Progress 01/13/14 to 09/30/14
Outputs
Target Audience: The plant science community was served through the development of cyberinfrastructure tools through the iPlant collaborative based on work from this project, the general scientific community was served by identifying mechanisms of plant adaption to environment and developing techniques for extracting small quantities of RNA from seedlings and by showing links of genes with crop models through journal publications. Three minority students were provided research internships through this program. Minority high school teachers were targeted to distribute educational materials at the Computational Biology Workshop at North Carolina A&T. Materials were provided to undergraduate students in STEM disciplines through improved lectures and laboratories on the applications of agriculture to biofuels in Agricultural and Biological Engineering courses at the University of Florida. In general this project targets plant breeders, agronomists, molecular biologists, engineering groups, and students. Changes/Problems: An extension to this project is being made, however since these projects require a maximum of five years reporting we will building a new project related to this project. What opportunities for training and professional development has the project provided? Three graduate students were either directly or indirectly involved in this project. Over 10 undergraduates were involved in collecting this data and analyzing the results.The dissemination of Workshop material related to modeling plant development was provieded toapproximately15 high school teachers/graduate studentseither minorities or serving minority schools.A workshop to bring plant breeders and crop modelers is being developed for 2014. How have the results been disseminated to communities of interest? Nine peer-reviewed publications have been completed with three more in progress. Approximately 10 poster/oral presentations have been given at National and International meetings. Over 100 undergraduate students have been taught about the research of this project through guest lectures and tours. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
IMPACT A grand challenge facing the plant science community is to link the genetic components of a plant (DNA) to their phenotypes (traits in the field) for a variety of environments. Linking genes to phenotypes will allow crop breeders and famers to select plants that are adapted for specific, often challenging, environments such as water or heat stress. In light of global climate change, understanding how different plants will grow based on their genes will keep US agricultural competitive in the global market since farmers and plant breeders can select only plants that will produce adequate crop yields in particular environments. This challenge was addressed in this project since we have begun to link genes to computational ecophysiological models for an economically important crop (i.e., the common bean). In addition, a model plant (Arabidopsis) has been studied to identify genes that are expressed in varying environments. Results from this project are building the tools that crop breeders, farmers and decision support users can implement to predict how different genotypes of plants will grow in different environments. We have applied and developed new modeling tools that can be used to predict parameters in a crop model. These methods will improve future models for predicting plant growth. The PD had nine peer-reviewed publications that supported this project and 11 abstracts and presentations were provided. Through this project three graduate students have been trained in agricultural sciences along with over 10 undergraduates. This includes three minority students. Workshop material was proved and disseminated to minority serving high school teachers in agricultural systems to provide computational biology tools for their classrooms. Overall this project has provided the foundational tools to link genes to models that are used in over 160 countries to predict crop development. Specific goals of this project addressed below. Goal 1. Characterize the growth and development of plants from different genotypes in varying environmental conditions. 1. Major activities completed / experiments conducted; We have grown over 160 genotypes of bean in five field locations around the world (FL, USA, Popayan and Palmira Colombia, Puerto Rico, and ND, USA), these studies were then used to characterize the growth of the common bean in greenhouses at the University of Florida. In addition, we have grown Arabidopsis on the International Space Station to characterize the growth of seedlings in microgravity. 2. Data collected Data was collected for approximately 15 physiological traits of the common bean for five field sites and greenhouse studies will be made publically available in 2015. Corresponding weather and field data were also collected. The results of the growth characteristics of Arabidopsis grown on the International Space Station have been published. 3. Summary statistics and discussion of results Node addition rate (leaf appearance rate) was found to be different between several field sites for the common bean, however, when data were “normalized” based on thermal units fewer differences were found. These results are not surprising since temperature is known to affect the rate of node addition. The growth of Arabidopsis in space was similar to that on the ground but with enhanced curvature responses to light signals. This is not surprising since in space the microgravity environment reduced the gravity signal in plants thus enhancing the response of plants to light signals. 4.Key outcomes or other accomplishments realized. Ninejournal articles were published related to this goal. *Three journal articles are in the process of being submitted for publication. Three graduate students were either directly or indirectly involved in this project. Over 10 undergraduates were involved in collecting this data and analyzing the results. Overall, this goal was accomplished used to accomplish goal 2 described below. Goal 2. Identify genes or genetic loci involved in differential plant adaptation to environmental conditions using gene expression analyses or Quantitative Trait Loci identification techniques. 1. Major activities completed / experiments conducted; We have identified approximately 3 genetic loci involved in node addition for the common bean based on data from five field sites. We have identified over on thousand genes that are differentially regulated in the harsh spaceflight environments compared to Earth grown seedlings. 2. Data collected Over 900 representative data points have been collected for the rate of node addition in the common bean which was used to calculate the quantitative trait loci for that trait. 3. Summary statistics and discussion of results Three loci have been identified to correspond with node addition rate one is the well-studied FIN gene which determines the growth habit of a plant (indeterminate/determinate). In addition to this loci, two others yet to be defined were identified. For plants grown in microgravity approximately 130 genes were identified to gravity-related and include genes involved in cell wall development and plant defense responses. Further characterization of these genes will allow us to understand how gravity is involved in building cell rigidity. 4.Key outcomes or other accomplishments realized. Ninejournal articles were published related to this goal. *Three journal articles are in the process of being submitted for publication. Three graduate students were either directly or indirectly involved in this project. Over 10 undergraduates were involved in collecting this data and analyzing the results. Goal 3. Link this genetic data with existing crop models to provide a more gene-based approach for predicting plant growth and development. 1. Major activities completed / experiments conducted; We have built a computational tool to estimate plant model parameters in a step-wise manner thus making a more accurate prediction of the parameter (two manuscripts in preparation). We have linked three genetic loci to a physiological model predicting node addition rate in the common bean (manuscript in preparation). 2. Data collected Over 900 representative data points have been collected for the rate of node addition in the common bean which was used to calculate the quantitative trait loci for that trait. Experiments with six genotypes in four different environments were grown in greenhouses to model node addition and leaf expansion based on temperature. 3. Summary statistics and discussion of results We have developed a tool that will predict parameters associated with the CROPGRO model in the DSSAT modeling platform for the common bean. We have used this technique to estimate the genetic coefficients of over 150 recombinant inbred lines. We have linked three loci to the rate of node addition model thus building the foundation of a gene-based model. 4.Key outcomes or other accomplishments realized. Ninejournal articles were published related to this goal. *Three journal articles are in the process of being submitted for publication. Three graduate students were either directly or indirectly involved in this project. Over 10 undergraduates were involved in collecting this data and analyzing the results. A workshop to bring plant breeders and crop modelers is being developed for 2014.
Publications
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Progress 01/13/14 to 09/30/14
Outputs
Target Audience: During this reporting period the plant science community was the target audience for this report period (2013). Changes/Problems: Major change in this project is anextension from 2013to 2016 based on an extension in associated funding. What opportunities for training and professional development has the project provided? Dr. Melanie Correll has mentored a minority student the University Minority Mentor Program at UF for the past year 2012-2013 and served as a Judge in the 4-H Congress Competitions for High School Students in Science Engineering Technology (Sumer 2013), A postdoctoralstudent on this project has been trained in three events Grant Writing Workshop for Teaching (Hosted by Dean Balser) Spring, 2013 and provided letters of support forinterviews for six different positions from assistant professor to international agencies in the last year. How have the results been disseminated to communities of interest? Results for this project are being dessiminated via oral presentations and peer reviewed articles. Poster presentations Li Zhang, Melanie Correll, C. Eduardo Vallejos, Kenneth J. Boote, Senthold Asseng, Wei Hou, Jim W. Jones, Jose A. Clavijo, Mehul Bhakta. Modeling early growth of the common bean (Phaseolus vulgaris) at the Sustaining Economies and Natural Resources in a Changing World: Key Role of Land Grant Universities. April 2-3, 2013 University of Florida, Gainesville, FL. Oral Presentations Melanie J. Correll Linking Genes to Phenotypes-NSF Project. Invited Speaker. Agricultural and Biological Engineering Class (ABE 2012C) Introduction to biological engineering (Fall 2012 and Spring 2013). Over 40 students in attendance at each semester (total: 90 students). Melanie Correll, Li Zhang, Raveendra Patil, Kenneth Boote, James Jones, Jose Clavijo-Michelangeli, Mehul Bhakta, Steve Bebe, Jaumer Ricaurte, Martin Otero, Idupulapati Rao, James Beaver, Abiezer Gonzalez, Elvin Roman-Paoli , and C. Eduardo Vallejos. 2013. An Ecophysiology Model to Link Genes to Phenotypes of the Common Bean at the Institute of Biological Engineers meeting in Raleigh, NC. What do you plan to do during the next reporting period to accomplish the goals? Five manuscripts are in preparation for 2014 and one workshop is planned (pending funding) to integrate crop modelers with plant breeders (estimated to be held August 2014).
Impacts
What was accomplished under these goals?
The entire set of phenotype data has been collected at five sites for the common bean and data from an experiment performed on the International Space Station has been analyzed for Arabidopsis thaliana. We are continuing model calibration and simulations to include all field sites and have been working on models for the vegetative growth phase, branching, and have a paper accepted on the results from the fruit and pod development. We are currently running (Spring/Summer 2013) a set of greenhouse experiments to study the effects of temperature on vegetative growth of the common bean to improve our model for node addition and leaf area. Partial support for this greenhouse study was provided by the Agronomy Department and IFAS at the University of Florida.We have adapted the Markov Chain-Monte Carlo (MCMC) simulation program staged approach for CROPGRO and have made minor modifications to the overall approach. For example, there is only a primary target for phenology events (e.g., emergence to flowering etc.) and we have adjusted the secondary targets for biomass variables. In this process we predict the first GSP (EM.FL) then hold that value constant for subsequent stages. This process continues until all GSPs are predicted holding the previous ones fixed. We tested this staged methodology with our synthetic data of common bean and compared results with the original approach (estimating all parameters at once). We saw marked improvement in the prediction of emergence to flowering (EM.FL) and other GSPs.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Correll, M.J., Pyle, T.P., Millar, K.D.L., Sun, Y., Yao, J, Edelmann, R.E., and J.Z. Kiss. 2013. Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes. Planta 238:519-533
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Progress 10/01/11 to 09/30/12
Outputs
OUTPUTS: Activities: Model Calibration a Markov Chain-Monte Carlo (MCMC) simulation program to solve for the Genotype Specific Parameters GSPs in the CROPGRO model from a "synthetic" set of recombinant inbred lines were performed/optimized. A new approach breaks the algorithm into pieces where GSPs most closely associated with specific observed variables are estimated at one time and in a logical sequence. Then, a series of these smaller scale estimations are used to estimate the remaining GSPs. Product: Environmental control and monitoring system developed for stand alone growth chambers to perform temperature analysis on growth of plants. Analysis: Data analysis from gene expression profiles from plants grown in extreme environments (i.e., spaceflight) were completed. UV light treatment on biological samples: Plants and shrimp. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Target Audiences: Plant breeders, agronomists, biology, engineering groups, students PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Improved Algorithm: A new MCMC approach breaks the problem into pieces where GSPs most closely associated with specific observed variables are estimated at one time and in a logical sequence. Then, a series of these smaller scale estimations are used to estimate the remaining GSPs. A successful version of the program for another crop is available for CROPGRO and the adaptation of this program to dry bean is underway. Identification of Stresses in Spaceflight for Plants: Our data analysis has identified unique problems associated with studying plants in space and guides engineers to develop improved technology for studying plants.
Publications
- Yang WW, Shriver SK, Chung SY, Percival S, Correll MJ, Rababah TM: In vitro gastric and intestinal digestions of pulsed light-treated shrimp extracts.Appl Biochem Biotechnol; 2012 Mar;166(6):1409-22 PMID: 22278049
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Progress 01/01/11 to 12/30/11
Outputs
OUTPUTS: Conducting and analyzing experiments: A field trial for the common bean was performed in Gainesville, FL in the Spring/Summer 2011 and a second field experiment was performed in North Dakota (Summer 2011). A third field trial in Colombia was conducted in Fall 2011. Data from this site is being analyzed. As a secondary aspect to this general effort (genotype to phenotype) Earth grown Arabidopsis seedlings trancriptome were compared to space samples from 2010. Mentoring: Two new graduate students and a postdoctoral associate have been added to this project. One minority undergraduate student was added. Models: A model has been developed to assist with parameter estimation and will be published in the upcoming year.Networks and/or collaborations fostered by the project or activity: Collaboration with industry in Florida has continued with 4Fronteirs Corp. and North Dakota. Students graduated in agricultural sciences: One M.S. student graduated. PARTICIPANTS: The following individuals have been added to the project David Peterside (undergraduate), Dr. Raveendra H. Patil was added as a postdoctoral associate. Zhengjun Hu is no longer on the project. Training for Dr. Patil was for the 2011 DSSAT modeling training in Alabama. All other participants remain as described in 2011 report. Participants in other sites North Dakota, Colombia are not included in this report. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Change in knowledge: Three additional publications on this research effort have been published with one more accepted. Based on our field data we have developed new techniques for collecting and analyzing data.
Publications
- Journal Articles: Kiss JZ, Millar KD, Kumar P, Edelmann RE, Correll MJ. Improvements in the re-flight of spaceflight experiments on plant tropisms. Adv Space Res. 2011 Feb 1;47(3):545-52.
- Gohil, H. L., M.J. Correll, and T. Sinclair. 2011. Predicting the effects of gas diffusivity on photosynthesis and transpiration of plants grown under hypobaria. Advances in Space Research. 47: 49-54
- Kratasyuk V., Esimbekova E., Correll M., Bucklin R. Bioluminescent enzyme assay for the indication of plant stress in enclosed life support systems Luminescence, 2011. V. 26, N 6. P. 543-546.
- Abstracts: Melanie J. Correll, R. A. Bucklin, J.Z. Kiss, H.L. Gohil, S. Smith, J. Truett, A.J. Stimpson, P. A. Fowler, V. Y. Rygalov, R. M. Wheeler, J. C. Sager S. Yeralan, Y. Mu, I. Hublitz, J. Palaia and E. G. Wilkerson. The Mars Greenhouse Projects and Lessons Learned About Growing Plants in Space on the ISS (TROPI 1 and 2). 14th Annual Mars Society Meeting Abstract Book. Houston, TX. 2011
- Tyler Pyle, K.D.L. Millar, P. Kumar, J.Z. Kiss, F. Souret, M.J. Correll. 2011. The Spaceflight Environment Induces Differential Gene Expression Including Cell-Wall-Related Genes of Arabidopsis thaliana. The Institute of Biological Engineers Abstract Book. Atlanta, GA.
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Progress 01/01/10 to 12/30/10
Outputs
OUTPUTS: Conducting and analyzing experiments: A field trial of the common bean was performed in Spring/Summer 2010 in Gainesville, FL. This is a foundational study to determine experimental layout and analysis for future experiments that will be used to link genotype to phenotype of plants. The analysis of transcriptome of Arabidopsis was performed using microarrays to study harsh environments on gene expression patterns from plants grown on the International Space Station on March 2010 during two separate experiments. Teaching: Updates were provided to the course ABE 3000c, Applications in Biological Engineering, and included materials such as lectures and lab modules related to biofuels and bioremediation including cellulosic ethanol, biodiesel and methane production in the agriculture communities. Mentoring: 7 undergraduate students were mentored during this period (including 4 women and 3 minorities) with two receiving HHMI fellowships and one receiving a University Scholars scholarship. All student projects were working in the area of phenotypic responses of plants to environments. A 1st place poster award was given to an undergraduate student at the 2010 ASGSB annual conference. Conferences: An oral presentation was given at The Institute of Biological Engineers Conference in March 2010 in Cambridge, MA. Posters (n=4)and an oral presentation (n=1) by students and advisors were given at the American Society for Gravitational and Space Biology Meeting in November 2010 in Washington, DC. Workshops: Correll was an instructor for a workshop at North Carolina A&T University on "Computational Biology for Biology Educators", sponsored by iPlantcollaborative and Shodor. Several high school teachers (12, including minorities) were in attendance and received training and educational materials. Curricula: The development of two learning modules in plant transpiration and photosynthesis were developed using VENSIM and MATLAB by Correll and Collaborators (Ann Stapleton, UNC Wilmington). Models: Two models were modified for photosynthesis and transpiration to be incorporated into curricula for biology educators. Networks and/or collaborations fostered by the project or activity: Collaboration with UNC Wilmington, North Carolina A&T, among other Universities. Students graduated in agricultural sciences: One Ph.D. graduated in Agricultural and Biological Engineering (now postdoctoral associate at California State University in viticulture research) and one M.S. student graduated. Dissemination: Educational materials were provided at the Computational Biology for Biology Educators in July 2010, these were targeted at high school teachers. PARTICIPANTS: Melanie Correll, involved in writing grants, reports, publications and mentoring of students working on the project. Correll assisted with identifying errors in programming codes for parameter estimation of crop models and linking genotype specific coefficients of crop models to each other. This identified potential overlap of genotype specific coefficients which may cause error when developing a gene-based ecophysiological model for crops. James Jones, coordinated simulation of bean cultivars for crop models and contributed to grant proposal writing, presentations reports. Carlos Eduardo Vallejos, PI on a NSF proposal, characterized genetic traits of the common bean, developed simulated recombinant inbred line family of the common bean, managed field experiments and began development of experimental plan for five field sites around the world. Kenneth Boote, involved in integrating the simulated recombinant inbred line for crop model simulations. Boote contributed to grant proposal writing, presentations and reports and identifying parameters to be measured in the field. Rongling Wu and Arthur Berg involved in performing statistical analysis on recombinant inbred population and assisting in grant proposal writing, presentation and reports. Zhengjun Hu, wrote R-programming code for Metropolis-Hasting Monte Carlo simulations to link with crop models, assisted in preparing reports and presentations. Ray Bucklin, assisted with methods for environmental control for monitoring plant growth and development. Bucklin assisted in writing grant proposals, reports and publications and supervising graduate and undergraduate students. John Kiss, collaborator from Miami University, led the project to study plant responses to extreme spaceflight environment. Graduate student, Pepe Michelangeli , Ph.D. student, was responsible for field experiments on the common bean. Graduate Ph.D. student, Hemant Gohil, and M.S. Student, John Truett, were involved in development of tools for measuring environmental effects on plant growth and development. Tyler Pyle and William Acosta, undergraduate students, were responsible for extraction of RNA, quality control and qPCR analysis from experiments performed in spaceflight. Samantha Smith, Ana Martin-Ryals, Stella Garcia, and Justin Townley, undergraduate students, were involved in testing materials for biocompatibility with plants and to identify possible materials for environmental systems to grow plants in harsh environments (UV radiation, large temperature fluctuations). Paul Heyliger Fonseca, an undergraduate student, was involved in preliminary studies to assess methods for measuring phenotypes in the field. TARGET AUDIENCES: Minority high school teachers were targeted to distribute educational materials at the Computational Biology Workshop at North Carolina A&T. Materials were provided to undergraduate students in STEM disciplines through improved lectures and laboratories on the applications of agriculture to biofuels in ABE courses. Three minority students were provided research internships through this program. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Change in knowledge: Three publications on this research effort have been published with one more accepted. Based on our field data we have developed new techniques for collecting and analyzing data.
Publications
- Smith,S.J., J. A. Townley, A. D. Martin-Ryals, J. Truett, J. E. Palaia, IV, A. E. Schuerger, R. A. Bucklin, M. J. Correll. 2011. Testing of Greenhouse Cladding Materials for Space Environments. Journal of Applied Engineering in Agriculture. in press.
- Gohil, H. L., M.J. Correll, and T. Sinclair. 2011. Predicting the effects of gas diffusivity on photosynthesis and transpiration of plants grown under hypobaria. Advances in Space Research. 47: 49-54.
- Millar, K.D.L., P. Kumar, M. J. Correll, J.L. Mullen, R.P. Hangarter, R.E. Edelmann, and J.Z. Kiss. 2010. A novel phototropic response to red light is revealed in microgravity. New Phytologist. 186:648-656.
- Smith , S.J. ,H.L. Gohil, J.R. Truett , R.A. Bucklin and M.J. Correll. 2010. Developing Engineering and Decision Support Tools for Growing Plants on Mars. Gravitational and Space Biology Bulletin, in press.
- Pyle, T., K.D.L. Millar, J.Z. Kiss, and M.J. Correll. 2010. The Effects of Gravity and the Spaceflight Environment on the Gene Expression Profile of Arabidopsis thaliana Seedlings. Gravitational and Space Biology Bulletin, in press.
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Progress 10/01/08 to 09/30/09
Outputs
OUTPUTS: A simulation project was used to test different aspects of the approach to link genes with existing crop models. The genetic analysis was carried out with a simulated recombinant inbred progeny derived from two synthetic parental genotypes of the common bean, Phaseolus vulgaris. The parental genotypes were assigned contrasting "Genotype-Specific Parameters" (GSPs) previously measured in field-grown plants from a diverse set of Andean and Mesoamerican cultivars. Each of 15 genotype coefficients used in the model were made into a linear function of the genotype at 3 to 6 loci (QTL). The RI coefficients were calculated according to the established functions, and then mapped. The simulated GSPs were used by the crop model to simulate "field data" based on weather data from Cali, Colombia. Finally, the "field data" was used to independently estimate the GSPs by implementation of a MCMC method using the Metropolis-Hastings algorithm with Gibbs sampler. Through this project a simulation of 202 cultivars of the common bean were simulated over 6000 times in a crop model to identify the original parameters. The analysis of gene expression in extreme environments was performed. Oral Presentations (4 total, * indicates graduate/undergraduate student); Correll, M.J., Vallejos, C.E., Jones, J., Boote, K.J., Berg, A., Wu, R., and Z. Hu. 2009. G2P: Prediction of Plant Phenotype from Genotype and Environmental Interactions. Agricultural and Biological Engineering Department Seminar Series, University of Florida. Gainesville, FL.; Correll, M.J., C.E. Vallejos, J.W. Jones, K.J. Boote, A.S. Berg, and R. Wu. 2009. Linking genes with genotype-specific coefficients in crop models. The 39th Biological Systems Simulation Group, at the University of Georgia-Griffin, GA.; Vallejos C.E., J.W. Jones, K.J. Boote, M.J. Correll, A.S. Berg, and R. Wu. 2009. Can we combine genetics and crop modeling approaches to predict the phenotype The 39th Biological Systems Simulation Group, at the University of Georgia-Griffin, GA.; *Gohil H.L., R.A. Bucklin, and M.J. Correll. 2009. The interacting effects of CO2 and hypobaria on growth and transpiration of radish. Gravitational and Space Biology in Raleigh, NC. Workshop (1 total); iPlant Collaborative workshop (www.iplantcollaborative.org ) in July 26-28, 2009 in Chicago, IL to discuss the development of tools for the plant science community. Demonstration (1 total);Hosted 5 members from St. John's County School District on Biotechnology. Educational materials about our Biotechnology Program at UF was provided to the attendees (January, 2009). Products (7 Total);Fellowships and Scholarships for Undergraduate Students (3 Total); Two students received a Howard Hughes Medical Fellowships for summer internships and one student received a University Scholars Award; Awards for undergraduate Students (3 Total) Software Program (1 Total); As part of this project a program for estimating parameters for crop models was developed PARTICIPANTS: Melanie Correll, involved in writing grants, reports, publications and mentoring of students working on the project. Performed crop modeling simulations on 202 recombinant inbred lines using a statistical software. Extracted and anaylzed plant growth and gene expression of plants from extreme environments using microarray technology. James Jones, coordinated simulation of bean cultivars for crop models and contributed to grant proposal writing, presentations reports. Assisted in simulation of hypothetical lines. Carlos Eduardo Vallejos, characterized genetic traits of the common bean, developed simulated recombinant inbred line family of the common bean, studied root development of common bean and contributed to grant prosal writing, presentations and reports. Kenneth Boote, involved in integrating the simulated recombinant inbred line for crop model simulations. Calibrated crop model CROPGRO to run 202 lines. Contributed to grant prosal writing, presentations and reports. Rongling Wu, involved in performing statistical analysis on recombinant inbred population and assisting in grant proposal writing, presentation and reports. Zhengjun Hu, wrote R-programming code for Metropolis-Hasting Monte Carlo simulations to link with crop models, assisted in preparing reports and presentations. Ray Bucklin, assisted with methods for environmental control for monitoring plant growth and development. Assisted in writing grant proposals, reports and publications. John Kiss, collaborator from Miami University, on project to study plant responses to extreme spaceflight environment. Steven Welch, Kansas State University, for the iPlant collaborative on developing cyberinfrastructure. Ruth Grene, Virginia Tech, for for the iPlant collaborative on developing cyberinfrastructure Joseph Palaia, from 4Frontiers assisted in producing website material for education purposes for growing plants in extreme environments. Training of 5 undergraduate students for summer internships (Stella Garcia, Paul Heyligher-Fonseca, Justin Townley, William Acosta, Samantha Smith) and two graduate students (Hemant Gohil and John Truett) TARGET AUDIENCES: Target groups; the plant science community was served through the development of cyberinfrastructure tools through the iPlant collaborative, general scientific community was served by identifying mechanisms of plant adaption to environment and developing techniques for extracting small quantities of RNA from seedlings. Three minority students were trained during this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Through this project, the development of cyberinfrastructure tools is underway with the iPlant Collaborative (www.iplantcollaborative.org). Simulation of the growth of 202 different genotypes of the common bean using existing crop models has been performed and new ways to handle and simulate plant growth have been developed. We now can better estimate parameters used to predict pant growth based in crop models using Metropolis-Hastings, within Gibbs Monte Carlo simulations. In addition, we have identified methods and gene mechanisms for growing plants in extreme environments (e.g., spaceflight) and extracting RNA from small amounts of plant tissue.
Publications
- Correll, M.J., C.E. Vallejos, J.W. Jones, K.J. Boote, A.S. Berg, and R. Wu. 2009. Linking genes with genotype-specific coefficients in crop models. The 39th Biological Systems Simulation Group, at the University of Georgia-Griffin, GA. p. 10-11.
- Vallejos C.E., J.W. Jones, K.J. Boote, M.J. Correll, A.S. Berg, and R. Wu. 2009. Can we combine genetics and crop modeling approaches to predict the phenotype The 39th Biological Systems Simulation Group, at the University of Georgia-Griffin, GA. p. 2-3.
- *Acosta W.A., J.Z. Kiss, and M.J. Correll. 2009. Characterizing the role of PIN4 in the red-light inhibition of root elongation. Gravitational and Space Biology Bulletin 23(1): 6.
- *Garcia S., R.A. Bucklin, and M.J. Correll. 2009. Optimization of the methodology for studying transpiration of Arabidopsis in hypobaria. Gravitational and Space Biology Bulletin 23(1): 6.
- *Smith S.J., H. Gohil, R.A. Bucklin, and M.J. Correll. 2009. Long term effects of hypobaria on radish growth and evapotranspiration. Gravitational and Space Biology Bulletin 23(1):7.
- *Gohil H.L., R.A. Bucklin, and M.J. Correll. 2009. The interacting effects of CO2 and hypobaria on growth and transpiration of radish. Gravitational and Space Biology Bulletin 23(1):15.
- *Truett J.R., R.A. Bucklin, and M.J. Correll. 2009. Humidity control for plant studies in a low pressure growth chamber. Gravitational and Space Biology Bulletin 23(1):5.
- Gohil, H.*, R.A. Bucklin, and M.J. Correll. 2009. The effects of CO2 and hypobaria on growth and transpiration of radish (Raphanus sativus). Advances in Space Research. Online publication complete: 22-DEC-2009 DOI information: 10.1016/j.asr.2009.11.015
- Kiss, J.Z., P. Kumar, K.D.L. Millar, R.E. Edelmann, and M.J. Correll. 2009. Operations of a spaceflight experiment to investigate plant tropisms. Advances in Space Research. 44: 879-886.
- Stimpson, A.J.*, R.S. Pereira*, J.Z. Kiss, and M.J. Correll. 2009. Extraction and labeling methods for microarrays using small amounts of plant tissue. Physiologia Plantarum. 135(3):229-236.
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