NSF 11-500: Plant Genome Research Program (PGRP) FY 2011 Competition

THIS DOCUMENT HAS BEEN REPLACED BY NSF 12-517

Program Solicitation NSF 11-500

National Science Foundation Directorate for Biological Sciences      Division of Integrative Organismal Systems

Full Proposal Target Date(s):

     January 28, 2011

Important Information And Revision Notes

A revised version of the NSF Proposal & Award Policies & Procedures Guide (PAPPG), NSF 11-1, was issued on October 1, 2010 and is effective for proposals submitted, or due, on or after January 18, 2011. Please be advised that the guidelines contained in NSF 11-1 apply to proposals submitted in response to this funding opportunity. Proposers who opt to submit prior to January 18, 2011, must also follow the guidelines contained in NSF 11-1.

Cost Sharing: The PAPPG has been revised to implement the National Science Board's recommendations regarding cost sharing.  Inclusion of voluntary committed cost sharing is prohibited. In order to assess the scope of the project, all organizational resources necessary for the project must be described in the Facilities, Equipment and Other Resources section of the proposal.  The description should be narrative in nature and must not include any quantifiable financial information.  Mandatory cost sharing will only be required when explicitly authorized by the NSF Director.  See the PAPP Guide Part I: Grant Proposal Guide (GPG) Chapter II.C.2.g(xi) for further information about the implementation of these recommendations.

Postdoctoral Researcher Mentoring Plan: As a reminder, each proposal that requests funding to support postdoctoral researchers must include, as a supplementary document, a description of the mentoring activities that will be provided for such individuals.  Please be advised that if required, FastLane will not permit submission of a proposal that is missing a Postdoctoral Researcher Mentoring Plan. See Chapter II.C.2.j of the GPG for further information about the implementation of this requirement.

Revision Notes

A new opportunity, Improving Plant Genome Annotation (IPGA) will be available in FY 2011.

The Comparative Plant Genome Sequencing (CPGS) opportunity will not be available in FY 2011.

Please note that proposals at all scales are welcome, from single investigator to multi-investigator consortium projects, commensurate with the scope of the proposed research.

Summary Of Program Requirements

General Information

Program Title:

Plant Genome Research Program (PGRP)

Synopsis of Program:

This program is a continuation of the Plant Genome Research Program (PGRP) that began in FY 1998 as part of the National Plant Genome Initiative (NPGI). A new five-year plan for the NPGI was published in January 2009 (https://www.nsf.gov/bio/pubs/reports/npgi_five_year_plan_2009_2013.pdf). The goal of the NPGI is to develop a basic knowledge of the structures and functions of plant genomes and translate this knowledge to a comprehensive understanding of all aspects of economically important plants and plant processes of potential economic value. By bridging basic research and plant performance in the field, the NPGI will accelerate basic discovery and innovation in economically important plants and enable enhanced management of agriculture, natural resources, and the environment to meet societal needs.

Since the inception of the PGRP, there has been a tremendous increase in the tools available for genomics in key crop plants and their models, including but not limited to, collections of expressed sequence resources, genome survey sequences, mutant collections, expression profiling resources, and tools for studying gene expression in situ. High quality whole genome sequences and downstream tools are available for a number of key crops as well as widely-used model systems. This wealth of genomic resources makes it possible for researchers to begin to address some of the major unanswered questions in plant biology that have been intractable using traditional approaches as well as transfer findings from model systems into plants of economic importance. At the same time, there is a continued need for novel and creative tools to allow development of new experimental approaches or new ways of analyzing genomic data. Proposals that present conceptually new and different ideas are encouraged, especially from investigators and institutions that have not participated in the PGRP before. In addition, proposals that provide strong and novel training opportunities integral to the research plan, and particularly across disciplines are especially encouraged.

Four kinds of activity will be supported in FY 2011: (1) Genome-Enabled Plant Research (GEPR) awards to tackle major unanswered questions in plant biology on a genome-wide scale; (2) Transferring Research from Model Systems (TRMS) awards to apply basic biological findings made using model systems to studying the basic biology of plants of economic importance; (3) Tools and Resources for Plant Genome Research (TRPGR) awards to support development of novel technologies and analysis tools to enable discovery in plant genomics; and (4) Improving Plant Genome Annotation (IPGA) to improve existing tools or develop new tools for improved annotation of the genomes of plants of economic importance.  Proposals addressing these opportunities are welcomed at all scales, from single-investigator projects through multi-investigator, multi-institution projects, commensurate with the scope of the work proposed.

The PGRP encourages proposals from early career investigators and also considers proposals submitted to the CAREER program (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503214&org=BIO). Early career investigators are strongly encouraged to contact a PGRP Program Director for further guidance.

Cognizant Program Officer(s):

Please note that the following information is current at the time of publishing. See program website for any updates to the points of contact.

• Diane Jofuku Okamuro, Program Director, 690N, telephone: (703) 292-4400, email: dbipgr@nsf.gov

• Rebecca Boston, 690N, telephone: (703) 292-4400, email: dbipgr@nsf.gov

• Nora Lapitan, 690N, telephone: (703) 292-4400, email: dbipgr@nsf.gov

Applicable Catalog of Federal Domestic Assistance (CFDA) Number(s):

• 47.074 --- Biological Sciences

Award Information

Anticipated Type of Award: Standard Grant or Continuing Grant or Cooperative Agreement

Estimated Number of Awards: 15 to 25 Approximately 15-25 new awards will be made, pending availability of funds.

Anticipated Funding Amount: $20,000,000 Up to $20 million is available for FY 2011 new awards, pending availability of funds.

Eligibility Information

Organization Limit:

Proposals may only be submitted by the following:

• Proposals may only be submitted by U.S. academic institutions accredited in, and having a campus located in the U.S., U.S. non-profit research organizations including museums, research laboratories, professional societies and similar organizations in the U.S. that are directly associated with educational or research activities, and consortia of only the eligible organizations listed here. When a consortium of eligible organizations submits a proposal, it must be submitted as a single proposal with one organization serving as the lead and all other organizations as subawardees. Separately submitted collaborative proposals will not be accepted and will be returned without review. Organizations ineligible to submit to this program solicitation may not receive subawards.

PI Limit:

None Specified

Limit on Number of Proposals per Organization:

None Specified

Limit on Number of Proposals per PI: 1

• Please note that there continues to be a limit on the number of proposals in which an investigator can be included. An investigator may only submit one proposal as a principal investigator or a co-principal investigator in response to this Program Solicitation. Proposals received in excess of this limit may be returned without review.

Proposal Preparation and Submission Instructions

A. Proposal Preparation Instructions

• Letters of Intent: Not Applicable

• Preliminary Proposal Submission: Not Applicable

• Full Proposals:
  • Full Proposals submitted via FastLane: NSF Proposal and Award Policies and Procedures Guide, Part I: Grant Proposal Guide (GPG) Guidelines apply. The complete text of the GPG is available electronically on the NSF website at: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=gpg.
  • Full Proposals submitted via Grants.gov: NSF Grants.gov Application Guide: A Guide for the Preparation and Submission of NSF Applications via Grants.gov Guidelines apply (Note: The NSF Grants.gov Application Guide is available on the Grants.gov website and on the NSF website at: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=grantsgovguide)

B. Budgetary Information

• Cost Sharing Requirements: Inclusion of voluntary committed cost sharing is prohibited.

• Indirect Cost (F&A) Limitations: Not Applicable

• Other Budgetary Limitations: Not Applicable

C. Due Dates

• Full Proposal Target Date(s): 

       January 28, 2011

Proposal Review Information Criteria

Merit Review Criteria: National Science Board approved criteria. Additional merit review considerations apply. Please see the full text of this solicitation for further information.

Award Administration Information

Award Conditions: Standard NSF award conditions apply.

Reporting Requirements: Standard NSF reporting requirements apply.

Agency Contacts

Other Information

I. Introduction

II. Program Description

The overarching goal of the NPGI is to develop a basic knowledge of the structures and functions of plant genomes and translate this knowledge to a comprehensive understanding of all aspects of economically important plants and plant processes of potential economic value. By bridging basic research and plant performance in the field, the NPGI will accelerate basic discovery and innovation in economically important plants and enable enhanced management of agriculture, natural resources, and the environment to meet societal needs.

In the thirteen years since the NPGI began, a wealth of genomic resources have been developed for plant biology. Given these resources and the advances that have been made in technology development and bioinformatics, it should be possible to begin to address major unanswered questions in plant biology. In addition, advances made using model systems can now be transferred into plants of agronomic importance. New tools and methodologies are also needed to advance the field of plant biology as well as to tackle questions that are intractable using current approaches. This Program Solicitation has been developed taking those objectives and the NSF’s mission and strengths into consideration.

The PGRP is committed to broadening participation. NSF believes that the available research tools and resources should enable any institution to take part in plant genome research. New investigators, investigators that have not participated in the PGRP in the past or from small institutions, are strongly encouraged to submit a proposal. Investigators from Primarily Undergraduate Institutions, Historically Black Colleges and Universities (HBCU), Hispanic Serving Institutions (HSI), and Tribal Colleges and Universities (TCU) as well as individuals and small groups are especially encouraged to apply. The PGRP encourages proposals from early-career investigators and also considers proposals submitted to the CAREER program (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503214&org=BIO). New investigators are strongly encouraged to contact a PGRP Program Director for further guidance.

PGRP Funding Opportunities

Four areas of opportunity will be offered as components of the PGRP in Fiscal Year 2011: (1) Genome-Enabled Plant Research (GEPR) awards to tackle major unanswered questions in plant biology on a genome-wide scale; (2) Transferring Research from Model Systems (TRMS) awards to transfer findings made using model systems to plants of economic importance; (3) Tools and Resources for Plant Genome Research (TRPGR) awards to support development of novel tools to enable discovery in plant biology and (4) Improving Plant Genome Annotation (IPGA) awards to improve existing tools or develop new tools for improved annotation of the genomes of plants of economic importance. 

The Program foci recognize the utility of genomics tools in addressing major unanswered questions in plant biology, the power of using model systems as an entree to understanding key plant pathways and processes, as well the continued need for new methodologies to tackle problems that remain intractable using existing approaches. Proposers are strongly encouraged to review the guidelines for each opportunity carefully and to contact a PGRP Program Director if there are any questions about the programmatic fit.

Genome-Enabled Plant Research (GEPR):

The NSF PGRP is evolving by increasing use of the new tools and resources that have become available through the NPGI. While there still remain some large community resources to be built, those available now are sufficient to begin to address major unanswered questions in plant biology, some of which have not been tractable using traditional approaches alone. To be eligible, projects should be developed on a whole genome, whole organelle or whole network scale. In FY 2011, proposals are especially encouraged in the following areas:

• Plant responses to environmental stress, especially as they relate to climate change
• Systems approaches to understanding plant-environmental and plant-plant interactions
• Systems approaches to understanding plant-pathogen/organism interactions from a plant perspective
• Systems approaches to understanding plant metabolic processes, including water use efficiency and nitrogen use efficiency
• Mechanisms of epigenetic regulation

Proposals are solicited from single investigators, small groups and multi-institution “virtual centers." The scale of the project in terms of personnel and budget should be developed in the context of the proposed activities. The management plan should be appropriate for the proposed activities and a carefully developed budget, research plan and timetable will strengthen a proposal. Proposers are encouraged to think outside the box and to put forward imaginative and creative ideas, selecting experimental systems best suited to the research focus and taking advantage of the available genomics tools and resources. Proposals should clearly justify the relevance of the research activities to the goals of the NSF PGRP.

Transferring Research from Model Systems (TRMS):

Model systems, whether non-plant (for example, yeast) or plant (for example, Arabidopsis and rice) are a powerful way to access complex biological pathways that may not be readily accessible in many plants of economic importance. Substantial investments have been made in model systems, including whole genome sequences, expressed sequence collections, mutant collections, whole genome expression data, metabolome and proteome resources. These resources have already enabled considerable progress in understanding the genomic basis of a range of complex biological processes, including traits of economic importance. For example, regulatory networks controlling complex traits such as plant size and cold tolerance have been identified in Arabidopsis. The time has come to transfer the knowledge gained in a model system to uncover basic mechanisms underlying important traits in plants of economic importance.

Proposers are encouraged to choose important problems and traits of economic importance that combine the strengths of the chosen model system or systems with the importance of the work in the chosen target crop plant(s) and should have a significant focus on a crop target(s).  Proposals should clearly justify the relevance of the research activities to the goals of the NSF PGRP as well as their potential downstream impacts. To be eligible, projects should include significant research activities in a crop plant(s) and be developed on a whole genome, whole organelle or whole network scale. Proposals focused entirely on the use of a non-crop model plant system are more appropriate for funding through other programs at NSF (https://www.nsf.gov/funding/pgm_list.jsp?org=BIO&ord=rect).  

Proposals are solicited from single investigators, small groups and multi-institution “virtual centers.” The scale of the project in terms of personnel and budget should be consistent with the proposed activities. The management plan should be appropriate for the proposed activities and a carefully developed budget, research plan and timetable will strengthen a proposal.

Tools and Resources for Plant Genome Research (TRPGR):

While tremendous advances have been made in the development of tools and technologies for plant genome research, there is still a demand for additional resources to tackle unmet needs. Proposers are encouraged to develop novel approaches focused on a specific problem or need. Risky proposals are welcome. Priority will be given to new or novel tools that are likely to contribute broadly to the advancement of the field of plant genomics. In FY 2011, proposals are especially encouraged in the following areas:

• Improved tools for sequence assembly and analysis, especially to enable effective use of sequence data produced by next-generation machines;
• Novel methodologies for high throughput plant phenotyping, especially under field conditions;
• Improved visualization tools.

Use of model systems in the development of tools and technologies is allowed if it is clear that the tools and technologies developed would be widely applicable for use in plants of economic importance.

Proposals are solicited from single investigators, small groups, and multi-institution “virtual centers”. The scale of the project in terms of personnel and budget should be consistent with the proposed activities. The management plan should be appropriate for the proposed activities and a carefully developed budget, research plan, and timetable will strengthen a proposal.

Projects that focus on development of community resources, either through production of research resources or novel tools or establishment of a service, must be justified in terms of potential demand, efficiency and cost-effectiveness. The plans for release of project outcomes, including the timing and form of released resources, tools or materials, must be described explicitly along with the terms of access. If appropriate, plans for continued maintenance or operation of such a service after the award should be described without assuming long-term NSF support.

Improving Plant Genome Annotation (IPGA):

Annotation significantly impacts the utility of the wealth of genome sequence resources available for economically important crop plants. The goal of this opportunity is to support the development of annotation tools that would contribute to a conceptual framework for the interpretation of the structure, function and evolution of genomes of economically important plants. Projects are solicited that focus on improvement of existing annotation software as well as development of new tools and algorithms. Proposers must provide clear justification for the approach(es)selected and the type of tool to be generated.  It is anticipated that the annotation tools to be developed would employ primarily existing sequence resources. Projects that focus solely on development of ancillary annotation resources such as full-length cDNAs are not encouraged. The plans for dissemination of the tools and end-user training will be review criteria for this opportunity.

Proposals are solicited from single investigators, small groups, and multi-institution "virtual centers". The scale of the project in terms of personnel and budget should be consistent with the proposed activities. The management plan should be appropriate for the proposed activities and a carefully developed budget, research plan, and timetable will strengthen a proposal.The plans for release of project outcomes, including the timing and form of release, must be described explicitly along with the terms of access.

Additional Considerations as Appropriate

• Integration of Research and Education and Broadening Participation Activities supported by the PGRP should provide an ideal environment for training young scientists in modern research technologies, introducing them to new paradigms in plant biology, and promoting increased participation by members of under-represented groups. Informatics skills are critical to making the maximum use of genome resources. Accordingly, proposers are expected to integrate this training into their projects at all levels, wherever appropriate. NSF expects proposers to take advantage of the unique opportunities the proposed project provides in terms of education and incorporate these into the plan at a scale that is commensurate with the scale of the proposed activity. Focused activities that fit well with the specific opportunities offered by the project would be viewed as a strength. Proposers are encouraged to take advantage of existing programs and networks where appropriate, building in additional opportunities unique to the project’s research goals. New activities that link ongoing PGRP-supported training and outreach efforts to enable them to go to the next level are encouraged.

• Data Sharing A massive amount of data continue to be generated through PGRP activities. Proposers are strongly encouraged to consider their project outcomes in the context of the whole field of plant biology and ensure maximal accessibility and visibility. Outcomes are expected to meet current community standards for genomic data and be deposited into the existing long-lived community databases where appropriate. Projects that produce resources of utility to other researchers, whether part of a large-scale community resource project or not, are expected to release outcomes as soon as appropriate quality standards have been met.

• Societal Impacts When appropriate, issues related to the societal impact of plant genome research should be addressed as an integral part of a proposal. These issues could be integrated into research (e.g., studies on horizontal gene transmission at a genomic scale, the genome-wide basis of pesticide resistance, development of selectable markers for transformation studies), or into an education and/or outreach activity designed to communicate the significance of the outcomes of plant genome research to society.

• International Collaboration Plant genome research is actively pursued all over the world. The Directorate for Biological Sciences encourages international research collaborations, particularly with investigators from developing countries, and especially where there is a common research focus or system. When applicable, proposed research activities should be coordinated with similar efforts in other countries to maximize efficiency and avoid unnecessary duplication of effort. However, foreign participants should secure support for their component of the collaboration from their own national programs. The PI is encouraged to contact a PGRP Program Director for guidance regarding allowable costs when considering international collaborations.

• Industrial Collaboration Private industry has already made a significant investment in plant genomic research. Innovative collaborations with industry are encouraged when they advance the goals of the PGRP. However, NSF funds may not be used to support the industrial collaborators. Participation of a company as a provider of a service should be managed according to the submitting institution's procurement policy. When private industry is involved, the proposer is responsible for ensuring that any intellectual property issues are handled according to NSF Policy (see section A-1 under Special Information and Supplementary Documentation below).

Other Funding Opportunities in Plant Genome Research at NSF

Additional funding opportunities may be found at https://www.nsf.gov/funding/pgm_list.jsp?org=BIO&ord=rcnt. Investigators are encouraged to contact the cognizant Program Directors directly regarding the fit of the proposed research into a particular program.

Developing Country Agriculture

Proposers are encouraged to consider inclusion of activities described in the Dear Colleague Letter for Developing Country Collaborations in Plant Genome Research (NSF 04-563: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=nsf04563). Proposed collaborative activities should focus on research problems important to developing countries that include scientist-to-scientist interactions potentially leading to long-term partnerships among participating laboratories. The exchange of ideas and people should be reciprocal and should be built on equal partnerships between U.S. scientists and scientists of developing nations. Examples of activities to be supported would include, but not be limited to, joint research projects and long-term (one year) or short-term (between one and three months) reciprocal exchange visits. Collaborations should be developed that bring complementary sets of expertise to bear on problems of importance to the participants from developing countries and that meet their identified needs. The described activities should meet the budgetary and organizational guidelines described in the Dear Colleague Letter.

The Basic Research to Enable Agricultural Development (BREAD) Program (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503403&org=DBI), a new partnership program with the Bill & Melinda Gates Foundation, also supports collaborative research with international partners.  The goal of BREAD is to build on the accomplishments of the NPGI, extending the opportunities to include international partners in efforts to generate sustainable, science-based solutions to problems of smallholder agriculture in developing countries. Through these new partnerships and projects, it is anticipated that the program will lead a change in the research culture to one that is more broadly inclusive of these needs. Proposers are encouraged to contact the BREAD Program Director for further guidance regarding programmatic fit.

Conferences, Workshops and Symposia

The PGRP supports conferences, symposia and workshops in plant genomics that bring experts together to discuss current research, to expose other researchers or students to new research methods, and to discuss future directions of major research activities in plant genomics and bioinformatics. Conferences will be supported only if equivalent results cannot be obtained at regular meetings of professional societies or the established conference series. More information about submission of these proposals can be found at https://www.nsf.gov/publications/pub_summ.jsp?ods_key=gpg. Proposers are encouraged to contact a Program Director about the suitability of the proposed activity for PGRP support prior to submission.

Early-concept Grants for Exploratory Research (EAGER)

The EAGER funding mechanism may be used to support exploratory work in its early stages on untested, but potentially transformative, research ideas or approaches. This work may be considered especially "high risk-high payoff" in the sense that it, for example, involves radically different approaches, applies new expertise, or engages novel disciplinary or interdisciplinary perspectives. These exploratory proposals may also be submitted directly to an NSF program, but the EAGER mechanism should not be used for projects that are appropriate for submission as "regular" (i.e., non-EAGER) NSF proposals. PI(s) must contact the NSF program officer(s) whose expertise is most germane to the proposal topic prior to submission of an EAGER proposal. This will aid in determining the appropriateness of the work for consideration under the EAGER mechanism; this suitability must be assessed early in the process. For guidelines, see the most recent version of the NSF Grant Proposal Guide (https://www.nsf.gov/publications/pub_summ.jsp?ods_key=gpg).

Grants for Rapid Response Research (RAPID)

The RAPID funding mechanism is used for proposals having a severe urgency with regard to availability of, or access to data, facilities or specialized equipment, including quick-response research on natural or anthropogenic disasters and similar unanticipated events. PI(s) must contact the NSF program officer(s) whose expertise is most germane to the proposal topic before submitting a RAPID proposal. This will facilitate determining whether the proposed work is appropriate for RAPID funding. For guidelines, see the most recent version of the NSF Grant Proposal Guide (https://www.nsf.gov/publications/pub_summ.jsp?ods_key=gpg).

Research Coordination Networks (RCN)

The goal of the RCN Program is to advance a field or create new directions in research or education. Innovative ideas for implementing novel networking strategies are especially encouraged. Groups of investigators will be supported to communicate and coordinate their research, training and educational activities across disciplinary, organizational, geographic and international boundaries. The objectives are to facilitate open communication and exchange of information and resources, to integrate research and/or education activities of scientists and engineers working independently on topics of common interest, to nurture a sense of community among young scientists and engineers, and to minimize isolation and maximize cooperation so as to eliminate unnecessary duplication of efforts. The Program Solicitation is accessible through https://www.nsf.gov/pubs/2010/nsf10566/nsf10566.htm.