Populus responses to edaphic and climatic cues: Emerging evidence from systems biology research

Critical Reviews in Plant Sciences

Volumn 28, Issue 5, 2009, Pages 368-374

  Wullschleger, Stan D ^a   Weston, David J ^a   Davis, John M ^b  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

Environmental stress; Forestry; Genomics; Molecular biology; Nutrients; Trees

Indexed keywords

POPULUS; POPULUS TRICHOCARPA;

EID: 77449141901     PISSN: 07352689     EISSN: 15497836     Source Type: Journal    
DOI: 10.1080/07352680903241246     Document Type: Article

References (63)

1. Andersson, A., Keskitalo, J., Sjodin, A., Bhalerao, R., Sterky, F., Wissel, K., Tandre, K., Aspeborg, H., Moyle, R., Ohmiya, Y., Bhalerao, R., Brunner, A., Gustafsson, P., Karlsson, J., Lundeberg, J., Nilsson, O., Sand-berg, G., Strauss, S., Sundberg, B., Uhlen, M., Jansson, S., and Nilsson, P. 2004. A transcriptional timetable of autumn senescence. Genome Biol. 5: R24.
2. Azri, W., Chambon, C., Herbette, S., Brunel, N., Coutand, C., Leple, J.-C., Rejeb, I.B., Ammar, S., Julien, J.-L., and Roeckel-Drevet, P. 2009. Proteome analysis of apical and basal regions of poplar stems under gravitrophic stimulation. Physiol. Plant. 136:193-208.
3. Benedict, C., Skinner, J. S., Meng, R., Chang, Y., Bhalerao, R., Huner, N.P.A., Finn, C. E., Chen, T.H.H., and Hurry, V. 2006. The CBF1-dependent low temperature signaling pathway, regulon and increase in freeze tolerance are conserved in Populus spp. Plant, Cell Environ. 29: 1259-1272.
4. Benfey, P.N., and Mitchell-Olds, T. 2008. From genotype to phenotype:Systems biology meets natural variation. Science 320: 495-497.
5. Bogeat-Triboulot, M. B., Brosché, M., Renaut, J., Jouve, L., Le Thiec, D., Fayyaz, P., Vinocur, B., Witters, E., Laukens, K., Teichmann, T., Altman, A., Hausman, J. F., Polle, A., Kangasjarvi, J., and Dreyer, E. 2007. Gradual soil water depletion results in reversible change of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions. Plant Physiol. 143: 876-892.
6. Bradshaw, H. D., Ceulemans, R., Davis, J., and Stettler, R. 2000. Emerging model systems in plant biology: Poplar (Populus) as a model forest tree. J. Plant. Growth Regul. 19: 306-313.
7. Bradshaw, H. D., and Stettler, R. F. 1993. Molecular-genetics of growth and development in Populus. 1. Triploidy in hybrid poplars. Theor. Appl. Genet. 86: 301-307.
8. Brosché, M., Vinocur, B., Alatalo, E. R., Lamminmaki, A., Teichmann, T., Ottow, E. A., Djilianov, D., Afif, D., Bogeat-Triboulot, M. B., Altman, A., Polle, A., Dreyer, E., Rudd, S., Lars, P., Auvinen, P., and Kangasjarvi, J. 2005. Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biol. 6: R101.
9. Brunner, A. M., Busov, V. B., and Strauss, S. H. 2004. Poplar genome sequence: functional genomics in an ecologically dominant plant species. Trends Plant Sci. 9: 49-56.
10. Chen, S., Li, J., Wang, S., Fritz, E., Huttermann, A., and Altman, A. 2003. Effects of NaCl on shoot growth, transpiration, ion compartmentalization, and transport in regenerated plants of Populus euphratica and Populus tomentosa. Can. J. For. Res. 33: 967-975.
11. Chinnusamy, V., Zhu, J., and Zhu J. K. 2007. Cold stress regulation of gene expression in plants. Trends in Plant Sci. 12: 444-451.
12. Coleman, G. D., Chen, T.H.H., and Fuchigami, L. H. 1992. Complementary DNA cloning of poplar bark storage protein and control of its expression by photoperiod. Plant Physiol. 98: 687-693.
13. Cooke, J.E.K., Brown, K. A., Wu, R., and Davis, J. M. 2003. Gene expression associated with N-induced shifts in resource allocation in poplar. Plant, Cell Environ. 26: 757-770.
14. Cooke, J.E.K., Martin, T.A., and Davis, J.M. 2005. Short-term physiological and developmental responses to nitrogen availability in hybrid poplar. New Phytol. 167: 41-52.
15. Cooke, J.E.K., and Weih, M. 2005. Nitrogen storage and seasonal nitrogen cycling in Populus: bridging molecular physiology and ecophysiology. New Phytol. 167: 19-30.
16. Coyle, D. R., Coleman, M. D., Durant, J. A., and Newman, L. A. 2006. Survival and growth of 31 Populus clones in South Carolina. Biomass Bioenergy 30: 750-758.
17. Dickmann, D. I., Liu, Z. J., and Nguyen, P. V. 1992. Photosynthesis, water relations, and growth of 2 hybrid Populus genotypes during a severe drought. Can. J. For. Res. 22: 1094-1106.
18. 14C in Populus deltoides during dormancy induction. Physiol. Plant. 54: 393-401.
19. DiFazio, S. P. 2005. A pioneer perspective on adaptation. New Phytol. 165: 661-664.
20. Druart, N., Johansson, A., Baba, K., Schrader, J., Sjodin, A., Bhalerao, R. R., Resman, L., Trygg, J., Moritz, T., and Bhalerao, R.P. 2007. Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stagespecific modulation of transcriptional and metabolic networks. Plant J. 50: 557-573.
21. Ferreira, S., HjernØ, K., Larsen, M., Wingsle, G., Larsen, P., Fey, S., Roepstorff, P., and Salomé Pais, M. 2006. Proteome profiling of Populus euphratica Oliv. upon heat stress. Ann. Bot. 98: 361-377.
22. Ghazalpour, A., Doss, S., Zhang, B., Wang, S., Plaisier, C., Castellanos, A. B., Schadt, E. E., Drake, T. A., Lusis, A., and Horvath, S. 2006. Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS 2:e130.
23. Goffinet, M. C. and Larson, P. R. 1981. Structural changes in Populus deltoides terminal buds and in the vascular transition zone of the stems during dormancy induction. Amer. J. Bot. 68: 118-129.
24. Guy, C., Kaplan, F., Kopka, J., Selbig, J., and Hincha, D. K. 2008. Metabolomics of temperature stress. Physiol. Plant. 132: 220-235.
25. Kieffer, P., Planchon, S., Oufir, M., Ziebel, J., Dommes, J., Hoffmann, L., Hausman, J.-F., and Renaut, J. 2009. Combining proteomics and metabolite analysis to unravel cadmium stress-response in poplar leaves. J. Proteome Res. 8: 400-417.
26. Hammer, G. L., Sinclair, T. R., Chapman, S. C., and van Oosterom, E. 2004. On systems thinking, systems biology, and the in silico plant. Plant Physiol. 134: 909-911.
27. He, C., Zhang, J., Duan, A., Zheng, S., Sun, H., and Fu, L. 2008. Proteins responding to drought and high-temperature stress in Populus x euramericana cv. 74/76. Trees 22: 803-813.
28. Howe, G. T., Gardner, G., Hackett, W. P., and Furnier, G. R. 1996. Phytochrome control of short-day-induced bud set in black cottonwood. Physiol. Plant. 97: 95-103.
29. 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-responsive path-way are conserved in Brassica napus and other plant species. Plant Physiol. 127: 910-917.
30. Jansson, S., and Douglas, C. J. 2007. Populus: A model system for plant biology. Annu. Rev. Plant Biol. 58: 435-458.
31. Lee, B. H., Henderson, D. A., and Zhu, J. K. 2005. The Arabidopsis cold- responsive transcriptome and its regulation by ICE1. Plant Cell 17: 3155-3175.
32. Li, L. G., Lu, S. F., and Chiang, V. 2006. A genomic and molecular view of wood formation. Crit. Rev. Plant Sci. 25: 215-233.
33. Lough, T. J., and Lucas, W. J. 2006. Integrative plant biology: Role of phloem long-distance macromolecular trafficking. Annu. Rev. Plant Biol. 57: 203-232.
34. Lu, S., Sun, Y.-H., and Chang, V. L. 2008. Stress-responsive microRNAs in Populus. Plant J. 55: 131-151.
35. Millard, P., Sommerkorn, M., and Grelet, G.-A. 2007. Environmental change and carbon limitation in trees: a biochemical, ecophysiological and ecosystem appraisal. New Phytol. 175: 11-28.
36. Monclus, R., Dreyer, E., Villar, M., Delmotte, F. M., Delay, D., Petit, J.-M., Barbaroux, C., Le Thiec, D., Bréchet, C., and Brignolas, F. 2005. Impact of drought on productivity and water use efficiency in 29 genotypes of Populus deltoides x Populus nigra. New Phytol. 169: 765-777.
37. Nanjo, T., Futamura, N., Nishiguchi, M., Igasaki, T., Shinozaki, K., and Shinohara, K. 2004. Characterization of full-length enriched expressed se- quencetagsofstress-treatedpoplarleaves.Plant Cell Physiol.45:1738-1748.
38. Nelson E. A. and Dickson, R. D. 1981 Accumulation of food reserves in cottonwood stems during dormancy induction. Can. J. For. Res. 11: 145-154.
39. Novaes, E., Osorio, L., Drost, D. R., Miles, B. L., Novaes, C.R.D.B., Benedict, C., Dervinis, C., Yu, Q., Sykes, R., Davis, M., Martin, T. A., Peter, G. F., and Kirst, M. 2009. Genetic analysis of nitrogen effect on biomass and wood chemistry of Populus identifies a major pleiotropic locus that links tree growth and wood properties. New Phytol. (in press).
40. Plomion, C., Lalanne, C., Claverol, S., Meddour, H., Kohler, A., Bogeat-Triboulot, M. B., Barre, A., Le Provost, G., Dumazet, H., Jacob, D., Bastien, C., Dreyer, E., de Daruvar, A., Guehl, J.M., Schmitter, J. M., Martin, F., and Bonneu, M. 2006. Mapping the proteome of poplar and application to the discovery of drought-stress responsive proteins. Proteomics 6: 6509-6527.
41. Rohde, A. and Bhalerao, R. P. 2007. Plant dormancy in the perennial context. Trends Plant Sci. 12: 217-223.
42. Rohde, A., Prinsen, E., DeRycke, R., Engler, G., VanMontagu, M., and Boerjan, W. 2002. PtABI3 impinges on the growth and differentiation of embryonic leaves during bud set in poplar. Plant Cell 14: 1885-1901.
43. Ruonala, R., Rinne, P.L.H., Baghour, M., Moritz, T., Tuominen, H., and Kangajarvi, J. 2006. Transitions in the functioning of the shoot apical meris- tem in birch (Betula pendula) involve ethylene. Plant J. 46: 628-640.
44. Ruttink, T., Arend, M., Morreel, K., Storme, V., Rombauts, S., Fromm, J., Bhalerao, R. P., Boerjan, W., and Rohde, A. 2007. A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell 19: 2370-2390.
45. Samuelson, L. J., Stokes, T. A., and Coleman, M. D. 2007. Influence of irri- gation and fertilization on transpiration and hydraulic properties of Populus deltoides. Tree Physiol. 27: 765-774.
46. Sterky, F., Regan, S., Karlsson, J., Hertzberg, M., Rohde, A., Holmberg, A., Amini, B., Bhalerao, R., Larsson, M., Villarroel, R., van Montagu, M., Sandberg, G., Olsson, O., Teeri, T.T., Boerjan, W., Gustafsson, P., Uhlen, M., Sundberg, B., and Lundeberg, J. 1998. Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags. Proc. Nat. Acad. Sci. USA 22: 13330-13335.
47. Street, N. R., Skogström, O., Sjödin, A., Tucker, J., Rodríguez-Acosta, M., Nilsson, P., Jansson, S., and Taylor, G. 2006. The genetics and genomics of the drought response in Populus. Plant J. 48: 321-341.
48. Taylor, G. 2002. Populus: Arabidopsis for forestry: Do we need a model tree? Ann. Bot. 90: 681-689.
49. Tschaplinski, T. J., Tuskan, G. A., Gebre, G. M., and Todd, D. E. 1998. Drought resistance of two hybrid Populus clones grown in a large-scale plantation. Tree Physiol. 18: 653-658.
50. 2 poplar pedigree grown in contrasting environments. Tree Phyiol. 26: 595-604.
51. Tuskan, G. A., DiFazio, S. P., and Teichmann, T. 2004. Poplar genomics is getting poplar: The impact of the poplar genome project on tree research. Plant Biol. 6: 2-4.
52. 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: 1596-1604.
53. Weston, D. J., Gunter, L. E., Rogers, A., and Wullschleger, S. D. 2008. Connecting genes, coexpression modular signatures to environmental stress phe- notypes in plants. BMC Sys. Biol. 2: 16.
54. Wisniewski, M., Suater, J., Fuchigami, L., and Stepien, V. 1997. Effects of near- lethal heat stress on bud break, heat-shock proteins and ubiquitin in dormant poplar (Populus nigra Charkowiensis x P. nigra incrassata). Tree Physiol. 17: 453-460.
55. Woolbright, S. A., DiFazio, S. P., Yin, T., Martinsen, G. D., Zhang, X., Allan, G.J., Whitham, T. G., and Keim, P. 2008. A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree. Heredity 100: 59-70.
56. Wu, R. L., Hu, X. S., and Han, Y. F. 2000. Molecular genetics and developmental physiology: Implications for designing better forest crops. Crit. Rev. Plant Sci. 5: 377-393.
57. Wullschleger, S. D., Jansson, S., and Taylor, G. 2002a. Genomics and forest biology: Populus emerges as the perennial favorite. Plant Cell 14: 2651-2655.
58. Wullschleger, S. D., Tuskan, G. A., and DiFazio, S. P. 2002b. Genomics and the tree physiologist. Tree Physiol. 22: 1273-1276.
59. Wullschleger, S. D., Yin, T. M., DiFazio, S. P., Tschaplinski, T. J., Gunter, L. E., Davis, M. F., and Tuskan, G. A. 2005. Phenotypic variation in growth and biomass distribution for two advanced-generation pedigrees of hybrid poplar. Can. J. For. Res. 35: 1779-1789.
60. Xiao, X., Yang, F., Zhang, S., Korpelainen, H., and Li, C. 2009. Physiological and proteomic responses of two contrasting Populus cathayana populations to drought stress. Physiol. Plant. 136: 150-168.
61. Yin, T. M., Zhang, X. Y., Gunter, L. E., Li, S. X., Wullschleger, S. D., Huang, M. R., and Tuskan, G. A. 2009. Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome. New Phytol. 181: 498-503.
62. Zhang, B. and Horvath, S. 2005. A general framework for weighted gene coexpression network analysis. Stat. Appl. Genet. Mol. Biol. 4:Article17.
63. Zhu, J., Dong, C. H., and Zhu, J. K. 2007. Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Cur. Opin. Plant Biol. 10: 290-295.