of transgenic papayas in Hawaii, Jamaica, and Venezuela. Methods Mol Biol 286:399–430. doi:10.1385/1-59259-827-7:399Google Scholar
  44. Fire A, Xu SQ, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811. doi:10.1038/35888PubMedGoogle Scholar
  45. Floyd SK, Bowman JL (2005) MicroRNAs: micro-managing the plant genome. In: Meyer P (ed) Plant epigenetics. Blackwell Scientific Publications, Oxford, pp 244–279Google Scholar
  46. Fransz PF, Alonso-Blanco C, Liharska TB, Peeters AJM, Zabel P, Hans de Jong J et al (1996) High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 9:421–430. doi:10.1046/j.1365-313X.1996.09030421PubMedGoogle Scholar
  47. Freese E (1959) The difference between spontaneous and base-analogue induced mutations of phage T4. Proc Natl Acad Sci USA 45:622–633. doi:10.1073/pnas.45.4.622PubMedGoogle Scholar
  48. Fu W, Wu K, Duan J (2007) Sequence and expression analysis of histone deacetylases in rice. Biochem Biophys Res Commun 356:843–850. doi:10.1016/j.bbrc.2007.03.010PubMedGoogle Scholar
  49. Galaud JP, Gaspar T, Boyer N (1993) Inhibition of internode growth due to mechanical stress in Bryonia dioica: relationship between changes in DNA methylation and ethylene metabolism. Physiol Plant 87:25–30. doi:10.1007/BF02912989Google Scholar
  50. Gavilano LB, Coleman NP, Burnley L-E, Bowman ML, Kalengamaliro NE, Hayes A, Bush L, Siminszky B (2006) Genetic Engineering of Nicotiana tabacum for Reduced Nornicotine Content. J Agric Food Chem 54:9071–9078. doi:10.1021/jf0610458PubMedGoogle Scholar
  51. Gethi JG, Labate JA, Lamkey KR, Smith ME, Kresovich S (2002) SSR variation in important U.S. maize inbred lines. Crop Sci 42:951–957Google Scholar
  52. Grant-Downton RT, Dickinson HG (2005) Epigenetics and its implications for plant biology. 1. The epigenetic network in plants. Ann Bot 96:1143–1164. doi:10.1093/aob/mci273Google Scholar
  53. Grant-Downton RT, Dickinson HG (2006) Epigenetics and its implications for plant biology. 2. The ‘epigenetic epiphany’: epigenetics, evolution and beyond. Ann Bot 97:11–27. doi:10.1093/aob/mcj001Google Scholar
  54. Griffiths AJF, Miller JH, Suzuki DT, Lewontin RC, Gelbart WM (1993) An introduction to genetic analysis. W.H. Freeman & Company, New YorkGoogle Scholar
  55. Gustafsson A, Gadd I (1965) Mutations and crop improvement. II. The genus Lupinus(Leguminosae). Hereditas 53:15–39. doi:10.1111/j.1601-5223.1965.tb01977Google Scholar
  56. Haig D, Westoby M (1989) Parent specific gene expression and the triploid endosperm. Am Nat 134:147–155. doi:10.1086/284971Google Scholar
  57. Hall IM, Grewal SI (2003) Structure and function of heterochromatin: implications for epigenetic gene silencing and genome organization. In: Hannon GJ (ed) RNAi: a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 205–232Google Scholar
  58. Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in post-transcriptional gene silencing in plants. Science 286:950–952. doi:10.1126/science.286.5441.950PubMedGoogle Scholar
  59. Hashida SN, Uchiyama T, Martin C, Kishima Y, Sano Y, Mikami T (2006) The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. Plant Cell 18:104–118. doi:10.1105/tpc.105.037655PubMedGoogle Scholar
  60. Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 44:418–424. doi:10.1038/nature05917Google Scholar
  61. Hollick JB, Dorweiler JE, Chandler VL (1997) Paramutation and related allelic interactions. Trends Genet 13:302–308. doi:10.1016/S0168-9525(97)01184-0PubMedGoogle Scholar
  62. Jacobsen SE, Meyerowitz EM (1997) Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277:1100–1103. doi:10.1126/science.277.5329.1100PubMedGoogle Scholar
  63. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080. doi:10.1126/science.1063127 DOI:dx.doi.orgPubMedGoogle Scholar
  64. Jiang C-X, Wright RJ, El-Zik KM, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci USA 95:4419–4424, PMID: 9539752, PMCID: PMC22504Google Scholar
  65. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569–573. doi:10.1038/nature02953PubMedGoogle Scholar
  66. John MC, Amasino RM (1989) Extensive changes in DNA methylation patterns accompany activation of a silent T-DNA ipt gene in Agrobacterium tumefaciens-transformed plant cells. Mol Cell Biol 9:4298–4303, PMID: 2479825, PMCID: PMC362510Google Scholar
  67. Jones PA, Rideout WM, Shen J-C, Spruck CH, Tsai YC (1992) Methylation, mutation and cancer. BioEssays 14:33–36. doi:10.1002/bies.950140107PubMedGoogle Scholar
  68. Jost JP, Siegmann M, Sun L, Leung R (1995) Mechanisms of DNA demethylation in chicken embryos. Purification and properties of a 5-methylcytosine-DNA glycosylase. J Biol Chem 270:9734–9739. doi:10.1074/jbc.270.17.9734Google Scholar
  69. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163:1109–1122, PMID: 12663548, PMCID: PMC1462485Google Scholar
  70. Kashkush K, Feldman M, Levy AA (2002) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160:1651–1659, PMID: 11973318, PMCID: PMC1462064Google Scholar
  71. Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303:1626–1632. doi:10.1126/science.1089670PubMedGoogle Scholar
  72. Kermicle JL, Alleman M (1990) Gametic imprinting in maize in relation to the angiosperm life cycle. Development 108 (Suppl):9–14. PMID: 2090436Google Scholar
  73. Khoshoo TN (1959) Polyploidy in gymnosperms. Evolution 13:24–39, http://www.jstor.org/ stable/2405943 Google Scholar
  74. Kidwell MG, Lisch D (2002) Transposable elements as sources of genomic variation. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Moblie DNA II. American Society for Microbiology Press, Washington, DC, pp 59–90Google Scholar
  75. Kinoshita T, Yadegari R, Harada JH, Goldberg RB, Fisher RL (1999) Imprinting of the MEDEA Polycomb gene in the Arabidopsis endosperm. Plant Cell 11:1945–1952. doi:10.1105/tpc.11.10.1945PubMedGoogle Scholar
  76. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, Kakutani T (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303:521–523. doi:10.1126/science.1089835PubMedGoogle Scholar
  77. Kovarik A, Koukalova B, Bezdek M, Opatrn Z (1997) Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor Appl Genet 95:301–306. doi:10.1007/s001220050563Google Scholar
  78. Kusaba M, Miyahara K, Iida S, Fukuoka H, Takano T, Sassa H, Nishimura M, Nishio T (2003) Low glutelin content 1: a dominant mutation that suppresses the glutelin multigene family via RNA silencing in rice. Plant Cell 15:1455–1467. doi:10.1105/tpc.011452PubMedGoogle Scholar
  79. Labra M, Ghiani A, Citterio S, Sgorbati S, Sala F, Vannini C, Ruffini-Castiglione M, Bracale M (2002) Analysis of cytosine methylation pattern in response to water deficitin pea roottips. Plant Biol 4:694–699. doi:10.1055/s-2002-37398Google Scholar
  80. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21:4663–4670. doi:10.1093/emboj/cdf476PubMedGoogle Scholar
  81. Lippman Z, Gendrel A-V, Black M, Vaughn M, Dedhla N, McComble R, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476. doi:10.1038/nature02651PubMedGoogle Scholar
  82. Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536. doi:10.1016/j.cell.2008.03.029PubMedGoogle Scholar
  83. Long JA, Ohno C, Smith ZR, Meyerowitz EM (2006) TOPLESS regulates apical embryonic fate in Arabidopsis. Science 312:1520–1523. doi:10.1126/science.1123841PubMedGoogle Scholar
  84. Louwers M, Haring M, Stam M (2005) When alleles meet: paramutation. In: Meyer P (ed) Plant epigenetics. Blackwell Scientific Publications, Oxford, pp 134–173Google Scholar
  85. Luger K, Mder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260. doi:10.1038/38444Google Scholar
  86. Ma X-F, Fang P, Gustafson JP (2004) Polyploidization-induced genome variation in triticale. Genome 47:839–848. doi:10.1139/G04-051PubMedGoogle Scholar
  87. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R, Tuschl T (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110:563–574. doi:10.1016/S0092-8674(02)00908-XPubMedGoogle Scholar
  88. Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJM (2004) Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 1677:129–141PubMedGoogle Scholar
  89. McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792–801. doi:10.1126/science.15739260PubMedGoogle Scholar
  90. McCormick S (2004) Control of male gametophyte development. Plant Cell 16(Suppl):S142–S153. doi:10.1105/tpc.016659PubMedGoogle Scholar
  91. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343–349. doi:10.1038/nature02873PubMedGoogle Scholar
  92. Mlynarova L, Nap JP, Bisseling T (2007) The SWI/SNF chromatin-remodeling gene AtCHR12 mediates temporary growth arrest in Arabidopsis thaliana upon perceiving environmental stress. Plant J 51:874–885. doi:10.1111/j.1365-313X.2007.03185.xPubMedGoogle Scholar
  93. Mochida K, Yamazaki Y, Ogihara Y (2003) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Gen Genet 270:371–377. doi:10.1007/s00438-003-0939-7Google Scholar
  94. Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marn MI, Martnez-Macas MI, Ariza RR, Roldán-Arjona T (2006) DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci USA 103:6853–6858. doi:10.1073/ pnas.0601109103PubMedGoogle Scholar
  95. Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, Feuerbach F, Proux F, Vaucheret H (2002) Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post -transcriptional gene silencing and virus resistance. Plant Cell 14:629–639. doi:10.1105/tpc.010358PubMedGoogle Scholar
  96. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997–1002. doi:10.1038/ng1615PubMedGoogle Scholar
  97. Muskens MWM, Vissers APA, Mol JNM, Kooter JM (2000) Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing. Plant Mol Biol 43:243–260. doi:10.1023/A:1006491613768PubMedGoogle Scholar
  98. Mysore KS, Nam J, Gelvin SB (2000) An Arabidopsis histoneH2Amutant is deficient in Agrobacterium T-DNA integration. Proc Natl Acad Sci USA 97:948–953, PMID: 10639185, PMCID: PMC15436Google Scholar
  99. Napoli C, Lemieux C, Jorgensen R (1990) Introduction of a chimeric chalcone synthase gene in to petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279–289. doi:10.1105/tpc.2.4.279PubMedGoogle Scholar
  100. Nishimura M, Morita R, Kusaba M (2009) Utilization and molecular characterization of seed protein composition mutants in rice plants. JARQ 43:1–5Google Scholar
  101. Ogita S, Uefuji H, Yamaguchi Y, Koizumi N, Sano H (2003) Producing decaffeinated coffee plants. Nature 423:823. doi:10.1038/423823aGoogle Scholar
  102. Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR (1997) Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 40:370–378. doi:10.1139/g97-050Google Scholar
  103. Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92–94. doi:10.1126/science.1180677PubMedGoogle Scholar
  104. Otto SP, Whitton J (2000) Polyploidy incidence and evolution. Annu Rev Genet 34:401–437. doi:10.1146/annurev.genet.34.1.401PubMedGoogle Scholar
  105. Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, van der Winden J, Matzke M, Matzke AJM (2003) Evidence for nuclear processing of plant microRNA and short interfering RNA precursors. Plant Physiol 132:1382–1390. doi:10.1104/pp.103.021980PubMedGoogle Scholar
  106. Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O (2004) In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev 18:2237–2242. doi:10.1101/gad.307804PubMedGoogle Scholar
  107. Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA (2003) Structure and evolution of cereal genomes. Curr Opin Genet Dev 13:644–650. doi:10.1016/j.gde.2003.10.002PubMedGoogle Scholar
  108. Patterson GI, Thorpe CJ, Chandler VL (1993) Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory gene. Genetics 135:881–894, PMID: 7507455, PMCID: PMC 1205727Google Scholar
  109. Paull TT, Rogakou EP, Yamazaki V, Kirchgessner CU, Gellert M, Bonner WM (2000) A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Curr Biol 10:886–895. doi:10.1016/S0960-9822(00)00610-2PubMedGoogle Scholar
  110. Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, Earley K, Lawrence RJ, Pikaard CS, Murfett J, Furner I, Vaucheret H, Mittelsten SO (2004) Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16:1021–1034. doi:10.1105/tpc.018754PubMedGoogle Scholar
  111. Prymakowska-Bosak M, Przewloka MR, Slusarczyk J, Kuras M, Lichota J, Kilianczyk B, Jerzmanowski A (1999) Linker histones play a role in male meiosis and the development of pollen grains in tobacco. Plant Cell 11:2317–2329. doi:10.1105/tpc.11.12.2317PubMedGoogle Scholar
  112. Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168:81–91. doi:10.1111/j.1469-8137.2005.01491PubMedGoogle Scholar
  113. Rasmusson DC, Phillips RL (1997) Plant breeding progress and genetic diversity from de novo variation and elevated epistasis. Crop Sci 37:303–310Google Scholar
  114. Regina A, Bird A, Topping D, Bowden S, Freeman J, Barsby T, Kosar-Hashemi B, Li Z, Rahman S, Morell M (2006) High-amylose wheat generated by RNA interference improves indices of large-bowel health in rats. Proc Natl Acad Sci USA 103:3546–3551. doi:10.1073/pnas.0510737103PubMedGoogle Scholar
  115. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626. doi:10.1101/gad.1004402PubMedGoogle Scholar
  116. Reuter G, Fischer A, Hofmann I (2005) Heterochromatin and the control of gene silencing in plants. In: Meyer P (ed) Plant epigenetics. Blackwell Scientific Publications, Oxford, pp 134–173Google Scholar
  117. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110:513–520. doi:10.1016/S0092-8674(02)00863-2PubMedGoogle Scholar
  118. Rideout WM 3rd, Coetzee G, Olumi A, Jones P (1990) 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science 249:1288–1290. doi:10.1126/science.1697983PubMedGoogle Scholar
  119. Roth BM, Pruss GJ, Vance VB (2004) Plant viral suppressors of RNA silencing. Virus Res 102:97–108. doi:10.1016/j.virusres.2004.01.020PubMedGoogle Scholar
  120. Rusche LN, Kirchmaier AL, Rine J (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72:481–516. doi:10.1146/annurev.biochem.72.121801.161547PubMedGoogle Scholar
  121. Schwartz YB, Pirrotta V (2008) Polycomb complexes and epigenetic states. Curr Opin Cell Biol 20:266–273. doi:10.1016/j.ceb.2008.03.002PubMedGoogle Scholar
  122. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199–208. doi:10.1016/S0092-8674(03)00759-1PubMedGoogle Scholar
  123. 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, PMID: 10072403, PMCID: PMC144185Google Scholar
  124. Shen JC, Rideout WM III, Jones PA (1994) The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res 22:972–976. doi:10.1093/nar/22.6.972PubMedGoogle Scholar
  125. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8:272–285. doi:10.1038/nrg2072PubMedGoogle Scholar
  126. Slotkin RK, Freeling M, Lisch D (2005) Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet 37:641–644. doi:10.1038/ng1576PubMedGoogle Scholar
  127. Smith WK, Gorz HJ (1965) Sweetclover improvement. Adv Agron 17:163–231Google Scholar
  128. Soltis DE, Soltis PS (1995) The dynamic nature of polyploid genomes. Proc Natl Acad Sci USA 92:8089–8091PubMedGoogle Scholar
  129. Stam M, Belele CL, Ramakrishna W, Dorweiler JE, Bennetzen JL, Chandler VL (2002) The regulatory regions required for B paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162:917–930, PMID: 12399399, PMCID: PMC 1462281Google Scholar
  130. Stebbins GL (1950) Variation and evolution in plants. Columbia University Press, ColumbiaGoogle Scholar
  131. Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H (2002) Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 277:37741–37746. doi:10.1074/jbc.M204050200PubMedGoogle Scholar
  132. Sung S, Amasino RM (2004) Vernalization and epigemetics: how plants remember winter. Curr Opin Plant Biol 7:4–10. doi:10.1016/j.pbi.2003.11.010PubMedGoogle Scholar
  133. Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019. doi:10.1105/tpc.104.022830PubMedGoogle Scholar
  134. Sunkar R, Kapoor A, Zhu J-K (2006) Post transcriptional induction of two cu/zn superoxide dismutase genes in Arabidopsis is mediated by down regulation of miR398 and important for oxidative stress tolerance. Plant Cell 18:2051–2065. doi:10.1105/tpc.106.041673PubMedGoogle Scholar
  135. Sweredoski M, DeRose-Wilson L, Gaut BS (2008) A comperative computational analysis of nonautonomous Helitron elements between maize and rice. BMC Genomics 9:467. doi:10.1186/1471-2164/9/467PubMedGoogle Scholar
  136. Takeda S, Sugimoto K, Otsuki H, Hirochika H (1999) A 13-bp cis-regulatory element in the LTR promoter of the tobacco retrotransposon Tto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal elicitors. Plant J 18:383–393. doi:10.1046/j.1365-313X.1999.00460.xPubMedGoogle Scholar
  137. Tatra GS, Miranda J, Chinnappa CC, Reid DM (2000) Effect of light quality and 5-azacytidine on genomic methylation and stem elongation in two ecotypes of Stellaria longipes. Physiol Plant 109:313–321. doi:10.1034/j.1399-3054.2000.100313.xGoogle Scholar
  138. Thomas BC, Pedersen B, Freeling M (2006) Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 16:934–946. doi:10.1101/gr.4708406PubMedGoogle Scholar
  139. Tian L, Chen ZF (2001) Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci USA 98:200–205. doi:10.1073/pnas.011347998PubMedGoogle Scholar
  140. Tokatlidis IS (2000) Variation within maize lines and hybrids in the absence of competition and relation between hybrid potential yield per plant with line traits. J Agric Sci 134:391–398. doi:10.1017/S0021859699007637Google Scholar
  141. Tokatlidis IS, Tsialtas JT, Xynias IN, Tamoutsidis E, Irakli M (2004) Variation within a bread wheat cultivar for grain yield, protein content, carbon isotope discrimination and ash content. Field Crops Res 86:33–42. doi:10.1016/S0378-4290(03)00169-2Google Scholar
  142. Tokatlidis IS, Xynias IN, Tsialtas JT, Papadopoulos II (2006) Single-plant selection at ultra low density to improve stability of a bread wheat cultivar. Crop Sci 46:90–97. doi:10.2135/cropsci2005.0125Google Scholar
  143. Tokatlidis IS, Tsikrikoni C, Tsialtas JT, Lithourgidis AS, Bebeli PJ (2008) Variability within cotton cultivars for yield, fibre quality and physiological traits. J Agric Sci 146:483–490. doi:10.1017/S0021859608007867Google Scholar
  144. Tokatlidis IS, Papadopoulos II, Baxevanos D, Koutita O (2010) Genotype ×environment effects on single-plant selection at low density for yield and stability in climbing dry bean populations. Crop Sci 50:775–783. doi:10.2135/cropsci2009.08.0459Google Scholar
  145. Tokatlidis IS, Tsikrikoni C, Lithourgidis AS, Tsialtas JT, Tzantarmas C (2011) Intra-cultivar variation in cotton: response to single-plant yield selection at low density. J Agric Sci 149:197–204. doi:10.1017/S0021859610000596Google Scholar
  146. Tranel PJ, Wright TR (2002) Resistance of weeds to ALS-inhibiting herbicides: what have we learned? Weed Sci 50:700–712. doi:10.1614/0043-1745(2002) 050[0700:RROWTA]2.0.CO;2Google Scholar
  147. Tsaftaris AS, Kafka M (1998) Mechanisms of heterosis in crop plants. J Crop Prod 1:95–111. doi:10.1300/J144v01n01_05Google Scholar
  148. Tsaftaris AS, Polidoros AN (2000) DNA methylation and plant breeding. Plant Breed Rev 18:87–176Google Scholar
  149. Tsaftaris AS, Polidoros AN, Kapazoglou A, Tani E, Kovacevic NM (2008) Epigenetics and plant breeding. Plant Breed Rev 30:49–178Google Scholar
  150. Tschiersch B, Hofmann A, Krauss V, Dorn R, Korge G, Reuter G (1994) The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)39 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J 13:3822–3831PubMedGoogle Scholar
  151. Turner BM (2000) Histone acetylation and an epigenetic code. BioEssays 22:836–845. doi:10.1002/1521-1878(200009)22:9 < 836::AID-BIES9 > 3.0.CO;2-XPubMedGoogle Scholar
  152. van der Krol AR, Mur LA, Beld M, Mol JNM, Stuitje AR (1990) Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2:291–299. doi:10.1105/tpc.2.4.291PubMedGoogle Scholar
  153. Van Holde KE (1988) Chromatin, Springer series in molecular biology. Springer, New YorkGoogle Scholar
  154. Vance V, Vaucheret H (2001) RNA silencing in plants-defense and counterdefense. Science 292:2277–2280. doi:10.1126/science.1061334PubMedGoogle Scholar
  155. Vaucheret H, Vazquez F, Crata P, Bartel DP (2004) The action of ARGONAUTE 1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18:1187–1197. doi:10.1101/gad.1201404PubMedGoogle Scholar
  156. Voinnet O (2001) RNA silencing as a plant immune system against viruses. Trends Genet 17:449–459. doi:10.1016/S0168-9525(01)02367-8PubMedGoogle Scholar
  157. Wang Q, Dooner HK (2006) Eukaryotic transposable elements and genome evolution special feature: remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 103:17644–17649. doi:10.1073/pnas.0603080103PubMedGoogle Scholar
  158. Wang J, Tian L, Lee H-S, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Jeffrey Chen ZJ (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507–517. doi:10.1534/genetics.105.047894PubMedGoogle Scholar
  159. Wassenegger M, Heimes S, Riedel L, Sanger HL (1994) RNA-directed de novo methylation of genomic sequences in plants. Cell 76:567–576. doi:10.1016/0092-8674(94)90119-8PubMedGoogle Scholar
  160. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249. doi:10.1023/A:1006392424384PubMedGoogle Scholar
  161. Wessler SR (1996) Plant retrotransposons: turned on by stress. Curr Biol 6:959–961. doi:10.1016/S0960-9822(02)00638-3PubMedGoogle Scholar
  162. Weterings K, Russell SD (2004) Experimental analysis of the fertilization process. Plant Cell 16(Suppl):S107–S118. doi:10.1105/tpc.016873PubMedGoogle Scholar
  163. Wolfe KH (2001) Yesterday’s polyploids and the mystery of diploidization. Nature Rev Genet 2:323–341. doi:10.1038/35072009Google Scholar
  164. Woodcock CL (2005) A milestone in the odyssey of higher-order chromatin structure. Nat Struct Mol Biol 12:639–640. doi:10.1038/nsmb0805-639PubMedGoogle Scholar
  165. Wu K, Zhang L, Zhou C, Yu CW, Chaikam V (2008) HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J Exp Bot 59:225–234. doi:10.1093/jxb/erm300PubMedGoogle Scholar
  166. Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL (2003) Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell 5:891–901. doi:10.1016/S1534-5807(03)00361-7PubMedGoogle Scholar
  167. Yadegari R, Drews GN (2004) Female gametophyte development. Plant Cell 16(Suppl):S133–S141. doi:10.1105/tpc.018192PubMedGoogle Scholar
  168. Ye J, Ai X, Eugeni EE, Zhang L, Carpenter LR, Jelinek MA, Freitas MA, Parthun MR (2005) Histone H4 lysine 91 acetylation. Mol Cell 18:123–130. doi:10.1016/j.molcel.2005.02.031 DOI:dx.doi.orgPubMedGoogle Scholar
  169. Zhang YX, Gentzbittel L, Vear F, Nicolas P (1995) Assessment of inter- and intra-inbred line variability in sunflower (Helianthus annuus) by RFLPs. Genome 38:1040–1048. doi:10.1139/g95-138PubMedGoogle Scholar
  170. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW-L, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201. doi:10.1016/j.cell.2006.08.003PubMedGoogle Scholar
  171. Zhang K, Sridhar VV, Zhu J, Kapoor A, Zhu JK (2007) Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS ONE 2:e1210. doi:doi:10.1371/journal.pone.0001210Google Scholar
  172. Zheng X, Pontes O, Zhu J, Miki D, Zhang F, Li WX, Iida K, Kapoor A, Pikaard CS, Zhu JK (2008) ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 455:1259–1262. doi:10.1038/nature07305PubMedGoogle Scholar
  173. Zhou C, Zhang L, Duan J, Miki B, Wu K (2005) HISTONE DEACETYLASE 19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell 17:1196–1204. doi:10.1105/tpc.104.028514PubMedGoogle Scholar
  174. Zhu JK (2008) Epigenome sequencing comes of age. Cell 133:395–397. doi:10.1016/j.cell.2008.04.016PubMedGoogle Scholar
  175. Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu J-K (2007) The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17:54–59. doi:10.1016/j.cub.2006.10.059PubMedGoogle Scholar
  176. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61–69. doi:10.1038/ng1929PubMedGoogle Scholar

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© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Department of Agricultural DevelopmentDemocritus University of ThraceOrestiadaGreece

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