11 Development and Systems Biology: Riding the Genomics Wave towards a Systems Understanding of Root Development
Annual Plant Reviews book series, Volume 35: Plant Systems Biology
II. Plant Systems Biology: Enumerating and Integrating the System Components
Siobhan M. Brady,
Philip N. Benfey,
Siobhan M. Brady
Duke University, Department of Biology and the Institute for Genome Science and Policy, Durham, NC, USA
Search for more papers by this authorPhilip N. Benfey
Duke University, Department of Biology and the Institute for Genome Science and Policy, Durham, NC, USA
Search for more papers by this authorSiobhan M. Brady,
Philip N. Benfey,
Siobhan M. Brady
Duke University, Department of Biology and the Institute for Genome Science and Policy, Durham, NC, USA
Search for more papers by this authorPhilip N. Benfey
Duke University, Department of Biology and the Institute for Genome Science and Policy, Durham, NC, USA
Search for more papers by this authorFirst published: 24 April 2018
This article was originally published in 2009 in Plant Systems Biology, Volume 35 (ISBN 9781405162838) of the Annual Plant Reviews book series, this volume edited by Gloria M. Coruzzi and Rodrigo A. Gutíerrez. The article was republished in Annual Plant Reviews online in April 2018.
Abstract
Systems biology approaches have recently garnered much interest in plant biology, primarily due to the massive increase of data obtained using genomic approaches. One advantage of using these approaches is the elucidation of emergent behaviour, or a complex pattern, which results from the interaction of simple components. The use of systems biology approaches to understand root development at various scales, including transcriptional networks that regulate cell identity, dynamic cellular behaviour that contributes to root growth and physical root architecture will be explored.
References
- Beemster, G.T.S. and Baskin, T.I. (1998) Analysis of cell division and elongation underlying the developmental acceleration of root growth in Arabidopsis thaliana . Plant Physiol 116 (4), 1515–1526.
- Benfey, P.N. and Scheres, B. (2000) Curr Biol 10 (22), R813.
- Benkova, E., Michniewicz, M., Sauer, M., Teichmann, T., Seifertova, D., Jurgens, G., et al. (2003) Cell 115 (5), 591.
- Bennett, M.J., Marchant, A., Green, H.G., May, S.T., Ward, S.P., Millner, P.A., et al. (1996) Science 273 (5277), 948.
- Birnbaum, K., Jung, J.W., Wang, J.Y., Lambert, G.M., Hirst, J.A., Galbraith, D.W., et al. (2005) Nat Methods 2 (8), 615.
- Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W., et al. (2003) Science 302 (5652), 1956.
- Blancaflor, E.B., Fasano, J.M. and Gilroy S. (1998) Plant Physiol 116 (1), 213.
- Blilou, I., Xu, J., Wildwater, M., Willemsen, V., Paponov, I., Friml, J., et al. (2005) Nature 433 (7021), 39.
- Brady, S.M., Orlando, D.A., Lee, J.-Y., Wang, J.Y., Koch, J., Dinneny, J.R., et al. (2007) 318 (5851), 801.
- Campilho, A., Garcia, B., Toorn, H.V.D., Wijk, H.V., Campilho, A. and Scheres, B. (2006) Plant J 48 (4), 619.
- Cannon, W.A. (1949) Ecology 30, 542.
- Cristina, M., Sessa, G., Dolan, L., Linstead, P., Baima, S., Ruberti, I., et al. (1996) Plant J 10 (3), 393.
- Cui, H., Levesque, M.P., Vernoux, T., Jung, J.W., Paquette, A.J., Gallagher, K.L., et al. (2007) Science 316 (5823), 421.
- Davuluri, R., Sun, H., Palaniswamy, S., Matthews, N., Molina, C., Kurtz, M., et al. (2003) BMC Bioinformatics 4 (1), 25.
- De Smet, I., Tetsumura, T., De Rybel, B., Frey, N.F.D., Laplaze, L., Casimiro, I., et al. (2007) Development 134 (4), 681.
- Deplancke, B., Dupuy, D., Vidal, M. and Walhout, A.J.M. (2004) Genome Res 14 (10b), 2093.
- Deplancke, B., Mukhopadhyay, A., Ao, W., Elewa, A.M., Grove, C.A., Martinez, N.J., et al. (2006) Cell 125 (6), 1193.
- Di Laurenzio, L., Wysocka-Diller, J., Malamy, J.E., Pysh, L., Helariutta, Y., Freshour, G., et al. (1996) Cell 86 (3), 423.
- Dolan, L., Janmaat, K., Willemsen, V., Linstead, P., Poethig, S., Roberts, K., et al. (1993) Development 119, 71.
- Eshel, A. (1998) Plant Cell Environ 21, 247.
- Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., et al. (2007) PLoS ONE 2 (2), e219, doi.1371/journal.pone.0000219.
- Friml, J., Wisniewska, J., Benkova, E., Mendgen, K. and Palme, K. (2002) Nature 415 (6873), 806.
- Goff, S.A., Ricke, D., Lan, T.-H., Presting, G., Wang, R., Dunn, M., et al. (2002) Science 296 (5565), 92.
- Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L., et al. (2005) Bioinformatics 21 (10), 2568.
- Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., et al. (2004) Nature 431 (7004), 99.
- Heidstra, R., Welch, D. and Scheres, B. (2004) Genes Dev 18 (16), 1964.
- Helariutta, Y., Fukaki, H., Wysocka-Diller, J., Nakajima, K., Jung, J., Sena, G., et al. (2000) Cell 101 (5), 555.
- Hocholdinger, F., Park, W.J., Sauer, M. and Woll, K. (2004) Trends Plant Sci 9 (1), 42.
- Ideker, T., Galitski, T. and Hood, L. (2001) Annu Rev Genom Human Genet 2 (1), 343.
- Ioio, R.D., Linhares, F.S., Scacchi, E., Casamitjana-Martinez, E., Heidstra, R., Costantino, P., et al. (2007) Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation. Curr Biol 17, 678–682.
- Itoh, H., Washio, T. and Tomita, M. (2004) RNA 10 (7), 1005.
- Jiang, K., Zhang, S., Lee, S., Tsai, G., Kim, K., Huang, H., et al. (2006) Plant Mol Biol 60 (3), 343.
- Jones-Rhoades, M.W. and Bartel, D.P. (2004) Mol Cell 14 (6), 787.
- Jones-Rhoades, M.W., Bartel, D.P. and Bartel, B. (2006) Annu Rev Plant Biol 57 (1), 19.
- Kawaguchi, R. and Bailey-Serres, J. (2005) Nucleic Acids Res 33 (3), 955.
- Keene, J.D. (2003) Nat Genet 33 (2), 111.
- Keene, J.D., Komisaraow, J.M. and Friedersdorf, M.B. (2006) Nat Protocols 1, 302.
- Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., et al. (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, 347–363.
- Kutschera, L. (1960) Wurzelatlas Mitteleuropaischer Ackerunkrauter und Kulturpflanzen (Frankfurt am main, Germany: DLG Verlag).
- Lee, J.-Y., Colinas, J., Wang, J.Y., Mace, D., Ohler, U. and Benfey, P.N. (2006) PNAS 103 (15), 6055.
- Lee, M.M. and Schiefelbein, J. (1999) Cell 99 (5), 473.
- Lee, M.M. and Schiefelbein, J. (2002) Plant Cell 14 (3), 611.
- Levesque, M.P., Vernoux, T., Busch, W., Cui, H., Wang, J.Y., Blilou, I., et al. (2006) PLoS Biol 4 (5), e143.
- Ljung, K., Hull, A.K., Celenza, J., Yamada, M., Estelle, M., Normanly, J., et al. (2005) Plant Cell 17 (4), 1090.
- Luschnig, C., Gaxiola, R.A., Grisafi, P. and Fink, G.R. (1998) Genes Dev 12 (14), 2175.
- Mahonen, A.P., Bonke, M., Kauppinen, L., Riikonen, M., Benfey, P.N. and Helariutta, Y. (2000) Genes Dev 14 (23), 2938.
- Masucci, J.D., Rerie, W.G., Foreman, D.R., Zhang, M., Galway, M.E., Marks, M.D., et al. (1996) Development 122 (4), 1253.
- Messerli, G., Partovi Nia, V., Trevisan, M., Kolbe, A., Schauer, N., Geigenberger, P., et al. (2007) Plant Physiol 143 (4), 1484.
- Nakajima, K., Sena, G., Nawy, T. and Benfey, P.N. (2001) Nature 413 (6853), 307.
- Nakano, M., Nobuta, K., Vemaraju, K., Tej, S.S., Skogen, J.W. and Meyers, B.C. (2006) Nucleic Acids Res 34 (Suppl 1), D731.
- Nawy, T., Lee, J.-Y., Colinas, J., Wang, J.Y., Thongrod, S.C., Malamy, J.E., et al. (2005) Plant Cell 17 (7), 1908.
- Nielsen, K.L., Lynch, J.P. and Weiss, H.N. (1997) Am J Bot 84 (1), 26.
- O'Connor, T.R., Dyreson, C. and Wyrick, J.J. (2005) Bioinformatics 21 (24), 4411.
- Pages, L., Vercambre, G., Drouet, J.-L., Lecompte, F., Collet, C. and Le Bot, J. (2004) Plant Soil 258, 103.
- Pitts, R.J., Cernac, A. and Estelle, M. (1998) Plant J 16 (5), 553.
- Przemeck, G.K.H., Mattson, J., Hardtke, C.S., Sung, Z.R. and Berleth, T. (1996) Planta 200, 229.
- Ryu, K.H., Kang, Y.H., Park, Y.-H., Hwang, I., Schiefelbein, J. and Lee, M.M. (2005) Development 132 (21), 4765.
- Sabatini, S., Beis, D., Wolkenfelt, H., Murfett, J., Guilfoyle, T., Malamy, J., et al. (1999) Cell 99 (5), 463.
- Sabatini, S., Heidstra, R., Wildwater, M. and Scheres, B. (2003) Genes Dev 17 (3), 354.
- Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., et al. (2005) Nat Genet 37 (5), 501.
- Spencer, M.W.B., Casson, S.A. and Lindsey, K. (2006) Plant Physiol 143, 924.
- Swarup, R., Friml, J., Marchant, A., Ljung, K., Sandberg, G., Palme, K., et al. (2001) Genes Dev 15 (20), 2648.
- Swarup, R., Kramer, E.M., Perry, P., Knox, K., Leyser, H.M.O., Haseloff, J., et al. (2005) Nat Cell Biol 7 (11), 1057.
- The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (6814), 796.
- Tian, Q. and Reed, J.W. (1999) Development 126 (4), 711.
- Van Der Weele, C.M., Jiang, H.S., Palaniappan, K.K., Ivanov, V.B., Palaniappan, K. and Baskin, T.I. (2003) A new algorithm for computational image analysis of deformable motion at high spatial and temporal resolution applied to root growth. Roughly uniform elongation in the meristem and also, after an abrupt acceleration, in the elongation zone. Plant Physiol 132, 1138–1148.
- Vanneste, S., De Rybel, B., Beemster, G.T.S., Ljung, K., De Smet, I., Van Isterdael, G., et al. (2005) Plant Cell 17 (11), 3035.
- Walk, T.C., Van Erp, E. and Lynch, J.P. (2004) Ann Bot 94 (1), 119.
- Woll, K., Borsuk, L.A., Stransky, H., Nettleton, D., Schnable, P.S. and Hochholdinger, F. (2005) Plant Physiol 139 (3), 1255.
- Yu, J., Hu, S., Wang, J., Wong, G.K.-S., Li, S., Liu, B., et al. (2002) Science 296 (5565), 79.
- Zanetti, M.E., Chang, I.-F., Gong, F., Galbraith, D.W. and Bailey-Serres, J. (2005) Plant Physiol 138 (2), 624.
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