Progress 09/01/08 to 08/31/11
Outputs
OUTPUTS: (1) Trained researchers at UC Riverside: postdoctoral researchers (Takeshi Fukao and Julian Pena-Castro), graduate students (Gregory Barding, Seung Cho Lee, Rejbana Alam, Erin Brinton), and undergraduate students (Elaine Yeung, Sumukh Sathnur, Patrick Salveson, Ryan Salditos). Trained researchers at UC Davis: postdoctoral researchers Ki-hong Jung, Harkamal Walia Su Young Seo, and undergraduate student (Sossi Hossein). (2) Over 100 presentations on the functional roles of SUB1A in adaptation responses to submergence and development of SUB1 rice lines with submergence tolerance at scientific conferences (national and international) and university/research institutes (domestic and foreign). Over 20 presentations on Sub1 rice to the lay public. (3) Regularly communicated unpublished data with collaborators at the International Rice Research Institute, who focus on providing farmers rice with improved submergence and anaerobic germination tolerance. (4) Published 11 peer-reviewed reports in the scientific literature, including one paper in the journal Nature. (5) Research highlights: Obtained new detailed information on the role of SUB1A in regulation of submergence tolerance in rice; Confirmed that Sub1 rice has improved survival of drought, suggesting that submergence and drought tolerance can be effectively combined; Identified a mechanism of direct low oxygen sensing in plants that regulated turnover of transcription factors that control gene expression during low oxygen stress. Demonstrated that SUB1A is unusual in that it evades this mechanism of turnover. (See Outcomes/Impacts for more details) (6) Overall impact: Research in this project has identified gene and metabolite networks differentially regulated by SUB1A, which can be targeted to further improve submergence tolerance in rice. It also provides evidence that pyramiding effective drought with submergence tolerance will prove successful. It also identified a mechanism of low oxygen sensing that can be manipulated in submergence sensitive plants. (7) Through efforts of the International Rice Research Institute, new Sub1 rice varieties with improved submergence tolerance is in the hands of over 100,000 south and southeast Asian farmers. This new rice is anticipated to significantly aid the stabilization of yields in flood-prone fields, accounting for 35% of worldwide rice acreage. PARTICIPANTS: Julia Bailey-Serres (Project Director): Project direction; conception and evaluation of experiments; involved in data analysis and manuscript preparation and submission from UC Riverside. Made presentations at conferences, research institutions, for undergraduates and in news releases on the project. Takeshi Fukao (Associate Researcher): Lead researcher at UC Riverside; conception, evaluation, and execution of experiments; initial data analysis; initial drafts of manuscripts; supervision of undergraduates; interacted with collaborator and postdocs at UC Davis and IRRI. Made presentations at research institutions on the project. Julian Pena-Castro (Postdoctoral Researcher): Conception, evaluation, and execution of Arabidopsis experiments; initial data analysis. Now Research Faulty, University of Papeloapen, Mexico Elaine Yeung (undergraduate researcher): Undergraduate student in Biochemistry; research performed under the direction of Takeshi Fukao. Completed UCR summer research internship in 2008. Now applying to graduate schools in plant biology. Pham Van Cuong (visiting scientist, Hanoi Agricultural University): performed physiological studies for six months 5/11-9/11 Cynthia Larive (collaborator): Project direction; conception and evaluation of experiments; involved in analysis of metabolome data. Made presentations at conferences and research institutes on the project. Gregory Barding (graduate student): assisted in the execution of plant growth, submergence treatment, and metabolite analysis experiments; initial data analysis. Seung Cho Lee (graduate student): assisted in study of oxygen sensing via the N-end rule pathway of proteolysis. Erin Brinton (graduate student): assisted in evaluation of mechanisms regulated by SUB1A. Now working on related project in maize. Rejbana Alam (graduate student): worked with ANAEROBIC GERMINATION 1 (AG1) near isogenic lines from IRRI, to study molecular and physiological basis of anaerobic germinability. Sumukh Sathnur (undergraduate student): assisted with submergence tolerance tests under the direction of Gregory Barding. Patrick Salveson (summer undergraduate intern from Riverside Community College): assisted in metabolite profiling under the direction of Gregory Barding; now undergraduate at UC Berkeley. Ryan Sumukh (undergraduate student): assisted with metabolite profiling studies under the direction of Gregory Barding. Pamela Ronald (collaborator): Project direction at UC Davis; conception and evaluation of experiments at UC Davis. Made presentations at conferences, research institutions for lay audiences and news releases on the project. Ki-hong Jung (Postdoctoral Researcher): Lead microarray experiment and data analysis. Harkamal Walia (Postdoctoral Researcher): Involved in microarray data analysis. Young Su Seo (Postdoctoral Researcher): Led rice interactome project that evaluated SUB1A and SUB1C interactors. Sossi Hossein (undergraduate student): assisted with submergence tolerance tests at UC Davis. International Collaborators: David Mackill, Abdel Ismail, Endang Septiningshi, and Sigrid Heuer at the International Rice Research Institute. TARGET AUDIENCES: During the reporting period, over 100 presentations on this project were made at scientific conferences and research institutes in various countries. The audiences for these presentations included non-scientists and scientists (i.e undergraduate students, graduate students, and professional researchers) The presentations emphasized how biological research and its application can foster real agricultural improvements. Based on the long term success of our work on Sub1 rice, several rice accessions with enhanced submergence tolerant were developed through breeding expedited by use of molecular markers at the International Rice Research Institute (IRRI). Through IRRI's efforts, these new cultivars have been certified by several countries and distributed to farmers in flood-prone areas in South and Southeast Asia. By 2010, over 100,000 India farmers had received a popular rice cultivar with improved submergence tolerance. PROJECT MODIFICATIONS: None
Impacts
The goal of this project was to elucidate the functional roles of the rice (Oryza sativa) gene SUB1A, which encodes a group VII ethylene responsive transcription factor, in survival of submergence. Towards this goal we: (1) identified proteins that interact directly with SUB1A and SUB1C. This ultimately led to evaluation of submergence tolerance of mutants in genes encoding interacting proteins (Seo et al., 2011). (2) Performed genome-scale gene expression analysis to determine the influence of SUB1A in the temporal transcriptional adaptation to submergence. Identified genes displaying SUBA-1-dependent regulation, including genes associated with anaerobic respiration, hormone responses, and antioxidant systems and SUB1A-regulated transcription factors (Jung et al., 2010; Mustroph et al., 2010). (3) Conducted a cross-species comparison of transcriptomic adjustments to low oxygen stress in organisms of four kingdoms, identifying evolutionarily conserved and species-specific responses to oxygen deprivation (Mustroph et al., 2010). (4) Identified genes that SUB1A binds using chromatin immunopurification and high-throughput sequencing technology. Performed a complementary analysis using Arabidopsis that expresses SUB1A and SUB1C. (Bailey-Serres lab unpublished data) (5) Completed developmental, physiological and molecular studies on transgenic Arabidopsis that ectopically expresses SUB1A-1 or SUB1C-1. Although ectopic SUB1A expression does not provide submergence tolerance, it causes several traits associated with SUB1A overexpression in rice, including altered ABA and GA responsiveness, delayed flowering and reduced seed production. Discovered SUB1A affects initiation of flowering during submergence in rice (Pena-Castro et al., 2011). (6) Completed metabolite analysis by 1H nuclear magnetic resonance spectroscopy (1H-NMR) (Barding et al., 2011); analyses on the same extracts using gas chromatography mass spectrometry GC-MS are underway. Metabolite changes in tolerant and intolerant genotypes to submergence, reoxygenation, ethylene and 1-MCP inhibition continue (Larive and Bailey-Serres labs) (7) Began characterization of anaerobic germination tolerance provided by a chromosome 9 locus called ANAEROBIC GERMINATION 1 (Bailey-Serres lab and IRRI collaborators) (8) Investigated the role of SUB1A in responses to other abiotic stresses. Determined that SUB1A benefits survival of re-oxygenation and post-submergence drought. (9) Identified a mechanism of low oxygen sensing in plants that involves transcription factors related to SUB1A. Confirmed stability of these proteins is regulated via the N-end rule pathway of targeted proteolysis in an oxygen dependent manner. SUB1A and SUB1C are not targets of this pathway, illustrating utility of circumvent a turnover mechanism limits low oxygen responses in plants (Gibbs et al., 2011). This new knowledge can be used to further improve submergence tolerance of rice and other crops.
Publications
- Fukao, T., Yeung, E. and Bailey-Serres, J. (2011) SUBMERGENCE 1A-mediated crosstalk of submergence and drought tolerance in rice. Plant Cell. 23:412-427.
- Pena-Castro, J.M., van Zanten, M., Lee, S.-C., Patel, M.R., Voesenek, L.A.C.J. Fukao, T. and Bailey-Serres, J. (2011) Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence-tolerance mechanism. Plant Journal. 67:434-446.
- Seo, Y.S., Chern M, Bartley LE, Han M, Jung KH, Lee I, Walia H, Richter T, Xu X, Cao P, Bai W, Ramanan R, Amonpant F, Arul L, Canlas PE, Ruan R, Park CJ, Chen X, Hwang S, Jeon JS and Ronald PC. (2011) Towards establishment of a rice stress response interactome. PLoS Genetics 7, e1002020.
- Gibbs, D.J., Lee, S.C., Isa, N.M., Gramuglia, S., Fukao, T., Bassel, G.W., Correia, C,S, Corbineau, F., Theodoulou, F.L., Bailey-Serres, J. and Holdsworth, M.J. (2011) Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature, doi:10.1038/nature10534.
- Barding, Jr., G.A., Fukao, T., Beni, S., Bailey-Serres, J. and Larive, C.K. (2011) Differential metabolic regulation governed by the rice SUB1A gene during submergence stress and identification of alanylglycine by 1H-NMR spectroscopy. Journal of Proteome Research, doi:10.1021/pr200919b.
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Progress 09/01/09 to 08/31/10
Outputs
OUTPUTS: Outputs: (1) Training of researchers at UC Riverside: postdoctoral researchers (Takeshi Fukao and Julian Pena-Castro), a graduate student (Gregory Barding), and undergraduate student (Elaine Yeung, UC Riverside). Training of researchers at UC Davis: postdoctoral researchers Ki-hong Jung and Harkamal Walia. (2) Presentation on the functional roles of Sub1A in adaptation responses to submergence and development of Sub1 rice lines with submergence tolerance at scientific conferences (national and international) and university/research institutes (domestic and foreign). Presentations on Sub1 rice to the lay public. (3) Communication with collaborators of research progress and results: Gene expression studies, IRRI development of new near isogenic lines with anaerobic germinability and submergence tolerance. (4) Arrangements made for Greg Barding to perform growth experiments at Utrecht University in the Plant Ecophysiology Group (Oct-Dec, 2010) to expand metabolite studies. (5) Five publications. PARTICIPANTS: Training of researchers at UC Riverside: postdoctoral researchers (Takeshi Fukao and Julian Pena-Castro), a graduate student (Gregory Barding), and undergraduate student (Elaine Yeung, UC Riverside). Training of researchers at UC Davis: postdoctoral researchers Ki-hong Jung and Harkamal Walia. TARGET AUDIENCES: Target audiences include research scientists and the lay-public. Since our work on submergence tolerance goes from the gene to the farmer's field, the research goals and achievements can be easily explained to the lay public. Professor Bailey-Serres and Ronald have given numerous talks during the project period to audiences that include the public and interviews with media. Our goal has been to use the success of this project to illustrate to the public the type of advances that can be achieved by through the NIFA competitive grants program. PROJECT MODIFICATIONS: None
Impacts
The primary goal of this project is to elucidate the functional roles of Sub1A and Sub1C in submergence tolerance and anaerobic germination. Towards this goal we: (1) Identified proteins (n=27) that interact directly with SUB1A and SUB1C by yeast two-hybrid screening. Selected interactions were re-confirmed through bi-molecular fluorescence complementation. One interacting protein is under further study. (Ronald Lab) (2) Performed genome-scale gene expression analysis to determine the influence of Sub1A in the temporal transcriptional adaptation to submergence (up to 6 d). The transcriptome analysis identified genes displaying Sub1A-1-dependent regulation, including genes associated with anaerobic respiration, hormone responses, and antioxidant systems. Of particular interest were AP2/ERF family transcription factors which are related to the regulation of the metabolic and hormonal adjustments to submergence. (Ronald and Bailey-Serres labs) (3) Conducted a cross-species comparison of transcriptomic adjustments to low oxygen stress in 21 organisms from four kingdoms (Plantae, Animalia, Fungi, and Bacteria). The datasets used for the analysis include Affymetrix-based rice transcriptome data obtained in this project. This meta-analysis successfully identified evolutionally conserved and species-specific responses to oxygen deprivation. (Bailey-Serres lab) (4) Identified genes that SUB1A binds using chromatin immunopurification and Illumina sequencing technology (ChIP-Seq). A complementary analysis was performed using Arabidopsis that expresses Sub1A and Sub1C. The analysis of these data is underway. (Bailey-Serres lab) (5) Expressed Sub1A-1 and Sub1C-1 from submergence tolerant rice in Arabidopsis. Developmental, physiological and molecular studies were performed. Although ectopic expression does not provide submergence tolerance, it emmulates many traits associated with Sub1A overexpression in rice, including altered ABA and GA responsiveness, delayed flowering and reduced seed production. The analysis led to the finding that Sub1A affects initiation of flowering during submergence. (Bailey-Serres lab) (6) Continued metabolite analysis by 1H nuclear magnetic resonance spectroscopy (1H-NMR) and gas chromatography mass spectrometry (GC-MS). Experimental methods for sample preparation and metabolite extraction have been optimized for 1H-NMR and GC-MS. Metabolite changes in tolerant and intolerant genotypes to submergence, reoxygenation, ethylene and 1-MCP inhibtion are under examination. (Larive and Bailey-Serres labs) (7) Still waiting to receive seed from IRRI for anaerobic germination analyses. (Bailey-Serres lab) (8) Investigation into the role of Sub1A in responses to other abiotic stresses led to the finding that Sub1A benefits reoxygenation and a post-submergence drought. This was demonstrated at physiological and molecular levels.
Publications
- Voesenek, L.A.C.J. and Bailey-Serres, J. (2009) Genetics of high-rise rice. Nature 460(20): 959-960.
- Mustroph, A., Lee, S.C., Oosumi, T., Zanetti, M.E., Yang, H., Ma, K., Yaghoubi-Mashi, A. Fukao, T. and Bailey-Serres, J. (2010) Cross-kingdom comparison of transcriptomic adjustments to low oxygen stress highlights conserved and plant-specific responses. Plant Physiology. 152(3): 1484-1500.
- Jung, K.-H. Seo, Y.-S., Walia, H , Cao, P., Amonpant, F., Fukao, T., Bailey-Serres, J. and Ronald, P.C. (2010) The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiology. 152(3): 1674-1692.
- Bailey-Serres J. and Voesenek L.A.C.J. (2010) Life in the balance: a signaling network controlling survival of flooding Current Opinion in Plant Biology. 13: 489-494.
- Bailey-Serres, J., Fukao, T., Ronald, P., Ismail, A., Heuer, S. and Mackill, D.J. (2011) Submergence tolerant rice: SUB1's journey from landrace to modern cultivar. Rice. 3: 138-147.
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Progress 09/01/08 to 08/31/09
Outputs
OUTPUTS: (1)Training of researchers at UC Riverside: postdoctoral researchers (Takeshi Fukao and Julian Pena-Castro), a graduate student (Gregory Barding), and undergraduate student (Elaine Yeung, UC Riverside). Training of researchers at UC Davis: postdoctoral researchers Ki-hong Jung and Harkamal Walia. (2)Presentation on the functional roles of Sub1A in adaptation responses to submergence and development of Sub1 rice lines with submergence tolerance at scientific conferences (national and international) and research institutes (domestic and foreign). (3)On-site investigation of flood-prone areas in India and Bangladesh and field trials of Sub1 rice lines in various countries of South and Southeast Asia. (4)Communication with collaborators of research progress and results: Gene expression studies, IRRI development of new near isogenic lines with anaerobic germinability and submergence tolerance. (5) Two manuscripts in preparation. PARTICIPANTS: Training of researchers at UC Riverside: postdoctoral researchers (Takeshi Fukao and Julian Pena-Castro), a graduate student (Gregory Barding), and undergraduate student (Elaine Yeung, UC Riverside). Training of researchers at UC Davis: postdoctoral researchers Ki-hong Jung and Harkamal Walia. TARGET AUDIENCES: Target audiences include research scientists and the lay-public. Since our work on submergence tolerance goes from the gene to the farmer's field, the research goals and achievements can be easily explained to the lay public. Professor Bailey-Serres and Ronald have given numerous talks during the project period to audiences that include the public and interviews with media. Our goal has been to use the success of this project to illustrate to the public the type of advances that can be achieved by through the USDA competitive grants program. PROJECT MODIFICATIONS: None.
Impacts
The primary goal of this project is to elucidate the functional roles of Sub1A and Sub1C in submergence tolerance and anaerobic germination. Thus far the project has identified 27 proteins which directly interact with SUB1A and SUB1C by yeast two hybrid (Y2H) screening. These interactions were re-confirmed through bi-molecular fluorescence complementation (BiFC). One of the interacting proteins, Os11g06410 (putative trihelix transcription factor) physically binds to both SUB1A and SUB1C. Overexpression lines of the gene have been created and are currently being tested for submergence response and tolerance. Using the NSF 45K rice oligoarrays, we performed genome-scale gene expression analysis to determine the influence of Sub1A in the temporal transcriptional adaptation to submergence (up to 6 d). The transcriptome analysis identified 898 genes displaying Sub1A-1-dependent regulation, including genes associated with anaerobic respiration, hormone responses, and antioxidant systems. Of particular interest were a set of AP2/ERF family transcription factors which are related to the regulation of the metabolic and hormonal adjustments to submergence. With combination of the microarray, Y2H, and published QTL work, new genes that might further improve submergence tolerance will be targeted using overexpression and mutant lines. We also conducted cross-species comparison of transcriptomic adjustments to low oxygen stress in 21 organisms from four kingdoms (Plantae, Animalia, Fungi, and Bacteria). The datasets used for the analysis include Affymetrix-based rice transcriptome data obtained in this project as well as published microarray data. This meta-analysis successfully identified evolutionally conserved and species-specific responses to oxygen deprivation. Identification of direct target genes for SUB1A transcription factor are being accomplished by a combination of chromatin immunopurification and Illumina sequencing technology (ChIP-Seq). Metabolite analysis by 1H nuclear magnetic resonance spectroscopy (1H-NMR) and gas chromatography mass spectrometry (GC-MS) is underway. Experimental methods for sample preparation and metabolite extraction have been optimized for 1H-NMR and GC-MS. QTL analysis identified a major locus which positively affects anaerobic germination on chromosome 7. This is under evaluation by our collaborators at IRRI. We are also analyzing the effect of rice Sub1A gene on development and hormone response in the dicot model plant, Arabidopsis. In accordance with rice, constitutive expression of Sub1A restricted gibberellic acid-mediated developmental processes, such as vegetative growth, flower development, and seed production in Arabidopsis. Application of exogenous GA3 rescued late flowering phenotype in the line. The Arabidopsis transgenic line is also being used to detect the direct target genes of SUB1A by ChIP-Seq.
Publications
- No publications reported this period
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