Progress 10/01/07 to 09/30/11
Outputs
OUTPUTS: During the project time the emphasis has changed from soybean performance under the influence of changing carbon dioxide amounts to looking in a more general way towards the genetic adaptation of plants to their environment. This idea was based on the increasing availability of genome and transcriptome information. Thus, we established a model system by asking how the genome of a close relative of Arabidopsis with a completely different "lifestyle" had been altered during recent evolutionary times. The plant is Thellungiella parvula, an extremely abiotic stress-tolerant species. Its genome is characterized by a large number of gene duplications, mostly for functions that are stress-related and stress relieving. Neo-functionalization of duplicated copies has also been obtained, e.g., that a gene expressed in roots of Arabidopsis now includes one root and one shoot expressed copy. Finally, we have seen subtle changes in amino acid composition for a number of proteins. This latter aspect, for example, provided altered ion uptake in the Thellungiella version of transporters in a way that the plant accomplished better use of nutrients (potassium, phosphate, nitrates). PARTICIPANTS: H.J. Bohnert, Professor emeritus, Dept. Plant Biologt and Dept. Crop Science, UIUC and R.L. Nelson, Professor, Dept. Crop Science, UIUC. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The work started with the search for Arabidopsis relatives - an ecological endevour. We found the plant T. parvula, living in salt flats (Lake Tuz) in central Turkey. To that we applied physiological techniques, measuring phtosynthesis, growth parameters, stress tolerances, etc. Finally, we established inbred lines (single seed, 8 generations) to obtain uniform material. The UIUC Center for Functional and Comparative Genomics sequenced nuclear DNA and transcriptomes, and over 10 months, we established the genome sequence and chromosome structure of the plant. A number of programs were used to establish this and in many cases these bioinformatics programs have been modified. The UIUC Center provided critical resources and the UIUC IT offices provided a platform for discussion and programming. Without these resources, the project would not have been successful. Out of the project, the comparison between the stress-sensitive Arabidopsis thaliana and the extremely stress-tolerant Thellungiella parvula, which is also able to grow in very degraded, resource-poor soils, allows us to draw several conclusions that can be applied to finding individuals in breeding programs that have qualities that support the growth, flowering and seed set of T. parvula. This knowledge will permit faster and precise identification of germ plasms that can be adapted to various soils and climates.
Publications
- Bressan, R.A., Reddy, M., Chung, S.H., Yun, D.J., Hardin, L.S. and Bohnert, H.J. 2010. Stress-adapted extremophiles provide energy without interference in food production. Food Security 3: e-pub, March 2011.
- Dassanayake, M., Oh, D.H., Haas, J., Hernandez, A., Ali, S., Shamimuzzaman, M., Hong, H., Yun, D.-J., Bressan, R.A., Zhu, J.-K., Bohnert, H.J. and Cheeseman, J.M. 2011. De novo genome assembly: From short reads to chromosomes for an extremophile crucifer. Nature Genetics, 43: 913-918
- Oh, D.-H., Dassanayake, M., Bohnert, H.J. and Cheeseman, J.M. 2012. Life at the extreme: Lessons from the genome. Genome Biology (Tentative Acceptance).
- Dassanayake, M., Oh, D.-H., Yun, D.-J., Bressan, R.A., Cheeseman, J.M. and Bohnert, H.J. 2011. The scope of things to come: New paradigms in biotechnology, plant biotechnology and agriculture, In: Plant Biotechnology 2011: Prospects for the 21st Century. Altman A, Hasegawa PM, eds., Academic Press (Sept 2011).
- Grene, R., Vasquez-Moreno, C. and Bohnert, H.J. 2011. Molecular biology and physiological genomics of dehydration stress. In: Desiccation Tolerance of Plants (Bartels D, Beck E, Luettge U, eds) Springer verlag, Heidelberg, Berlin, New York.
- Oh, D.H., Ali, Z., Park, H.C., Bressan, R.A., Yun, D.J. and Bohnert, H.J. 2010. Consequences of SOS1 Deficiency - Intracellular Physiology and Transcription. Plant Signaling Behaviour 5: June 2010
- Choi, W., Baek, D., Oh, D.H., Park, J., Hong, H., Bohnert, H.J., Bressan, R.A., Park, H.C. and Yun, D.J. 2010. NKS1, Na+- and K+-sensitive 1, regulates ion homeostasis in an SOS-independent pathway in Arabidopsis. Phytochemistry 72: 330-336.
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: The project has evolved into a more general study on the differences in N-use efficiency in plants. Especially, we are comapring closely related species that are distinctly different in how they are able to acquire nitrogen. One aspect that became quite clear is that micornutrient uptake capacity seems to include several categories of nutrients, i.e., effciency in N-uptake seems to be coupled to P- and Fe-uptake. PARTICIPANTS: Dr. Dong-Ha Oh, postdoctoral fellow, UIUC; Dr. Maheshi Dassanayake, postdoctoral fellow, UIUC; Ms. Hyewon Hong, graduate student, UIUC; Professor John M Cheeseman, UIUC; Professor Ray A Bressan, Pudrdue University and several people in his lab; Professor Jian-JKang Zhu, UC Riverside and KAUST Saudi Arabia; and Professor Dae-Jin Yun, Gyeongsang Natl University Korea, and people in his lab. TARGET AUDIENCES: Nutrient uptake in plants that experience stressful conditions is of utmost importance so that the yield potential is not reduced by a stress condition. PROJECT MODIFICATIONS: Suggested is a stronger focus on model species whose entire genome sequence is known, and to plants that are more easily manipulated both in their growth conditions and in terms of their biology. For both suggested species entire genome sequences are available, as are mutant colllections.
Impacts
This recognition from physiological work has then been transfered to a model in which we could do genetic and molecular work fast - Arabidopsis and Thellungiella, the latter being a relative of Arabidopsis with extremely efficient nutrient uptake capabilities. From Arabidopsis we have now defined a pathway that includes a WRKY transcripotion factor which activates three different bHLH transcription factors, one of which activates Fe- and Zn-transporters, and a second one is associated with NO3 reduction. We have no phenotype for the third bHLH factor yet. In Thellungiella, several of these components exist as tandemly repeated ORFS.
Publications
- Oh, D.-H., Lee, S.-Y., Bressan, R.A., Yun, D.-J. and Bohnert, H.J. 2010. Intracellular consequences of SOS1 deficiency during salt stress. Journal of Experimental Botany 61: 1205-1213.
- Orsini, F., Paino-dUrzo, M., Inan, G., Serra, S., Oh, D.-H., Mickelbart, M.V., Consiglio, F., Li, X., Jeong, J.C., Yun, D.-J., Bohnert, H.J., Bressan, R.A. and Maggio, A. 2010. Emerging new Arabidopsis-Relative Model Systems (ARMS): A comparative study of salt tolerance parameters in eleven wild relatives of Arabidopsis thaliana. J. Experimental Botany 61: 3787-3798.
- Oh, D.H., Dasanayake, M., Kropornika, A., Paino-dUrzo, M., Lambert, G., Galbraith, D., Bressan, R.A., Zhu, J.-K., Yun, D.-J., Cheeseman, J.M. and Bohnert, H.J. 2010. Chromosome structures of the extreme halophyte Thellungiella parvula distinguished from Thellungiella salsuginea (T. halophila) and Arabidopsis thaliana. Plant Physiology 154: 1040-1052.
- Dassanayke, M., Oh, D.H. and Cheeseman, J.M. 2010. Importance of transcription control for halophytic life. Trends Plant Science (In Press).
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Progress 11/01/08 to 10/31/09
Outputs
OUTPUTS: Because of turnover of lab personnel, the work on soybean was pushed into the background for the 2009 growing season (Dr. Indu Rupassara left the lab - see report for 2008). A manuscript is being prepared, but has not been submiteed, describing metabolite transport in the phloem and xylem for soybeans grown in the field in ambient and elevated CO2. Dissemination is through the thesis of Dr. Rupassara at present. Several other sub-projects have been advanced: One is about a comparison of different wheat lines during mild drought stresses, using Sanger-type sequencing of cDNAs and microarray hybridizations. A second topic, more important for the future, has been a focus on the newly available sequencing tools that will revolutionize how genomics studies will be conducted . manuscripts have been published. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: See project outputs section.
Impacts
In principle, the year has been used for re-tooling and preparation for another round in 2010.
Publications
- Ergen, N.Z., Thimmapuram, J., Bohnert, H.J., Budak, H. 2009. Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Funct Integrative Genomics 9: 377-396.
- Cheong, M.S., Park, H.C., Lee, S.Y., Bohnert, H.J., Bressan, R.A. and Yun, D.J. 2009. Specific domain structures control ABA, SA, and stress mediated SIZ1 phenotypes. Plant Physiology, Oct 16 [Epub ahead of print].
- Chen, K., Valiyodan, B., Trupti, J., LeNoble, M.E., Bohnert, H.J., Xu, D., Sharp, R.E. and Nguyen, H.T. 2010. Transcript regulation in the growth zone of the maize primary root during early water deficit. Journal of Experimental Botany, submitted November 2009.
- Ali, S., Wright, C.L., Lane, A., Vlach, E., Hetrick, L., Bachman, S., Vullaganti, D.R., Thimmapuram, J., Drnevich, J., Band, M., Hernandez, A.G., Avivi, A., Mikel, M.A. and Bohnert, H.J. 2010. Development of adapter free-transcriptome sequencing procedures on the GS FLX/Titanium next-generation DNA sequencing system. PLOS Biology, revised submitted December 2009.
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Progress 01/01/08 to 10/15/08
Outputs
OUTPUTS: The output for this year is two-fold. First, the garduate student working on the project has graduated in August 2008 (PhD). Ms. Rupassara has studied phleom and xylem contents, as well as leaf metabolites, of soybean varieties grown in eleveated CO2 in the FACE rings. The thesis includes a very large list of metabolites, 327 in total, many still unknown, that are found in one or the other or in all tissues. We are still working on evaluating these data for publication. Second, we have conducted and published a test experiment - growing Arabidopsis in FACE high CO2 rings. The results indicate that enetic varability is large so that some ecotypes are doing very well in high CO2. Many reactions by the plants are strictly dependent on the local weather conditions, no change in development was observed. It must however be considered that Arabidopsis has an extremely short developmental time in the field. The data have been published. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Plant breeders are the primary target audience. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The impact of the data is that this is the largest, most complete compilation of metabolites in soybeans grown in FACE rings. In addition, the detection of ecotypic variability in the response to eleveated CO2 in Arabidopsis most certainly will also be found in other crop species. While elevated CO2 can be detrimental - especially for species that do not have the possibility of diverting the excess carbon into large sinks (such as trees) - for some species, breeding can be expected to circumvent the problem. One particularly interesting outcome of our Arabidopsis experiment was the following. In high CO2 we find several genes induced that have eben associated with N-sensing, or C:N quorum sensing. These genes may be candidates to look for in breeding programs.
Publications
- Li, P., Ainsworth, E., Leakey, A.D., Ulanov, A., Lozovaya, V., Ort, D. and Bohnert, H.J. 2008. Arabidopsis in an open-air FACE facility: Transcript and metabolite profiles identify the nature of ecotype-specific acclimation to elevated [CO2]. Plant Cell and Environment, e-pub Sept 2008.
- Rupassara, S.I. 2008. Metabolite profiling of leaves and vascular exudates in soybean grwon under free-air concentration enrichment. University of Illinois, Ph.D. thesis, 2008, 187 pages.
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: This project is in the first year of activity. We have been using metabolite analysis for roots (xylem) and leaves (phloem) and total leaf metabolites with leaves of different ages.
PARTICIPANTS: Indu Rupassara, graduate student and also undergraduate students.
Impacts
We are interested in studying how different soybean lines respond in elevated CO2. The difference in these lines is their abiity to carry out nitrogen fixation.
Publications
- No publications reported this period
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