The National Science Foundation (NSF) announces its intention to continue to support plant genome research through the Plant Genome Research Program (PGRP). Since its inception in 1998 as part of the National Plant Genome Initiative (NPGI), the NSF PGRP has followed the long-range plans for the NPGI and, working closely with the other agencies participating in the NPGI, has contributed to tremendous advances in plant genomics and plant sciences. The program is currently following the third five-year plan (National Plant Genome Initiative: 2009-2013;http://www.nsf.gov/bio/pubs/reports/npgi_five_year_plan_2009_2013.pdf). Following the goals set out in this plan, the PGRP encourages new, innovative ideas in the form of basic research and tool development projects that will advance the whole field of plant biology and accelerate basic discovery and innovation in economically important crop plants to meet societal needs. Potentially high-risk, high-payoff proposals or proposals that present unconventional ideas are especially encouraged. The list of ongoing projects available at http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5338&org=BIO should be consulted to ensure that, if funded, a planned project would make a significantly new scientific contribution to the field.
Proposals that focus on individual genes or gene families should be sent to other BIO programs (see web pages available through http://www.nsf.gov/dir/index.jsp?org=BIO for listing of programs and funding opportunities). Proposers are strongly encouraged to contact a Program Director prior to submission to determine the suitability of the project for the PGRP.
Simultaneous submission of proposals to this program and another federal agency is permissible with prior written approval of the agencies involved. A proposal from the same submitter that is a duplicate of, or substantially similar to, a proposal already under consideration by NSF will be returned without review.
II. PROGRAM DESCRIPTION
In the sixteen years since the NPGI and the PGRP began, a wealth of genomic resources has been developed for plant biology. Using these resources and building on the advances that have been made in technology development and bioinformatics, it is now possible to address fundamental questions in plant biology and begin to achieve a systems-level understanding of economically important plant processes. This is achievable in the context of the physiology of the plant in a changing environment and will allow improvement of the practice of agriculture, reduction of the demands on environmental resources, and addressing of challenges posed by global climate change. In addition, new tools and methodologies continue to be needed to advance the field of plant biology as well as to tackle questions that are intractable using current approaches. There continues to be a critical need for training in the use of these new tools and technologies, especially for those scientists who possess expertise in traditional fields of plant biology, such as plant anatomy, physiology and biochemistry.
Activities in four focus areas will be supported in FY 2014: (1) Genomics-empowered plant research to tackle fundamental questions in plant sciences on a genome-wide scale; (2) Development of tools and resources for plant genome research including novel technologies and analysis tools to enable discovery; (3) Mid-Career Investigator Awards in Plant Genome Research (MCA-PGR) to increase participation of investigators trained primarily in fields other than plant genomics; and, (4) Advancing Basic Research in Economically Important Crop Plants (ABR-PG) to develop sequence resources that are critically needed to enable or advance basic research in crop plants.
Proposals are solicited from single investigators, small groups, or multi-institution "virtual centers." 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. 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 the experimental systems best suited to the research focus and taking advantage of all available genomics tools and resources. This could include the limited use of model plant systems to rapidly test hypotheses and/or gene function. Proposers should clearly justify the relevance of the research activities to the overarching goals of the PGRP as well as their potential downstream impacts. Proposals focused entirely on the use of a non-crop model plant system are more appropriate for funding through other programs at NSF (http://www.nsf.gov/funding/pgm_list.jsp?org=BIO&ord=rect).
The PGRP is committed to broadening participation and the available research tools and resources should enable any institution to take part in plant genome research. New investigators and investigators who have not participated in the PGRP in the past, or are from small institutions, are strongly encouraged to submit a proposal. Individuals and small groups of investigators from Primarily Undergraduate Institutions (PUI), Historically Black Colleges and Universities (HBCU), Hispanic Serving Institutions (HSI), and Tribal Colleges and Universities (TCU) are especially encouraged to apply. The PGRP encourages proposals from early-career investigators and also considers proposals submitted to the CAREER program (http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503214). New investigators or mid-career investigators considering submission of a proposal for training in the use of genomic tools/approaches are strongly encouraged to contact a PGRP Program Director for further guidance.
Focus Areas for FY 2014
Genomics-empowered plant research to tackle fundamental questions in plant sciences on a genome-wide scale
The whole field of plant biology is being advanced by increased 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 more than sufficient to address many of the major unanswered questions in plant biology, some of which have not been tractable using traditional approaches. In keeping with the focus of the PGRP, projects should be developed on a whole genome, whole organelle or whole network scale. In FY 2014, proposals are especially encouraged in the following areas:
- Development of a genome-level understanding to link genes and pathways to physiological functions and phenotypes in crop plants
- Development of a genome to systems-level understanding of plant-environmental interactions, especially with respect to adaptation to climate change and response to abiotic and biotic stresses
- Systems-level approaches to understanding the interaction between the genome and the epigenome in the regulation of economically important processes in crop plants
Development of tools and resources for plant genome research including novel technologies and analysis tools to enable discovery
While tremendous advances have been made in the development of tools and technologies for plant genome research, there still remains a need for additional resources, particularly for innovations in high-throughput, high resolution phenotyping platforms to alleviate the constraint for effective utilization of genomics data and tools in the study of plants and plant processes. Proposers are encouraged to develop novel approaches focused on a specific problem or need. Potentially high-risk, high-payoff proposals or proposals that present unconventional ideas are welcomed. Priority will be given to the development of new or novel tools that are likely to contribute broadly to the advancement of the field of plant genomics. In FY 2014, proposals are especially encouraged in the following areas:
- Improved tools for data integration and analysis, especially to enable linkage of sequence data with data generated using high throughput phenotyping, proteomic and metabolomic technologies
- Novel methodologies for high-throughput, semi-automated and automated plant phenotyping, especially under field conditions and over time
- Improved tools for high-throughput gene function analysis and validation, especially to enable targeted manipulation of plant gene activity required to test novel hypotheses
- Improved tools for genome sequence assembly and analysis to enable effective use of data produced by next- generation sequencing technologies in the absence of physical maps
- Improved data 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.
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.
Mid-Career Investigator Awards in Plant Genome Research (MCA-PGR)
New ideas, approaches and technologies are needed to advance the field of plant genomics to meet societal needs. Opportunities for mid-career plant researchers/scientists to move into genomics, or adopt genomics tools and technologies to solve relevant questions will greatly enhance the whole field. The PGRP continues to offer the Mid-Career Investigator Awards in Plant Genome Research (MCA-PGR) opportunity which seeks to increase participation of mid-career investigators primarily trained in fields other than plant genomics. Especially encouraged are proposals from investigators trained in plant anatomy, physiology or biochemistry. A "mid-career" investigator is defined here as any researcher who is post-tenure and not retired. Mid-career investigators trained in genomics of non-plant systems, informatics, and other disciplines that are critical to advancing the field of plant genome research (engineering, mathematics/statistics, physiology and quantitative genetics), are also encouraged to apply. Proposals submitted to the MCA-PGR opportunity should have a research theme that is consistent with the overall goals of the PGRP as well as critical training components proposed for the applicant. Proposers are encouraged to take advantage of opportunities to develop new curriculum or course offerings that build on outcomes of the MCA-PGR activities.
NSF expects that MCA-PGR projects will take full advantage of data, materials, information, expertise, and facilities available through PGRP funded projects. Whenever appropriate, the applicant should network with existing PGRP-supported activities (consult http://www.nsf.gov/bio/pubs/awards/pgr.htm?WT.si_n=ClickedAbstractsRecentAwards&WT.si_x=1&WT.si_cs=1&WT.z_pims_id=5338& for a list of active projects). Funds may be requested to support research visits to existing PGRP-supported laboratories, for participation in training opportunities offered by existing PGRP projects, and for use of genome research facilities not available at the applicant's institution. If necessary, funds may also be requested for salary support of the applicant during the training period(s).
Investigators interested in the MCA-PGR opportunity are strongly encouraged to contact a Program Director for further guidance prior to submission of a proposal.
Advancing Basic Research in Economically Important Crop Plants (ABR-PG)
Over its sixteen-year history as part of the NPGI, the PGRP has supported the development of tools and biological resources that have enabled plant genomics communities to generate significant new insight into economically important plant pathways and processes through basic research. Advances in next generation sequencing technologies and public access to computational tools provide an opportunity for the PGRP to cost-effectively and strategically add sequence resources that would enable basic research in currently underfunded or understudied crop plants. The Advancing Basic Research in Plants of Economic Importance opportunity (ABR-PG) specifically solicits proposals that focus on biological questions in crop plant systems that could be addressed using a particular sequence or sequences. Sequence resources may include, but are not limited to, whole genome sequences, survey sequences, physical maps, and sequences that could improve genome annotations and assemblies Proposers must provide clear justification for the plant or plants selected, the type of resources to be generated and why the resources are essential to the specific question being posed. Any crop plant system may be chosen as long as it is well justified for the proposed research and the outcomes of the research will advance the goals of the PGRP. Amounts of up to $1,500,000 total for a period of up to two years may be requested for an ABR-PG project. Proposals must describe clearly how the sequence data will be disseminated and accessible to the public. Proposers are encouraged to consider the available resources and to leverage existing resources as much as possible. If other projects are under way that have overlapping goals, including international projects, proposers should present a clear plan for coordination.
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 of 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 these kinds of 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 and/or enhance ongoing PGRP-supported training and outreach efforts and enable them to increase visibility and impact are encouraged.
Massive amounts 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 to be deposited into 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, once specified quality standards have been met.
Plant genome research is actively pursued all over the world. The PGRP encourages international research collaborations, particularly with investigators from developing countries, and especially where there is a common research focus or system. When applicable, the proposed research activities should be coordinated with similar efforts in other countries to maximize efficiency and avoid unnecessary duplication of effort.
It is expected that non-US participants will 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.
Private industry has already made significant investments 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).
Additional Funding Opportunities
The PGRP will accept Research in Undergraduate Institution (RUI) proposals. Information on the scope of RUI projects and the format of these proposals can be found athttp://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5518&from=fund.
The PGRP will also accept Research Coordination Network (RCN) Proposals. Information on the scope of RCN projects and the format of these proposals can be found athttp://www.nsf.gov/funding/pgm_summ.jsp?pims_id=11691&org=BIO.
Proposals are encouraged from early-career investigators and proposals submitted to the CAREERprogram (http://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.
Finally, 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:http://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.
Proposers are encouraged to contact a Program Director about the suitability of the activity for PGRP support prior to submission of these types of proposals.
Supplemental Funding Requests
March 1 annually (or next business day if that is a weekend or holiday) is the target date for most IOS programs for Research Experiences for Undergraduates (REU), Research Experiences for Teachers (RET), Research Assistantships for High School Students (RAHSS), and Research Opportunity Award (ROA) supplement requests as well as proposals for Conferences, Symposia and Workshops (Meetings). Please note that supplemental funding is intended for unanticipated opportunities only and should be justified on this basis. Guidance for IOS PIs preparing supplemental requests is posted at http://www.nsf.gov/bio/ios/suppopp.jsp. Proposers are encouraged to contact a Program Director about the suitability of the activity for PGRP support prior to submission of supplement proposals. Requests for support of planned REU, RET, RAHSS, and ROA activities can be included in full proposals submitted in response to this solicitation. Proposers should follow guidance in the current REU solicitation (http://www.nsf.gov/pubs/2013/nsf13542/nsf13542.pdf) when including a request for a supplement (REU, RET, RAHSS or ROA) as part of the proposal.
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 approaches, and to discuss future directions of major research activities in plant genomics and bioinformatics. Conferences will be supported only if equivalent results cannot be achieved at regular meetings of professional societies or an established conference series. More information about submission of these proposals can be found at http://www.nsf.gov/publications/pub_summ.jsp?ods_key=gpg. Proposers are encouraged to contact a Program Director prior to submission of these types of proposals.
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 (http://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 (http://www.nsf.gov/publications/pub_summ.jsp?ods_key=gpg).
Grant Opportunities for Academic Liaison with Industry (GOALI)
Grant Opportunities for Academic Liaison with Industry (GOALI) promotes university-industry partnerships by making project funds or fellowships/traineeships available to support an eclectic mix of industry-university linkages. Special interest is focused on affording the opportunity for:
- Faculty, postdoctoral fellows, and students to conduct research and gain experience in an industrial setting;
- Industrial scientists and engineers to bring industry's perspective and integrative skills to academe; and,
- Interdisciplinary university-industry teams to conduct research projects.
GOALI targets high-risk/high-gain research with a focus on fundamental research, new approaches to solving generic problems, development of innovative collaborative industry-university educational programs, and direct transfer of new knowledge between academe and industry. GOALI seeks to fund transformative research that lies beyond that which industry would normally fund. More information can be found at http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504699.