When we think of evolution, we often think about physical changes, like a plant developing broader leaves to collect more solar energy. Such evolution actually occurs within the plant’s DNA. I am using computational analysis and modeling to visualize how plant genomes have evolved over time, particularly those of staple crops. We are learning from this work to improve the range and yield of modern plants.
Using multidisciplinary approaches that combine computational analysis, modeling, and prediction with experimental verification, Doreen Ware’s lab seeks a deeper understanding of the evolution of genome sequences in plants and their implications for agricultural improvement. By looking comparatively across the genomes of plants in the same lineage, they seek answers to the following questions: How are genes conserved and lost over time? What are the fates of duplicated genes? What is the impact of structural variation on phenotypic variation? Ware’s team also studies gene regulation in plants, focusing on gene regulatory networks, targeting transcription factors and microRNA genes with the objective of understanding how these parts of the plant genome work together in determining spatial and temporal expression of genes. The lab had an important role in the project to produce a haplotype map reference genome of maize, spearheading the most comprehensive analysis of the crop yet. This has provided important information on the variation of the reference genome, as well as comparative data showing changes in the genome acquired through domestication and breeding. They have devoted special attention to examining diversity within maize, grape, and tomato, aiming to accelerate the development of strategies to introduce new germplasm that is needed to meet demands of increasing population and a changing environment. The lab also has brought fully sequenced genomes into an integrated data framework, to enhance the power of their comparative studies. This past year, Ware was named as its principal investigator for the National Science Foundation-funded Gramene project, a comparative genomics resource for agriculturally important crops and models to support sustainable food and fuel production. Ware, as principal investigator for plants, has also helped lead an effort funded by the Department of Energy to create—out of many separate streams of biological information—a single, integrated cyber-“knowledgebase” for plants and microbial life.
Liu, Z. J. and Kumari, S. and Zhang, L. F. and Zheng, Y. L. and Ware, D. (2012) Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays. PLoS ONE, 7(6) pp. e39786.
Chia, J. M. and Song, C. and Bradbury, P. J. and Costich, D. and de Leon, N. and Doebley, J. and Elshire, R. J. and Gaut, B. and Geller, L. and Glaubitz, J. C. and Gore, M. and Guill, K. E. and Holland, J. and Hufford, M. B. and Lai, J. and Li, M. and Liu, X. and Lu, Y. and McCombie, R. and Nelson, R. and Poland, J. and Prasanna, B. M. and Pyhajarvi, T. and Rong, T. and Sekhon, R. S. and Sun, Q. and Tenaillon, M. I. and Tian, F. and Wang, J. and Xu, X. and Zhang, Z. and Kaeppler, S. M. and Ross-Ibarra, J. and McMullen, M. D. and Buckler, E. S. and Zhang, G. and Xu, Y. and Ware, D. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet, 44(7) pp. 803-U238.
Brady, S. M. and Zhang, L. and Megraw, M. and Martinez, N. J. and Jiang, E. and Yi, C. S. and Liu, W. and Zeng, A. and Taylor-Teeples, M. and Kim, D. and Ahnert, S. and Ohler, U. and Ware, D. H. and Walhout, A. J. M. and Benfey, P. N. (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Molecular Systems Biology, 7 pp. 459.
Youens-Clark, K. and Buckler, E. and Casstevens, T. and Chen, C. and DeClerck, G. and Derwent, P. and Dharmawardhana, P. and Jaiswal, P. and Kersey, P. and Karthikeyan, A. S. and Lu, J. and McCouch, S. R. and Ren, L. and Spooner, W. and Stein, J. C. and Thomason, J. and Wei, S. and Ware, D. H. (2011) Gramene database in 2010: Updates and extensions. Nucleic Acids Research, 39(SUPPL.)
Paterson, A. H. and Bowers, J. E. and Bruggmann, R. and Dubchak, I. and Grimwood, J. and Gundlach, H. and Haberer, G. and Hellsten, U. and Mitros, T. and Poliakov, A. and Schmutz, J. and Spannagl, M. and Tang, H. and Wang, X. and Wicker, T. and Bharti, A. K. and Chapman, J. and Feltus, F. A. and Gowik, U. and Grigoriev, I. V. and Lyons, E. and Maher, C. A. and Martis, M. and Narechania, A. and Otillar, R. P. and Penning, B. W. and Salamov, A. A. and Wang, Y. and Zhang, L. and Carpita, N. C. and Freeling, M. and Gingle, A. R. and Hash, C. T. and Keller, B. and Klein, P. and Kresovich, S. and McCann, M. C. and Ming, R. and Peterson, D. G. and Mehboob ur, R. and Ware, D. H. and Westhoff, P. and Mayer, K. F. X. and Messing, J. and Rokhsar, D. S. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229) pp. 551-556.Additional materials of the author at
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