2009 — 2014 |
Grene, Ruth Yang, Yinong (co-PI) [⬀] Crasta, Oswald Pereira, Andy Baisakh, Niranjan |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Cereal Drought Stress Response and Resistance Networks @ Virginia Polytechnic Institute and State University
PI: Andy Pereira (Virginia Polytechnic and State University)
Co-PIs: Ruth Grene and Oswald Crasta (Virginia Polytechnic and State University), Yinong Yang (Pennsylvania State University), Niranjan Baisakh (Louisiana State University Agricultural Center)
Collaborators: Guy Davenport and Jianbing Yan (CIMMYT, Mexico), Hei Leung (IRRI, Philippines)
Water scarcity causing drought during essential periods of plant growth can limit stable crop production. Cereal crops such as maize, wheat, rice and barley are most affected by drought during the time of flowering and initiation of grain formation, causing drastic yield losses. The goal of this project is to develop a systems biology view of drought responses in cereals to understand this complex process and improve drought resistance and water use efficiency. Genome-wide comparative transcriptome analysis of drought responses in rice and maize will be integrated into a cereal drought gene interaction network, using ortholog information to predict conserved functional relationships as a basis for cereals. Conserved orthologous regulatory genes between rice and maize involved in drought responses and resistance will be identified comprising transcription factors (TFs), protein kinases and phosphatases, genes in hormone signaling pathways, chromatin binding proteins, protein degradation and small RNA pathways. As proof of principle, a set of these putative conserved rice and maize genes will be tested by genetic analysis of mutants and natural allelic variants, assessing them for altered drought response phenotypes and perturbation in the drought gene interaction network. These analyses will validate and improve the cereal gene interaction network predictions, and provide candidate genes for improvement of drought resistance/tolerance in cereals.
With respect to broader impacts, this project will contribute through the generation of information key to the development of stable food production systems worldwide and through the creation of a transdisciplinary educational environment. Scientifically, the project will demonstrate the use of an integrated network approach to understand complex plant responses such as drought response and resistance. Outreach and training activities are integrated within the transdisciplinary plant-lab-bioinformatics project and will be made accessible to high school and underrepresented undergraduate students from institutions across Virginia and North Carolina through established programs at Virginia Tech and other nearby universities. An outreach program developed as part of a NSF-Cyberinfrastructure Training, Education, Advancement, and Mentoring for Our 21st Century Workforce (CI-TEAM) project will provide modules for quantitative data analysis for teachers and students using socio-environmental case studies from research data. An integrated mentor program for postdoctoral researchers will be used to facilitate career development. International research collaborations with the Generation Challenge Program and CGIAR institutes involved in drought research will add capacity building to agricultural systems worldwide. Plant genotypes and all data developed in the project will be made available through a project website (http://cereal-drought.vbi.vt.edu/) that will allow interactive access to data and networks. Other publicly available genetic stocks used will be distributed by the respective originators with long term public repositories. Microarray and EST data will be deposited at GEO and NCBI, respectively. All functional genomics data generated will be periodically deposited in Gramene and other public databases.
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1 |
2011 — 2015 |
Grene, Ruth Pereira, Andy Collakova, Eva [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
A Systems Biology Approach to Cellular Regulation of Seed Filling @ Virginia Polytechnic Institute and State University
Intellectual merit. Seeds storage reserves, such as oils, proteins, and sugars are essential for plant reproduction as a source of nutrients and energy during seed germination. Seed composition is a genetically malleable trait that has been, and can be further, modified to our advantage. The seed crop domestication process has involved the selection of varieties containing different amounts of storage reserves primarily for nutritional purposes. Now, and for future needs, the genetic potential of seeds is being tapped as a source for industrial chemicals and biofuel. The goal of this research program is to identify the specific genetic regulators that determine seed composition in the model plant Arabidopsis thaliana by using modern experimental and computational approaches. This research will lead to a deeper understanding of specific cellular functions and metabolic processes that underlie the accumulation of seed storage reserves.
Broader impacts. From the practical point of view, the outcomes of this project will provide the basis for controlling seed composition in Arabidopsis (e.g. to produce more oil or protein) and crops optimized for future economic needs (biofuels and oil-based chemical feedstocks) beyond the traditional nutritional needs of humans and domesticated animals. From the educational point of view, high school students will be provided with research opportunities via the Partnership for Research and Education in Plants (PREP)program to enhance student interest and involvement in science. PREP targets diverse ethnic groups. Students participating in this program tend to improve dramatically in critical reasoning by asking basic biological questions, designing and executing experiments, and interpreting results. Involvement in this outreach program will provide a direct connection between research laboratories and high school science education and thereby contribute significantly to the improvement of scientific literacy in our society.
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1 |
2011 — 2017 |
Heath, Lenwood [⬀] Grene, Ruth Pereira, Andy |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Abi Development: Representation, Visualization, and Modeling of Signaling Pathways in Higher Plants @ Virginia Polytechnic Institute and State University
An award is made to Virginia Polytechnic Institute and State University to build the community-based Beacon system to provide computational support for biologists' questions about signaling pathways. Signal transduction pathways hold the key to understanding the early response of higher plants to abiotic stresses, such as drought, flooding, heat, cold, ozone, and salt. For crop plants, the ability to cope with such abiotic stresses can drastically affect productivity. Traditionally, signaling pathways have been difficult to synthesize and impossible to manipulate computationally. Current pathway tools and databases provide only limited support for manipulating pathways as networks. In particular, it is not possible for a biologist to take an existing signaling pathway and ask hypothetical questions that are answered computationally. The project includes the training of recognized authorities by Beacon staff on the system, thereby empowering plant biologists to curate and archive signaling pathways for abiotic stress responses in the Beacon database. Usability of the tool will be addressed via a continual feedback loop between users and developers.
The user interface is an editing environment that represents and manipulates a pathway in a standard graphical notation called SBGN Activity Flow language, built on the network visualization tool VANTED and SBGN-ED, an extension of VANTED. Research herein will extend SBGN-ED to create Beacon. The result will be a curation tool that will allow authorities to enter pathways in SBGN Activity Flow language, edit them, annotate them, and save them to an initial Beacon database. The database representation allows the biologist to impose a semantic, such as Boolean semantics, on a pathway. The Beacon simulation engine is then able to computationally implement those semantics and provide results that can be queried and visualized. The Beacon inference engine provides tools to allow biologist to develop testable hypotheses about pathway components. The Beacon system will interest undergraduate students in computational sciences as well as experimental biologists. Well-established outreach programs at Virginia Tech will be used to provide training and educational outreach activities. An experimental component will be implemented in the final years of the project, where Beacon-based predictions concerning phenotype will be tested in the laboratory. At https://bioinformatics.cs.vt.edu/beacon/, users will have access to project outcomes.
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1 |
2017 — 2020 |
Naithani, Kusum (co-PI) [⬀] Pereira, Andy |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Systems Genetics Analysis of Photosynthetic Carbon Metabolism in Rice
The aim of this project is to discover mutations in rice that increase photosynthesis efficiency. Plants capture the energy of sunlight through photosynthesis to produce sugars, starch, and a multitude of biologically active energy-rich molecules of life. Improving the efficiency of photosynthesis in plants, making it stable to environmental stresses, would provide us with a sustainable supply of food and nutrition as well as renewable energy to maintain the needs of the growing population. This interdisciplinary project will offer practical training to graduate and undergraduate students. This project also will produce hands-on laboratory exercises to improve knowledge of undergraduate and graduate students on plant diversity and environmental challenges affecting food security, and broadening the impact of plant sciences in STEM education. In addition, K-12 students from the Arkansas agricultural areas in the Delta region will be engaged by a STEM literacy outreach program providing experience in experimental plant sciences aimed at caring for the environment. The project will use an integrated systems genetics approach to dissect the complex pathways of plant photosynthesis driving plant development and productivity. Genome wide association analysis of a diverse rice population identified single nucleotide polymorphism (SNP) markers associated with several parameters for photosynthetic efficiency. These SNPs will be used to identify the key genes determining important natural variation for photosynthesis. To understand the regulation of these interacting processes, it is essential to go beyond individual gene action or biochemical pathways. The integrated network approach employed will help place multiple genetically defined photosynthetic parameters in the context of gene regulatory pathways that underpin response to external factors, growth and development. A diverse set of computational formulations will be integrated into a consensus network using rank-based protocols, an approach proven to be robust for prediction of functional relationships. Predicted transcription factors will be tested in high throughput assays for their ability to activate photosynthesis genes in vivo, and confirmed in transgenic plants to unravel their downstream regulatory pathways. The systems genetic information from these genotypes will be used to reconstruct improved plants and crops with modular improvements in photosynthetic-based processes for diverse needs.
This project is co-funded by the Systems and Synthetic Biology Program in the Division of Molecular and Cellular Biosciences and by the NSF EPSCoR Program.
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0.943 |
2018 — 2022 |
Srivastava, Vibha (co-PI) [⬀] Pereira, Andy Khodakovskaya, Mariya Famoso, Adam Sunkar, Ramanjulu (co-PI) [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Rii Track-2 Fec: Systems Genetics Studies On Rice Genomes For Analysis of Grain Yield and Quality Under Heat Stress
Non-technical Description The basic knowledge and understanding of how environmental stressors, such as high temperatures, affect cereal crop production is important for global food security. Rice, a model cereal plant and a major world staple crop, is grown in the southern United States, and is threatened by increased night temperatures that contribute to unstable production, resulting in lower grain yield and quality, which result in decreased market value. This project will identify individual rice lines that are tolerant to high nighttime temperatures and will use a variety of genetic and biochemical techniques to identify potential mechanisms that underlie the ability of these plants to be high temperature tolerant. These mechanisms will be tested in the plant using gene editing technologies to confirm that these mechanisms and thus the underling causative alleles are responsible for the plant's resistance to high nighttime temperatures. Knowing the actual mechanisms will aid breeders to develop new lines that can help decrease the risk of major crop losses due to high temperatures in the future. This project will be a collaborative effort among the University of Arkansas campuses at Fayetteville and Little Rock, Louisiana State University, and Oklahoma State University and will help develop the careers of six early career research faculty, train undergraduate and graduate students, and postdocs. In addition, the projects will build educational resources for STEM at the undergraduate level as well as K-12.
Technical description The japonica rice subspecies is the basis of most US varieties currently in production and have been used in US breeding efforts with other rice introductions from all over the world to select varieties that are tolerant to high night temperature. In this project, a diverse collection of rice lines critical to U.S. production will be screened in the field, including environments differing in night temperature, and replicated under controlled greenhouse conditions, to identify heat tolerant genotypes with contributing genes and novel mechanisms that are of interest to use in improvement of rice and other cereals for their resilience to high night temperatures. The genetic changes or identification of alleles ascribed to the desired phenotypes will be characterized at multi-systems levels: the transcriptome, metabolome, proteome, and the physiological response. Information from these analyses will be integrated into gene regulatory networks that can provide a biological understanding of plant adaptations to the changing environment documented in independent genotypes. Wildtype or mutant alleles identified from the population studies will be validated by transformation and CRISPR/Cas9 mediated allele engineering, followed by phenotypic validation to identify alleles associated with heat tolerance, as proof of concept for use in cultivar development. This Research Infrastructure Improvement Track-2 Focused EPSCoR Collaboration (RII Track-2 FEC) project brings together complementary expertise comprising senior and junior faculty from the University of Arkansas campuses at Fayetteville and Little Rock, Louisiana State University, and Oklahoma State University, to address this complex challenge in an interdisciplinary manner. The participants include six early career faculty from different institutions, who will be integrated into the interdisciplinary program to develop expertise in cross-disciplinary research projects. The project will include training of postdocs, graduate and undergraduate students, participation of 10-12th grade students in STEM girl's leadership events, and of High School teachers and students for training in Plant Genetics and Physiology.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
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0.943 |