Translational Biology Approaches to Improve Abiotic Stress Tolerance in Crops

Improving Crop Resistance to Abiotic Stress

Volumn 1, Issue , 2012, Pages 207-239

  Iannacone, Rina ^a   Cellini, Francesco ^a   Morelli, Giorgio ^a,b   Ruberti, Ida ^b  

^a ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

^b CNR   (Italy)

Author keywords

Abiotic stress tolerance; Genomic revolution; Osmolytes; Phenomics; Translational biology

Indexed keywords

EID: 84885821378     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527632930.ch9     Document Type: Chapter

References (185)

1. Acquaah, G. (2007) Principles of Plant Genetics and Breeding, Blackwell, Oxford, UK.
2. Delmer, D.P. (2005) Agriculture in the developing world: connecting innovations in plant research to downstream applications. Proc. Natl. Acad. Sci. USA, 102 (44), 15739-15746.
3. Hua, J. (2009) From freezing to scorching: transcriptional responses to temperature variations in plants. Curr. Opin. Plant Biol., 12 (5), 568-573.
4. Thomashow, M.F. (2010) Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol., 154 (2), 571-577.
5. Miura, K., Jin, J.B., Lee, J., Yoo, C.Y., Stirm, V., Miura, T., Ashworth, E.N., Bressan, R.A., Yun, D.J., and Hasegawa, P.M. (2007) SIZ1-mediated sumoylation of ICE1 controls CBF3/ DREB1A expression and freezing tolerance in Arabidopsis. Plant Cell, 19 (4), 1403-1414.
6. Doherty, C.J., Van Buskirk, H.A., Myers, S.J., and Thomashow, M.F. (2009) Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. Plant Cell, 21 (3), 972-984.
7. Fowler, S.G., Cook, D., and Thomashow, M.F. (2005) Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol., 137 (3), 961-968.
8. Franklin, K.A. and Whitelam, G.C. (2007) Light-quality regulation of freezing tolerance in Arabidopsis thaliana. Nat. Genet., 39 (11), 1410-1413.
9. Koornneef, M., Alonso-Blanco, C., and Vreugdenhil, D. (2004) Naturally occurring genetic variation in Arabidopsis thaliana. Annu. Rev. Plant Biol., 55, 141-172.
10. Zhen, Y. and Ungerer, M.C. (2008) Relaxed selection on the CBF/DREB1 regulatory genes and reduced freezing tolerance in the southern range of Arabidopsis thaliana. Mol. Biol. Evol., 25 (12), 2547-2555.
11. Gilmour, S.J., Fowler, S.G., and Thomashow, M.F. (2004) Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities. Plant Mol. Biol., 54 (5), 767-781.
12. Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K., and Shinozaki, K. (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought-and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell, 10 (8), 1391-1406.
13. Achard, P., Gong, F., Cheminant, S., Alioua, M., Hedden, P., and Genschik, P. (2008) The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLAproteins via its effect on gibberellin metabolism. Plant Cell, 20 (8), 2117-2129.
14. Harberd, N.P., Belfield, E., and Yasumura, Y. (2009) The angiosperm gibberellin-GID1-DELLA growth regulatory mechanism: how an "inhibitor of an inhibitor" enables flexible response to fluctuating environments. Plant Cell, 21 (5), 1328-1339.
15. Jaglo, K.R., Kleff, S., Amundsen, K.L., Zhang, X., Haake, V., Zhang, J.Z., Deits, T., and Thomashow, M.F. (2001) Components of the Arabidopsis C-repeat/dehydration-responsive element binding factor cold-response pathway are conserved in Brassica napus and other plant species. Plant Physiol., 127 (3), 910-917.
16. Nakashima, K., Fujita, Y., Kanamori, N., Katagiri, T., Umezawa, T., Kidokoro, S., Maruyama, K., Yoshida, T., Ishiyama, K., Kobayashi, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2009) Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/ OST1 and SRK21/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. Plant Cell Physiol., 50 (7), 1345-1363.
17. Chew, Y.H. and Halliday, K.J. (2011) A stress-free walk from Arabidopsis to crops. Curr. Opin. Biotechnol., 22 (2), 281-286.
18. Mittler, R. and Blumwald, E. (2010) Genetic engineering for modern agriculture: challenges and perspectives. Annu. Rev. Plant Biol., 61, 443-462.
19. Cutler, S.R., Rodriguez, P.L., Finkelstein, R.R., and Abrams, S.R. (2010) Abscisic acid: emergence of a core signaling network. Annu. Rev. Plant Biol., 61, 651-679.
20. Sirichandra, C., Wasilewska, A., Vlad, F., Valon, C., and Leung, J. (2009) The guard cell as a single-cell model towards understanding drought tolerance and abscisic acid action. J. Exp. Bot., 60 (5), 1439-1463.
21. Park, S.Y., Fung, P., Nishimura, N., Jensen, D.R., Fujii, H., Zhao, Y., Lumba, S., Santiago, J., Rodrigues, A., Chow, T.F., Alfred, S.E., Bonetta, D., Finkelstein, R., Provart, N.J., Desveaux, D., Rodriguez, P.L., McCourt, P., Zhu, J.K., Schroeder, J.I., Volkman, B.F., and Cutler, S.R. (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science, 324 (5930), 1068-1071.
22. Ma, Y., Szostkiewicz, I., Korte, A., Moes, D., Yang, Y., Christmann, A., and Grill, E. (2009) Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science, 324 (5930), 1064-1068.
23. Santiago, J., Rodrigues, A., Saez, A., Rubio, S., Antoni, R., Dupeux, F., Park, S.Y., Marquez, J.A., Cutler, S.R., and Rodriguez, P.L. (2009) Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs. Plant J., 60 (4), 575-588.
24. Nishimura, N., Sarkeshik, A., Nito, K., Park, S.Y., Wang, A., Carvalho, P.C., Lee, S., Caddell, D.F., Cutler, S.R., Chory, J., Yates, J.R., and Schroeder, J.I. (2010) PYR/PYL/RCAR family members are major in-vivo AB11 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant J., 61 (2), 290-299.
25. Hubbard, K.E., Nishimura, N., Hitomi, K., Getzoff, E.D., and Schroeder, J.I. (2010) Early abscisic acid signal transduction mechanisms: newly discovered components and newly emerging questions. Genes Dev., 24 (16), 1695-1708.
26. Iyer, L.M., Koonin, E.V., and Aravind, L. (2001) Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins., 43 (2), 134-144.
27. Radauer, C., Lackner, P., and Breiteneder, H. (2008) The Betv 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. BMC Evol. Biol., 8, 286.
28. Melcher, K., Ng, L.M., Zhou, X.E., Soon, F.F., Xu, Y., Suino-Powell, K.M., Park, S.Y., Weiner, J.J., Fujii, H., Chinnusamy, V., Kovach, A., Li, J., Wang, Y., Peterson, F.C., Jensen, D.R., Yong, E.L., Volkman, B.F., Cutler, S.R., Zhu, J.K., and Xu, H.E. (2009) A gate-latch-lock mechanism for hormone signalling by abscisic acid receptors. Nature, 462 (7273), 602-608.
29. Santiago, J., Dupeux, F., Round, A., Antoni, R., Park, S.Y., Jamin, M., Cutler, S.R., Rodriguez, P.L., and Marquez, J.A. (2009) The abscisic acid receptor PYR1 in complex with abscisic acid. Nature, 462 (7273), 665-668.
30. Nishimura, N., Hitomi, K., Arvai, A.S., Rambo, R.P., Hitomi, C., Cutler, S.R., Schroeder, J.I., and Getzoff, E.D. (2009) Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science, 326 (5958), 1373-1379.
31. Yin, P., Fan, H., Hao, Q., Yuan, X., Wu, D., Pang, Y., Yan, C., Li, W., Wang, J., and Yan, N. (2009) Structural insights into the mechanism of abscisic acid signaling by PYL proteins. Nat. Struct. Mol. Biol., 16 (12), 1230-1236.
32. Miyazono, K., Miyakawa, T., Sawano, Y., Kubota, K., Kang, H.J., Asano, A., Miyauchi, Y., Takahashi, M., Zhi, Y., Fujita, Y., Yoshida, T., Kodaira, K.S., Yamaguchi-Shinozaki, K., and Tanokura, M. (2009) Structural basis of abscisic acid signalling. Nature., 462 (7273), 609-614.
33. Mustilli, A.C., Merlot, S., Vavasseur, A., Fenzi, F., and Giraudat, J. (2002) Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production. Plant Cell, 14 (12), 3089-3099.
34. Yoshida, R., Umezawa, T., Mizoguchi, T., Takahashi, S., Takahashi, F., and Shinozaki, K. (2006) The regulatory domain of SRK2E/OST1/SnRK2.6 interacts with AB11 and integrates abscisic acid (ABA) and osmotic stress signals controlling stomatal closure in Arabidopsis. J. Biol. Chem., 281 (8), 5310-5318.
35. Fujii, H. and Zhu, J.K. (2009) Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress. Proc. Natl. Acad. Sci. USA, 106 (20), 8380-8385.
36. Fujita, Y., Nakashima, K., Yoshida, T., Katagiri, T., Kidokoro, S., Kanamori, N., Umezawa, T., Fujita, M., Maruyama, K., Ishiyama, K., Kobayashi, M., Nakasone, S., Yamada, K., Ito, T., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2009) Three SnRK2 protein kinases are the main positive regulators of abscisic acid signaling in response to water stress in Arabidopsis. Plant Cell Physiol., 50 (12), 2123-2132.
37. Nakashima, K. and Yamaguchi-Shinozaki, K. (2006) Regulons involved in osmotic stress-responsive and cold stress-responsive gene expression in plants. Physiol. Plant., 126 (1), 62-71.
38. Belin, C., de Franco, P.O., Bourbousse, C., Chaignepain, S., Schmitter, J.M., Vavasseur, A., Giraudat, J., Barbier-Brygoo, H., and Thomine, S. (2006) Identification of features regulating OST1 kinase activity and OST1 function in guard cells. Plant. Physiol., 141 (4), 1316-1327.
39. Umezawa, T., Sugiyama, N., Mizoguchi, M., Hayashi, S., Myouga, F., Yamaguchi-Shinozaki, K., Ishihama, Y., Hirayama, T., and Shinozaki, K. (2009) Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis. Proc. Natl. Acad. Sci. USA, 106 (41), 17588-17593.
40. Vlad, F., Rubio, S., Rodrigues, A., Sirichandra, C., Belin, C., Robert, N., Leung, J., Rodriguez, P.L., Lauriere, C., and Merlot, S. (2009) Protein phosphatases 2C regulate the activation of the Snf1-related kinase OST1 by abscisic acid in Arabidopsis. Plant. Cell., 21 (10), 3170-3184.
41. Weiner, J.J., Peterson, F.C., Volkman, B.F., and Cutler, S.R. (2010) Structural and functional insights into core ABA signaling. Curr. Opin. Plant. Biol., 13 (5), 495-502.
42. Fujii, H., Chinnusamy, V., Rodrigues, A., Rubio, S., Antoni, R., Park, S.Y., Cutler, S.R., Sheen, J., Rodriguez, P.L., and Zhu, J.K. (2009) In vitro reconstitution of an abscisic acid signalling pathway. Nature, 462 (7273), 660-664.
43. Kline, K.G., Sussman, M.R., and Jones, A.M. (2010) Abscisic acid receptors. Plant. Physiol., 154 (2), 479-482.
44. Klingler, J.P., Batelli, G., and Zhu, J.K. (2010) ABA receptors: the START of a new paradigm in phytohormone signalling. J. Exp. Bot., 61 (12), 3199-3210.
45. Melcher, K., Xu, Y., Ng, L.M., Zhou, X.E., Soon, F.F., Chinnusamy, V., Suino-Powell, K.M., Kovach, A., Tham, F.S., Cutler, S.R., Li, J., Yong, E.L., Zhu, J.K., and Xu, H.E. (2010) Identification and mechanism of ABA receptor antagonism. Nat. Struct. Mol. Biol., 17 (9), 1102-1108.
46. Peterson, F.C., Burgie, E.S., Park, S.Y., Jensen, D.R., Weiner, J.J., Bingman, C.A., Chang, C.E., Cutler, S.R., Phillips, G.N., Jr., and Volkman, B.F. (2010) Structural basis for selective activation of ABA receptors. Nat. Struct. Mol. Biol., 17 (9), 1109-1113.
47. Eckardt, N.A., Cominelli, E., Galbiati, M., and Tonelli, C. (2009) The future of science: food and water for life. Plant Cell, 21 (2), 368-372.
48. Bartels, D. and Sunkar, R. (2005) Drought and salt tolerance in plants. Crit. Rev. Plant Sci., 24 (1), 23-58.
49. Bartels, D. and Salamini, F. (2001) Desiccation tolerance in the resurrection plant Craterostigma plantagineum. A contribution to the study of drought tolerance at the molecular level. Plant Physiol., 127 (4), 1346-1353.
50. Ashraf, M. (2010) Inducing drought tolerance in plants: recent advances. Biotechnol. Adv., 28 (1), 169-183.
51. Xoconostle-Cazares, B., Ramirez-Ortega, F.A., Flores-Elenes, L., and Ruiz-Medrano, R. (2010) Drought tolerance in crop plants. Am. J. Plant Physiol., 5 (5), 241-256.
52. Century, K., Reuber, T.L., and Ratcliffe, O.J. (2008) Regulating the regulators: the future prospects for transcription-factor-based agricultural biotechnology products. Plant Physiol., 147 (1), 20-29.
53. Bray, E.A. (1993) Molecular responses to water deficit. Plant Physiol., 103 (4), 1035-1040.
54. Kishor, P., Hong, Z., Miao, G.H., Hu, C., and Verma, D. (1995) Overexpression of [delta]-pyrroline-5-carboxylate synthetase increases proline production and confers osmotolerance in transgenic plants. Plant Physiol., 108 (4), 1387-1394.
55. Zhu, B., Su, J., Chang, M., Verma, D.P.S., Fan, Y.-L., and Wu, R. (1998) Overexpression of a D1-pyrroline-5-carboxylate synthetase gene and analysis of tolerance to water- and salt-stress in transgenic rice. Plant Sci., 139 (1), 41-48.
56. Molinari, H.B.C., Marur, C.J., Daros, E., De Campos, M.K.F., De Carvalho, J.F.R.P., Filho, J.C.B., Pereira, L.F.P., and Vieira, L.G.E. (2007) Evaluation of the stress-inducible production of proline in transgenic sugarcane (Saccharum Saccharum): osmotic adjustment, chlorophyll fluorescence and oxidative stress. Physiol. Plant., 130 (2), 218-229.
57. Rathinasabapathi, B., McCue, K.F., Gage, D.A., and Hanson, A.D. (1994) Metabolic engineering of glycine betaine synthesis: plant betaine aldehyde dehydrogenases lacking typical transit peptides are targeted to tobacco chloroplasts where they confer betaine aldehyde resistance. Planta, 193 (2), 155-162.
58. Sakamoto, A. and Murata, N. (2002) The role of glycine betaine in the protection of plants from stress: clues from transgenic plants. Plant Cell Environ., 25 (2), 163-171.
59. Yancey, P.H., Clark, M.E., Hand, S.C., Bowlus, R.D., and Somero, G.N. (1982) Living with water stress: evolution of osmolyte systems. Science., 217 (4566), 1214-1222.
60. Mattioli, R., Costantino, P., and Trovato, M. (2009) Proline accumulation in plants: not only stress. Plant. Signal. Behav., 4 (11), 1016-1018.
61. Szabados, L. and Savoure, A. (2010) Proline: a multifunctional amino acid. Trends Plant Sci., 15 (2), 89-97.
62. Verbruggen, N. and Hermans, C. (2008) Proline accumulation in plants: a review. Amino Acids, 35 (4), 753-759.
63. Hong, Z., Lakkineni, K., Zhang, Z., and Verma, D.P. (2000) Removal of feedback inhibition ofdelta(1)-pyrroline-5-carboxylate synthetase results in increased proline accumulation and protection of plants from osmotic stress. Plant Physiol., 122 (4), 1129-1136.
64. Kumar, V., Varsha, S., Kavi Kishor, P.B., Jawali, N., and Shitole, M.G. (2010) Enhanced proline accumulation and salt stress tolerance of transgenic indica rice by over-expressing P5CSF129A gene. Plant Biotechnol. Rep., 4, 37-48.
65. Nanjo, T., Kobayashi, M., Yoshiba, Y., Kakubari, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (1999) Antisense suppression of proline degradation improves tolerance to freezing and salinity in Arabidopsis thaliana. FEBS Lett., 461 (3), 205-210.
66. Mani, S., Van De Cotte, B., Van Montagu, M., and Verbruggen, N. (2002) Altered levels of proline dehydrogenase cause hypersensitivity to proline and its analogs in Arabidopsis. Plant Physiol., 128 (1), 73-83.
67. Banu, M.N., Hoque, M.A., Watanabe-Sugimoto, M., Islam, M.M., Uraji, M., Matsuoka, K., Nakamura, Y., and Murata, Y. (2010) Proline and glycinebetaine ameliorated NaCl stress via scavenging of hydrogen peroxide and methylglyoxal but not superoxide or nitric oxide in tobacco cultured cells. Biosci. Biotechnol. Biochem., 74 (10), 2043-2049.
68. Papageorgiou, G.C. and Murata, N. (1995) The unusually strong stabilizing effects of glycine betaine on the structure and function of the oxygen-evolving photosystemII complex. Photosynth. Res., 44 (3), 243-252.
69. Rhodes, D. and Hanson, A.D. (1993) Quaternary ammonium and tertiary sulfonium compounds in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol., 44 (1), 357-384.
70. Nyyssola, A., Kerovuo, J., Kaukinen, P., von Weymarn, N., and Reinikainen, T. (2000) Extreme halophiles synthesize betaine from glycine by methylation. J. Biol. Chem., 275 (29), 22196-22201.
71. Landfald, B. and Strom, A.R. (1986) Choline-glycine betaine pathway confers a high level of osmotic tolerance in Escherichia coli. J. Bacteriol., 165 (3), 849-855.
72. Holmstrom, K.O., Somersalo, S., Mandal, A., Palva, T.E., and Welin, B. (2000) Improved tolerance to salinity and low temperature in transgenic tobacco producing glycine betaine. J. Exp. Bot., 51 (343), 177-185.
73. Deshnium, P., Los, D.A., Hayashi, H., Mustardy, L., and Murata, N. (1995) Transformation of Synechococcus with a gene for choline oxidase enhances tolerance to salt stress. Plant Mol. Biol., 29 (5), 897-907.
74. Sakamoto, A. and Murata, N. (1998) Metabolic engineering of rice leading to biosynthesis of glycinebetaine and tolerance to salt and cold. Plant Mol. Biol., 38 (6), 1011-1019.
75. Shirasawa, K., Takabe, T., and Kishitani, S. (2006) Accumulation of glycinebetaine in rice plants that overexpress choline monooxygenase from spinach and evaluation of their tolerance to abiotic stress. Ann. Bot., 98 (3), 565-571.
76. McNeil, S.D., Nuccio, M.L., Ziemak, M.J., and Hanson, A.D. (2001) Enhanced synthesis of choline and glycine betaine in transgenic tobacco plants that overexpress phosphoethanolamine N-methyltransferase. Proc. Natl. Acad. Sci. USA, 98 (17), 10001-10005.
77. Quan, R., Shang, M., Zhang, H., Zhao, Y., and Zhang, J. (2004) Engineering of enhanced glycine betaine synthesis improves drought tolerance in maize. Plant Biotechnol. J, 2 (6), 477-486.
78. Quan, R., Shang, M., Zhang, H., Zhao, Y., and Juren, Z. (2004) Improved chilling tolerance by transformation with betA gene for the enhancement of glycinebetaine synthesis in maize. Plant Sci., 166 (1), 141-149.
79. Park, E.J., Jeknic, Z., Pino, M.T., Murata, N., and Chen, T.H. (2007) Glycinebetaine accumulation is more effective in chloroplasts than in the cytosol for protecting transgenic tomato plants against abiotic stress. Plant Cell Environ., 30 (8), 994-1005.
80. Doebley, J.F., Gaut, B.S., and Smith, B.D. (2006) The molecular genetics of crop domestication. Cell, 127 (7), 1309-1321.
81. Yu, H., Chen, X., Hong, Y.Y., Wang, Y., Xu, P., Ke, S.D., Liu, H.Y., Zhu, J.K., Oliver, D.J., and Xiang, C.B. (2008) Activated expression of an Arabidopsis HD-START protein confers drought tolerance with improved root system and reduced stomatal density. Plant Cell, 20 (4), 1134-1151.
82. Jaglo-Ottosen, K.R., Gilmour, S.J., Zarka, D.G., Schabenberger, O., and Thomashow, M.F. (1998) Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science, 280 (5360), 104-106.
83. Gilmour, S.J., Sebolt, A.M., Salazar, M.P., Everard, J.D., and Thomashow, M.F. (2000) Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiol., 124 (4), 1854-1865.
84. Ding, Z., Li, S., An, X., Liu, X., Qin, H., and Wang, D. (2009) Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana. J. Genet. Genomics, 36 (1), 17-29.
85. Jung, C., Seo, J.S., Han, S.W., Koo, Y.J., Kim, C.H., Song, S.I., Nahm, B.H., Choi, Y.D., and Cheong, J.J. (2008) Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol., 146 (2), 623-635.
86. Wu, Y., Deng, Z., Lai, J., Zhang, Y., Yang, C., Yin, B., Zhao, Q., Zhang, L., Li, Y., and Xie, Q. (2009) Dual function of Arabidopsis ATAF1 in abiotic and biotic stress responses. Cell Res., 19 (11), 1279-1290.
87. Hsieh, T.H., Lee, J.T., Charng, Y.Y., and Chan, M.T. (2002) Tomato plants ectopically expressing Arabidopsis CBF1 show enhanced resistance to water deficit stress. Plant Physiol., 130 (2), 618-626.
88. Oh, S.J., Song, S.I., Kim, Y.S., Jang, H.J., Kim, S.Y., Kim, M., Kim, Y.K., Nahm, B.H., and Kim, J.K. (2005) Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiol., 138 (1), 341-351.
89. Hsieh, T.H., Lee, J.T., Yang, P.T., Chiu, L.H., Charng, Y.Y., Wang, Y.C., and Chan, M.T. (2002) Heterology expression of the Arabidopsis C-repeat/dehydration response element binding factor 1 gene confers elevated tolerance to chilling and oxidative stresses in transgenic tomato. Plant Physiol., 129 (3), 1086-1094.
90. Yang, J.S., Wang, R., Meng, J.J., Bi, Y.P., Xu, P.L., Guo, F., Wan, S.B., He, Q.W., and Li, X.G. (2010) Overexpression of Arabidopsis CBF1 gene in transgenic tobacco alleviates photoinhibition ofPSII and PSI during chilling stress under low irradiance. J. Plant Physiol., 167 (7), 534-539.
91. Dubouzet, J.G., Sakuma, Y., Ito, Y., Kasuga, M., Dubouzet, E.G., Miura, S., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J., 33 (4), 751-763.
92. Ito, Y., Katsura, K., Maruyama, K., Taji, T., Kobayashi, M., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol., 47 (1), 141-153.
93. Orellana, S., Yanez, M., Espinoza, A., Verdugo, I., González, E., Ruiz-Lara, S., and Casaretto, J.A. (2010) The transcription factor SlAREB1 confers drought, salt stress tolerance and regulates biotic and abiotic stress-related genes in tomato. Plant Cell Environ., 33 (12), 2191-2208.
94. Hsieh, T.H., Li, C.W., Su, R.C., Cheng, C.P., Sanjaya, Tsai, Y.C., and Chan, M.T. (2010) A tomato bZIP transcription factor, SlAREB, is involved in water deficit and salt stress response. Planta, 231 (6), 1459-1473.
95. Navarro, M., Ayax, C., Martinez, Y., Laur, J., El Kayal, W., Marque, C., and Teulieres, C. (2011) Two EguCBF1 genes overexpressed in Eucalyptus display a different impact on stress tolerance and plant development. Plant Biotechnol. J., 9 (1), 50-63.
96. Kang, J.Y., Choi, H.I., Im, M.Y., and Kim, S.Y. (2002) Arabidopsis basic leucine zipper proteins that mediate stress-responsive abscisic acid signaling. Plant Cell., 11 (2), 343-357.
97. Oh, S.J., Kwon, C.W., Choi, D.W., Song, S.I., and Kim, J.K. (2007) Expression of barley HvCBF4 enhances tolerance to abiotic stress in transgenic rice. Plant Biotechnol. J., 5 (5), 646-656.
98. Kiang, J.G. and Tsokos, G.C. (1998) Heat shock protein 70 kDa: molecular biology, biochemistry, and physiology. Pharmacol. Ther., 80 (2), 183-201.
99. Wu, X., Shiroto, Y., Kishitani, S., Ito, Y., and Toriyama, K. (2009) Enhanced heat and drought tolerance in transgenic rice seedlings overexpressing OsWRKY11 under the control of HSP101 promoter. Plant Cell Rep., 28 (1), 21-30.
100. Raho, G., Lupotto, E., Hartings, H., Della Torre A., Perrotta, C., and Marmiroli, N. (1996) Tissue-10Hvhsp17 gene promoter in transgenic tobacco plants. J. Exp. Bot., 47 (10), 1587-1594.
101. Kasuga, M., Miura, S., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2004) A combination of the Arabidopsis DREB1A gene and stress-inducible rd29A promoter improved drought-and low-temperature stress tolerance in tobacco by gene transfer. Plant Cell Physiol., 45 (3), 346-350.
102. Lee, J.T., Prasad, V., Yang, P.T., Wu, J.F., David Ho, T.H., Charng, Y.Y., and Chan, M.T. (2003) Expression of Arabidopsis CBF1 regulated by an ABA/ stress inducible promoter in transgenic tomato confers stress tolerance without affecting yield. Plant Cell Environ., 26 (7), 1181-1190.
103. Umezawa, T., Fujita, M., Fujita, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr. Opin. Biotechnol., 17 (2), 113-122.
104. Jakab, G., Ton, J., Flors, V., Zimmerli, L., Métraux, J.-P., and Mauch-Mani, B. (2005) Enhancing Arabidopsis salt and drought stress tolerance by chemical priming for its abscisic acid responses. Plant Physiol., 139 (1), 267-274.
105. Srivastava, A.K., Ramaswamy, N.K., Suprasanna, P., and D'Souza, S.F. (2010) Genome-wide analysis of thiourea-modulated salinity stress-responsive transcripts in seeds of Brassica juncea: identification of signalling and effector components of stress tolerance. Ann. Bot., 106 (5), 663-674.
106. Hiratsu, K., Matsui, K., Koyama, T., and Ohme-Takagi, M. (2003) Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. Plant J., 34 (5), 733-739.
107. Staudt, A.C. and Wenkel, S. (2011) Regulation of protein function by "microproteins". EMBO Rep., 12 (1), 35-42.
108. Minoia, S., Petrozza, A., D'Onofrio, O., Piron, F., Mosca, G., Sozio, G., Cellini, F., Bendahmane, A., and Carriero, F. (2010) A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Res. Notes, 3, 69.
109. Kariola, T., Brader, G., Helenius, E., Li, J., Heino, P., and Palva, E.T. (2006) Early responsive to dehydration 15, a negative regulator of abscisic acid responses in Arabidopsis. Plant Physiol., 142 (4), 1559-1573.
110. Alexandre, C., Moller-Steinbach, Y., Schonrock, N., Gruissem, W., and Hennig, L. (2009) Arabidopsis MS11 is required for negative regulation of the response to drought stress. Mol. Plant, 2 (4), 675-687.
111. Cominelli, E., Galbiati, M., Vavasseur, A., Conti, L., Sala, T., Vuylsteke, M., Leonhardt, N., Dellaporta, S.L., and Tonelli, C. (2005) A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Curr. Biol., 15 (13), 1196-1200.
112. Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., and Xiong, L. (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc. Natl. Acad. Sci. USA, 103 (35), 12987-12992.
113. Huang, X.Y., Chao, D.Y., Gao, J.P., Zhu, M.Z., Shi, M., and Lin, H.X. (2009) A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev., 23 (15), 1805-1817.
114. Covarrubias, A.A. and Reyes, J.L. (2010) Post-transcriptional gene regulation of salinity and drought responses by plant microRNAs. Plant Cell Environ., 33 (4), 481-489.
115. Bohnert, H., Gong, Q., Li, P., and Ma, S. (2006) Unraveling abiotic stress tolerance mechanisms - getting genomics going. Curr. Opin. Plant Biol., 9 (2), 180-188.
116. De Vos, M., Van Oosten, V.R., Van Poecke, R.M.P., Van Pelt, J.A., Pozo, M.J., Mueller, M.J., Buchala, A.J., Métraux, J.-P., Van Loon, L.C., Dicke, M., and Pieterse, C.M.J. (2005) Signal signature and transcriptome changes of Arabidopsis during pathogen and insect attack. Mol. Plant Microbe Interact., 18 (9), 923-937.
117. Fujita, M., Fujita, Y., Noutoshi, Y., Takahashi, F., Narusaka, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. (2006) Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr. Opin. Plant Biol., 9 (4), 436-442.
118. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., and Harter, K. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J., 50 (2), 347-363.
119. Ma, S. and Bohnert, H.J. (2007) Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol., 8 (4), R49.
120. Walley, J.W., Coughlan, S., Hudson, M.E., Covington, M.F., Kaspi, R., Banu, G., Harmer, S.L., and Dehesh, K. (2007) Mechanical stress induces biotic and abiotic stress responses via a novel cis element. PLoS Genet., 3 (10), 1800-1812.
121. Kultz, D. (2005) Molecular and evolutionary basis of the cellular stress response. Annu. Rev. Physiol., 67, 225-257.
122. Mittler, R. (2006) Abiotic stress, the field environment and stress combination. Trends Plant Sci., 11 (1), 15-19.
123. Cheong, Y.H., Chang, H.S., Gupta, R., Wang, X., Zhu, T., and Luan, S. (2002) Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis. Plant Physiol., 129 (2), 661-677.
124. Fowler, S. and Thomashow, M.F. (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell., 14 (8), 1675-1690.
125. Rizhsky, L., Liang, H., and Mittler, R. (2002) The combined effect of drought stress and heat shock on gene expression in tobacco. Plant Physiol., 130 (3), 1143-1151.
126. Rizhsky, L., Liang, H., Shuman, J., Shulaev, V., Davletova, S., and Mittler, R. (2004) When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol., 134 (4), 1683-1696.
127. Larkindale, J. and Huang, B. (2004) Thermotolerance and antioxidant systems in Agrostis stolonifera: involvement of salicylic acid, abscisic acid, calcium, hydrogen peroxide, and ethylene. J. Plant Physiol., 161 (4), 405-413.
128. Hewezi, T., Leger, M., and Gentzbittel, L. (2008) A comprehensive analysis of the combined effects of high light and high temperature stresses on gene expression in sunflower. Ann. Bot., 102 (1), 127-140.
129. Keles, Y. and Öncel, I. (2002) Response of antioxidative defence system to temperature and water stress combinations in wheat seedlings. Plant Sci., 163 (4), 783-790.
130. Hirayama, T. and Shinozaki, K. (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J., 61 (6), 1041-1052.
131. Munns, R. and Tester, M. (2008) Mechanisms of salinity tolerance. Annu. Rev. Plant Biol., 59, 651-681.
132. Werner, T., Nehnevajova, E., Kollmer, I., Novak, O., Strnad, M., Kramer, U., and Schmulling, T. (2010) Root-specific reduction of cytokinin causes enhanced root growth, drought tolerance, and leaf mineral enrichment in Arabidopsis and tobacco. Plant Cell, 22 (12), 3905-3920.
133. Yuan, J.S., Galbraith, D.W., Dai, S.Y., Griffin, P., and Stewart, C.N. (2008) Plant systems biology comes of age. Trends Plant Sci., 13 (4), 165-171.
134. Chenu, K., Chapman, S.C., Tardieu, F., McLean, G., Welcker, C., and Hammer, G.L. (2009) Simulating the yield impacts of organ-level quantitative trait loci associated with drought response in maize: a "gene-to-phenotype" modeling approach. Genetics, 183 (4), 1507-1523.
135. Granier, C., Aguirrezabal, L., Chenu, K., Cookson, S.J., Dauzat, M., Hamard, P., Thioux, J.J., Rolland, G., Bouchier-Combaud, S., Lebaudy, A., Muller, B., Simonneau, T., and Tardieu, F. (2006) Phenopsis: an automated platform for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis thaliana permitted the identification of an accession with low sensitivity to soil water deficit. New Phytol., 169 (3), 623-635.
136. Hammer, G., Cooper, M., Tardieu, F., Welch, S., Walsh, B., van Eeuwijk, F., Chapman, S., and Podlich, D. (2006) Models for navigating biological complexity in breeding improved crop plants. Trends Plant Sci., 11 (12), 587-593.
137. Poorter, H., Niinemets, U., Walter, A., Fiorani, F., and Schurr, U. (2010) A method to construct dose-response curves for a wide range of environmental factors and plant traits by means of a meta-analysis of phenotypic data. J. Exp. Bot., 61 (8), 2043-2055.
138. Tardieu, F. and Tuberosa, R. (2010) Dissection and modelling of abiotic stress tolerance in plants. Curr. Opin. Plant Biol., 13 (2), 206-212.
139. Eckardt, N.A., Araki, T., Benning, C., Cubas, P., Goodrich, J., Jacobsen, S.E., Masson, P., Nambara, E., Simon, R., Somerville, S., and Wasteneys, G. (2001) Arabidopsis research 2001. Plant Cell., 13 (9), 1973-1982.
140. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36 (Database issue), D480-D484
141. Matsuda, F., Hirai, M.Y., Sasaki, E., Akiyama, K., Yonekura-Sakakibara, K., Provart, N.J., Sakurai, T., Shimada, Y., and Saito, K. (2010) AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiol., 152 (2), 566-578.
142. Zhang, P., Foerster, H., Tissier, C.P., Mueller, L., Paley, S., Karp, P.D., and Rhee, S.Y. (2005) MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol., 138 (1), 27-37.
143. Matsui, A., Ishida, J., Morosawa, T., Mochizuki, Y., Kaminuma, E., Endo, T.A., Okamoto, M., Nambara, E., Nakajima, M., Kawashima, M., Satou, M., Kim, J.M., Kobayashi, N., Toyoda, T., Shinozaki, K., and Seki, M. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol., 49 (8), 1135-1149.
144. Matzke, M., Kanno, T., Huettel, B., Daxinger, L., and Matzke, A.J. (2007) Targets of RNA-directed DNA methylation. Curr. Opin. Plant Biol., 10 (5), 512-519.
145. Zeller, G., Henz, S.R., Widmer, C.K., Sachsenberg, T., Ratsch, G., Weigel, D., and Laubinger, S. (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J., 58 (6), 1068-1082.
146. Chinnusamy, V. and Zhu, J.K. (2009) Epigenetic regulation of stress responses in plants. Curr. Opin. Plant Biol., 12 (2), 133-139.
147. Jaenisch, R. and Bird, A. (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet, 33 (Suppl.), 245-254.
148. Salazar, J.D., Saithong, T., Brown, P.E., Foreman, J., Locke, J.C.W., Halliday, K.J., Carre, I.A., Rand, D.A., and Millar, A.J. (2009) Prediction of photoperiodic regulators from quantitative gene circuit models. Cell, 139 (6), 1170-1179.
149. Li, Y., Roycewicz, P., Smith, E., and Borevitz, J.O. (2006) Genetics of local adaptation in the laboratory: flowering time quantitative trait loci under geographic and seasonal conditions in Arabidopsis. PLoS one, 1 (1), e105.
150. Scarcelli, N., Cheverud, J.M., Schaal, B.A., and Kover, P.X. (2007) Antagonistic pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus. Proc. Natl. Acad. Sci. USA, 104 (43), 16986-16991.
151. Scarcelli, N. and Kover, P.X. (2009) Standing genetic variation in FRIGIDA mediates experimental evolution of flowering time in Arabidopsis. Mol. Ecol., 18 (9), 2039-2049.
152. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408 (6814), 796-815.
153. Project, I.R.G.S. (2005) The map-based sequence of the rice genome. Nature, 436 (7052), 793-800.
154. Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., Depamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C.J., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G. Van de Peer, Y., and Rokhsar, D. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313 (5793), 1596-1604.
155. Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyere, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pe, M.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A.F., Weissenbach, J., Quetier, F., and Wincker, P. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449 (7161), 463-467.
156. Zharkikh, A., Troggio, M., Pruss, D., Cestaro, A., Eldrdge, G., Pindo, M., Mitchell, J.T., Vezzulli, S., Bhatnagar, S., Fontana, P., Viola, R., Gutin, A., Salamini, F., Skolnick, M., and Velasco, R. (2008) Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: problems and solutions. J. Biotechnol., 136 (1-2), 38-43.
157. Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J.H., Senin, P., Wang, W., Ly, B.V., Lewis, K.L., Salzberg, S.L., Feng, L., Jones, M.R., Skelton, R.L., Murray, J.E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Tang, H., Lyons, E., Paull, R.E., Michael, T.P., Wall, K., Rice, D.W., Albert, H., Wang, M.L., Zhu, Y.J., Schatz, M., Nagarajan, N., Acob, R.A., Guan, P., Blas, A., Wai, C.M., Ackerman, C.M., Ren, Y., Liu, C., Wang, J., Na, J.K., Shakirov, E.V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J.E., Gschwend, A.R., Delcher, A.L., Singh, R., Suzuki, J.Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Perez, R., Torres, M.J., Feltus, F.A., Porter, B., Li, Y., Burroughs, A.M., Luo, M.C., Liu, L., Christopher, D.A., Mount, S.M., Moore, P.H., Sugimura, T., Jiang, J., Schuler, M.A., Friedman, V., Mitchell-Olds, T., Shippen, D.E., dePamphilis, C.W., Palmer, J.D., Freeling, M., Paterson, A.H., Gonsalves, D., Wang, L., and Alam, M. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Carica papaya). Nature, 452 (7190), 991-996.
158. Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A.K., Chapman, J., Feltus, F.A., Gowik, U., Grigoriev, I.V., Lyons, E., Maher, C.A., Martis, M., Narechania, A., Otillar, R.P., Penning, B.W., Salamov, A.A., Wang, Y., Zhang, L., Carpita, N.C., Freeling, M., Gingle, A.R., Hash, C.T., Keller, B., Klein, P., Kresovich, S., McCann, M.C., Ming, R., Peterson, D.G., Mehboobur, R., Ware, D., Westhoff, P., Mayer, K.F., Messing, J., and Rokhsar, D.S. (2009) The sorghum bicolor genome and the diversification of grasses. Nature, 457 (7229), 551-556.
159. Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W.J., Wang, X., Xie, B., Ni, P., Ren, Y., Zhu, H., Li, J., Lin, K., Jin, W., Fei, Z., Li, G., Staub, J., Kilian, A., van der Vossen, E.A., Wu, Y., Guo, J., He, J., Jia, Z., Tian, G., Lu, Y., Ruan, J., Qian, W., Wang, M., Huang, Q., Li, B., Xuan, Z., Cao, J., Asan, Wu, Z., Zhang, J., Cai, Q., Bai, Y., Zhao, B., Han, Y., Li, Y., Li, X., Wang, S., Shi, Q., Liu, S., Cho, W.K., Kim, J.Y., Xu, Y., Heller-Uszynska, K., Miao, H., Cheng, Z., Zhang, S., Wu, J., Yang, Y., Kang, H., Li, M., Liang, H., Ren, X., Shi, Z., Wen, M., Jian, M., Yang, H., Zhang, G., Yang, Z., Chen, R., Ma, L., Liu, H., Zhou, Y., Zhao, J., Fang, X., Fang, L., Liu, D., Zheng, H., Zhang, Y., Qin, N., Li, Z., Yang, G., Yang, S., Bolund, L., Kristiansen, K., Li, S., Zhang, X., Wang, J., Sun, R. Zhang, B., Jiang, S., and Du, Y. (2009) The genome of the cucumber, Cucumis sativus L. Nat. Genet., 41 (12), 1275-1281.
160. Schnable, P.S., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T.A., Minx, P., Reily, A.D., Courtney, L., Kruchowski, S.S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S.M., Belter, E., Du, F., Kim, K., Abbott, R.M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S.M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M.J., McMahan, L., Van Buren, P., Vaughn, M.W., Ying, K., Yeh, C.T., Emrich, S.J., Jia, Y., Kalyanaraman, A., Hsia, A.P., Barbazuk, W.B., Baucom, R.S., Brutnell, T.P., Carpita, N.C., Chaparro, C., Chia, J.M., Deragon, J.M., Estill, J.C., Fu, Y., Jeddeloh, J.A., Han, Y., Lee, H., Li, P., Lisch, D.R., Liu, S., Liu, Z., Nagel, D.H., McCann, M.C., SanMiguel, P., Myers, A.M., Nettleton, D., Nguyen, J., Penning, B.W., Ponnala, L., Schneider, K.L., Schwartz, D.C., Sharma, A., Soderlund, C., Springer, N.M., Sun, Q., Wang, H., Waterman, M., Westerman, R., Wolfgruber, T.K., Yang, L., Yu, Y., Zhang, L., Zhou, S., Zhu, Q., Bennetzen, J.L., Dawe, R.K., Jiang, J., Jiang, N., Presting, G.G., Wessler, S.R., Aluru, S., Martienssen, R.A., Clifton, S.W., McCombie, W.R., Wing, R.A., and Wilson, R.K. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956), 1112-1115.
161. Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D.L., Song, Q., Thelen, J.J., Cheng, J., Xu, D., Hellsten, U., May, G.D., Yu, Y., Sakurai, T., Umezawa, T., Bhattacharyya, M.K., Sandhu, D., Valliyodan, B., Lindquist, E., Peto, M., Grant, D., Shu, S., Goodstein, D., Barry, K., Futrell-Griggs, M., Abernathy, B., Du, J., Tian, Z., Zhu, L., Gill, N., Joshi, T., Libault, M., Sethuraman, A., Zhang, X.C., Shinozaki, K., Nguyen, H.T., Wing, R.A., Cregan, P., Specht, J., Grimwood, J., Rokhsar, D., Stacey, G., Shoemaker, R.C., and Jackson, S.A. (2010) Genome sequence of the palaeopolyploid soybean. Nature, 463 (7278), 178-183.
162. Initiative, T.I.B. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463 (7282), 763-768.
163. Delseny, M., Han, B., and Hsing, Y.I. (2010) High throughput DNA sequencing: the new sequencing revolution. Plant Sci., 179 (5), 407-422.
164. Edwards, D. and Batley, J. (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J., 8 (1), 2-9.
165. Varshney, R.K., Nayak, S.N., May, G.D., and Jackson, S.A. (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol., 27 (9), 522-530.
166. Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., Fontana, P., Bhatnagar, S.K., Troggio, M., Pruss, D., Salvi, S., Pindo, M., Baldi, P., Castelletti, S., Cavaiuolo, M., Coppola, G., Costa, F., Cova, V., Dal Ri, A., Goremykin, V., Komjanc, M., Longhi, S., Magnago, P., Malacarne, G., Malnoy, M., Micheletti, D., Moretto, M., Perazzolli, M., Si-Ammour, A., Vezzulli, S., Zini, E., Eldredge, G., Fitzgerald, L.M., Gutin, N., Lanchbury, J., Macalma, T., Mitchell, J.T., Reid, J., Wardell, B., Kodira, C., Chen, Z., Desany, B., Niazi, F., Palmer, M., Koepke, T., Jiwan, D., Schaeffer, S., Krishnan, V., Wu, C., Chu, V.T., King, S.T., Vick, J., Tao, Q., Mraz, A., Stormo, A., Stormo, K., Bogden, R., Ederle, D., Stella, A., Vecchietti, A., Kater, M.M., Masiero, S., Lasserre, P., Lespinasse, Y., Allan, A.C., Bus, V., Chagne, D., Crowhurst, R.N., Gleave, A.P., Lavezzo, E., Fawcett, J.A., Proost, S., Rouze, P., Sterck, L., Toppo, S., Lazzari, B., Hellens, R.P., Durel, C.E., Gutin, A., Bumgarner, R.E., Gardiner, S.E., Skolnick, M., Egholm, M., Van de Peer, Y., Salamini, F., and Viola, R. (2010) The genome of the domesticated apple (Malus x domestica Malus x domestica). Nat. Genet., 42 (10), 833-839.
167. Argout, X., Salse, J., Aury, J.M., Guiltinan, M.J., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S.N., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier-Goud, M., Barbosa-Neto, J.F., Sabot, F., Kudrna, D., Ammiraju, J.S., Schuster, S.C., Carlson, J.E., Sallet, E., Schiex, T., Dievart, A., Kramer, M., Gelley, L., Shi, Z., Berard, A., Viot, C., Boccara, M., Risterucci, A.M., Guignon, V., Sabau, X., Axtell, M.J., Ma, Z., Zhang, Y., Brown, S., Bourge, M., Golser, W., Song, X., Clement, D., Rivallan, R., Tahi, M., Akaza, J.M., Pitollat, B., Gramacho, K., D'Hont, A., Brunel, D., Infante, D., Kebe, I., Costet, P., Wing, R., McCombie, W.R., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., and Lanaud, C. (2011) The genome of Theobroma cacao. Nat. Genet., 43 (2), 101-108.
168. Shulaev, V., Sargent, D.J., Crowhurst, R.N., Mockler, T.C., Folkerts, O., Delcher, A.L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S.P., Burns, P., Davis, T.M., Slovin, J.P., Bassil, N., Hellens, R.P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O.R., Jensen, R.V., Allan, A.C., Michael, T.P., Setubal, J.C., Celton, J.M., Rees, D.J., Williams, K.P., Holt, S.H., Rojas, J.J., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S.A., Troggio, M., Viola, R., Ashman, T.L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H.D., Bryant, D.W. Jr., Fox, S.E., Givan, S.A., Wilhelm, L.J., Naithani, S., Christoffels, A., Salama, D.Y., Carter, J., Girona, E.L., Zdepski, A., Wang, W., Kerstetter, R.A., Schwab, W., Korban, S.S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J.L., Salzberg, S.L., Dickerman, A.W., Velasco, R., Borodovsky, M., Veilleux, R.E., and Folta, K.M. (2010) The genome of woodland strawberry (Fragaria vesca). Nat. Genet., 43, 109-116.
169. Ganal, M.W., Altmann, T., and Roder, M.S. (2009) SNP identification in crop plants. Curr. Opin. Plant Biol., 12 (2), 211-217.
170. Imelfort, M., Duran, C., Batley, J., and Edwards, D. (2009) Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol. J., 7 (4), 312-317.
171. You, F.M., Huo, N., Deal, K.R., Gu, Y.Q., Luo, M.C., McGuire, P.E., Dvorak, J., and Anderson, O.D. (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics, 12 (1), 59.
172. Myles, S., Chia, J.M., Hurwitz, B., Simon, C., Zhong, G.Y., Buckler, E., and Ware, D. (2010) Rapid genomic characterization of the genus Vitis. PLoS One, 5 (1), e8219.
173. Hyten, D.L., Cannon, S.B., Song, Q., Weeks, N., Fickus, E.W., Shoemaker, R.C., Specht, J.E., Farmer, A.D., May, G.D., and Cregan, P.B. (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics, 11, 38.
174. Barbazuk, W.B., Emrich, S.J., Chen, H.D., Li, L., and Schnable, P.S. (2007) SNP discovery via 454 transcriptome sequencing. Plant J., 51 (5), 910-918.
175. Salekdeh, G.H., Reynolds, M., Bennett, J., and Boyer, J. (2009) Conceptual framework for drought phenotyping during molecular breeding. Trends Plant Sci., 14 (9), 488-496.
176. Finkel, E. (2010) Genetic resources. Parlous times for seed banks spell trouble for Australian agriculture. Science, 329 (5999), 1591.
177. Furbank, R.T. (2009) Plant phenomics: from gene to form and function. Funct. Plant Biol., 36 (11), v-vi
178. Nagel, K.A., Kastenholz, B., Jahnke, S., van Dusschoten, D., Aach, T., Muhlich, M., Truhn, D., Scharr, H., Terjung, S., Walter, A., and Schurr, U. (2009) Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping. Funct. Plant Biol., 36 (11), 947-959.
179. Yazdanbakhsh, N. and Fisahn, J. (2009) High throughput phenotyping of root growth dynamics, lateral root formation, root architecture and root hair development enabled by PlaRoM. Funct. Plant Biol., 36 (11), 938-946.
180. Jansen, M., Gilmer, F., Biskup, B., Nagel, K.A., Rascher, U., Fischbach, A., Briem, S., Dreissen, G., Tittmann, S., Braun, S., De Jaeger, I., Metzlaff, M., Schurr, U., Scharr, H., and Walter, A. (2009) Simultaneous phenotyping of leaf growth and chlorophyll fluorescence via GROWSCREEN FLUORO allows detection of stress tolerance in Arabidopsis thaliana and other rosette plants. Funct. Plant Biol., 36 (11), 902-914.
181. Moran, M.S., Inoue, Y., and Barnes, E.M. (1997) Opportunities and limitations for image-based remote sensing in precision crop management. Remote Sens. Environ., 61 (3), 319-346.
182. Möller, M., Alchanatis, V., Cohen, Y., Meron, M., Tsipris, J., Naor, A., Ostrovsky, V., Sprintsin, M., and Cohen, S. (2007) Use of thermal and visible imagery for estimating crop water status of irrigated grapevine. J. Exp. Bot., 58 (4), 827-838.
183. Berger, B., Parent, B., and Tester, M. (2010) High-throughput shoot imaging to study drought responses. J. Exp. Bot., 61 (13), 3519-3528.
184. Rajendran, K., Tester, M., and Roy, S.J. (2009) Quantifying the three main components of salinity tolerance in cereals. Plant Cell Environ., 32 (3), 237-249.
185. Sadok, W., Naudin, P., Boussuge, B., Muller, B., Welcker, C., and Tardieu, F. (2007) Leaf growth rate per unit thermal time follows QTL-dependent daily patterns in hundreds of maize lines under naturally fluctuating conditions. Plant Cell Environ., 30 (2), 135-146.