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Agriculture and Food Research InitiativeCompetitive Grants Program

oundational ProgramF

Y 2010 Request for Applications F


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NATIONAL INSTITUTE OF FOOD AND AGRICULTUREU.S. DEPARTMENT OF AGRICULTURE

AGRICULTURE AND FOOD RESEARCH INITIATIVECOMPETITIVE GRANTS PROGRAMFOUNDATIONAL PROGRAM

INITIAL ANNOUNCEMENT

CATALOG OF FEDERAL DOMESTIC ASSISTANCE: This program is listed in the Catalog of FederalDomestic Assistance under 10.310.

DATES: Applications must be submitted via Grants.gov by 5:00 p.m. Eastern Time on the deadline dateindicated in the Program Area Descriptions section beginning in Part I, C (page 4). Applications receivedafter the deadline will normally not be considered for funding. Comments regarding this request for applications (RFA) are requested within six months from the issuance of this notice. Comments receivedafter this date will be considered to the extent practicable.

STAKEHOLDER INPUT: The National Institute of Food and Agriculture (NIFA) is requesting commentsregarding this RFA from any interested party. These comments will be considered in the d developmentof the next RFA for the program, if applicable, and will be used to meet the requirements of section103(c)(2) of the Agricultural Research, Extension, and Education Reform Act of 1998 (7 U.S.C.7613(c)(2)). This section requires the Secretary to solicit and consider input on a current RFA frompersons who conduct or use agricultural research, education, and extension for use in formulating futureRFAs for competitive programs. Written stakeholder comments directed toward this RFA should besubmitted in accordance with the deadline set forth in the DATES portion of this notice.

Written stakeholder comments should be submitted by mail to: Policy and Oversight Branch; Office of Extramural Programs; National Institute of Food and Agriculture; USDA; STOP 2299; 1400 IndependenceAvenue, SW; Washington, DC 20250-2299; or via e-mail to: [email protected] . (This e-mailaddress is intended only for receiving comments regarding this RFA and not for requesting information or forms.) In your comments, please state that you are responding to the Agriculture and Food ResearchInitiative Foundational Program RFA.

EXECUTIVE SUMMARY: The Department of Agriculture established the Agriculture and Food ResearchInitiative (AFRI) under which the Secretary of Agriculture may make competitive grants for fundamentaland applied research, extension, and education to address food and agricultural sciences (as definedunder section 1404 of the National Agricultural Research, Extension, and Teaching Policy Act of 1977(NARETPA) (7 U.S.C. 3103)), as amended, in six priority areas. The six priority areas include: 1) planthealth and production and plant products; 2) animal health and production and animal products; 3) foodsafety, nutrition, and health; 4) renewable energy, natural resources, and environment; 5) agriculturesystems and technology; and 6) agriculture economics and rural communities.

In fiscal year (FY) 2010, approximately $262 million is available to support the AFRI program. Of thisamount, no less than 30 percent will be made available to fund integrated research, education, andextension programs.

For FY 2010, approximately $64 million is available for support for the Foundational Program within AFRI.This RFA focuses on building a foundation of knowledge critical for solving current and future societalchallenges.

Projects supported by AFRI within this RFA include single-function Research Projects and Food andAgricultural Science Enhancement (FASE) Grants. This RFA identifies research program objectives,eligibility criteria, and matching requirements for each type of project.

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******************************************************************PLEASE READ

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Important Information about the Agriculture and Food Research Initiative

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AFRI RFAs: In FY 2010, NIFA will issue seven RFAs for the AFRI Program:(1) Foundational Program addressing the six AFRI priority areas(2) Challenge Areas:

a. Childhood Obesity Preventionb. Climate Changec. Food Safetyd. Global Food Securitye. Sustainable Bioenergy

(3) NIFA Fellowships Grant Program soliciting Pre- and Postdoctoral Fellowship Grantapplications

Applications for AFRI funds may also be solicited through other announcements including supplementalAFRI RFAs or in conjunction with multi-agency programs.

AllAFRI program information is available on the NIFA Web site at: www.nifa.usda.gov/afri .

FY 2010 NIFA Fellowships Grant Program: Beginning in FY 2010, all Pre- and Postdoctoral FellowshipGrants will be solicited via a separate NIFA Fellowships Grant Program RFA. AFRI invites applicationsfrom doctoral candidates and individuals who will soon receive or have recently received their doctoraldegree for a Pre- or Postdoctoral Fellowship Grant, as appropriate, for research, education, extension, or integrated activities. The AFRI program anticipates awarding at least $6 million in Pre- and PostdoctoralFellowship Grants. Information on the NIFA Fellowship Grants Program RFA, including the anticipatedrelease date, is available at www.nifa.usda.gov/afri .

Eligibility: Since NIFA is only soliciting Research Projects under this RFA, eligible applicants for theprograms implemented under this RFA include: (1) State Agricultural Experiment Stations; (2) collegesand universities (including junior colleges offering associate degrees or higher); (3) university researchfoundations; (4) other research institutions and organizations; (5) Federal agencies, (6) nationallaboratories; (7) private organizations or corporations; (8) individuals who are U.S. citizens, nationals, or permanent residents; and (9) any group consisting of 2 or more entities identified in (1) through (8).Eligible institutions do not include foreign and international organizations.

Award Instrument: All awards made under this RFA will be made as standard awards. A standard awardis an award instrument by which NIFA agrees to support a specified level of effort for a predetermined project

period without the announced intention of providing additional support at a future date. Award Duration: All grants (excluding Conference, Sabbatical, Equipment, and Seed Grants) haveaward duration of up to five years. Please note the procedures for no-cost extensions of time that extendthe project period beyond five years under Part VIII, B. 2. e) (page 47).

Letters of Intent: In FY 2010, certain Program Areas within AFRI require a Letter of Intent for submissionof an application. For those programs requiring a Letter of Intent, a letter is required for all grant typesexcept Conference Grant applications. Refer to the Program Area Descriptions beginning in Part I, C

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(page 4) to determine if a Letter of Intent is required for a specific Program Area. Refer to Part IV, A (page29) for instructions on the preparation of a Letter of Intent.

Annual Investigator Meetings: Beginning in FY 2010, if a Seed Grant application is funded, the ProjectDirector is required to attend annual investigator meetings starting in the second year of funding,.Reasonable travel expenses should be included as part of the project budget. For all other grant types(excluding Conference, Sabbatical, and Equipment Grants), Project Directors will continue to be requiredto attend annual investigator meetings beginning in the first year of funding.

Logic Model Requirements: There are NO logic model requirements for applications submitted to theAFRI Foundational Program. However, information and resources related to logic model planning processare provided at www.nifa.usda.gov/funding/integrated/integrated_logic_model.html . Integrated Projectsfound in other AFRI solicitations will continue to require the inclusion of a Logic Model.

Indirect Cost Limitations: NIFA is prohibited from paying indirect costs exceeding 22 percent of the totalFederal funds provided under each award. This limitation is equivalent to 0.28205 of the total direct costsof an award. See Part IV, E (page 38) for additional information.

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TABLE OF CONTENTS

PART I FUNDING OPPORTUNITY DESCRIPTION ................................................................................. 1

A. Legislative Authority and Background .................................................................................................. 1

B. Purpose and Priorities .......................................................................................................................... 1

C. Program Area Descriptions .................................................................................................................. 4

PART II Award Information ...................................................................................................................... 22

A. Available Funding ............................................................................................................................... 22

B. Types of Applications ......................................................................................................................... 22

C. Project Types ..................................................................................................................................... 22

D. Grant Types........................................................................................................................................ 23

PART III ELIGIBILITY INFORMATION .................................................................................................... 27

A. Eligible Applicants .............................................................................................................................. 27

B. Request for Determination ................................................................................................................. 27

C. Cost Sharing or Matching ................................................................................................................... 28 PART IV APPLICATION AND SUBMISSION INFORMATION ................................................................ 29

A. Letter of Intent Instructions ................................................................................................................. 29

B. Electronic Application Package .......................................................................................................... 29

C. Content and Form of Application Submission .................................................................................... 30

D. Submission Dates and Time .............................................................................................................. 38

E. Funding Restrictions ........................................................................................................................... 38

F. Other Submission Requirements ....................................................................................................... 39

PART V APPLICATION REVIEW REQUIREMENTS .............................................................................. 41

A. General ............................................................................................................................................... 41 B. Evaluation Criteria .............................................................................................................................. 41

C. Conflicts of Interest and Confidentiality .............................................................................................. 42

D. Organizational Management Information ........................................................................................... 42

PART VI AWARD ADMINISTRATION ..................................................................................................... 43

A. General ............................................................................................................................................... 43

B. Award Notice ...................................................................................................................................... 43

C. Administrative and National Policy Requirements ............................................................................. 43

D. Expected Program Outputs and Reporting Requirements ................................................................ 44

PART VII AGENCY CONTACTS ............................................................................................................. 46

PART VIII OTHER INFORMATION ......................................................................................................... 47

A. Access to Review Information ............................................................................................................ 47

B. Use of Funds; Changes ...................................................................................................................... 47

C. Confidential Aspects of Applications and Awards .............................................................................. 47

D. Regulatory Information ....................................................................................................................... 48

E. Application Disposition ....................................................................................................................... 48

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F. Materials Available on the Internet ..................................................................................................... 48

G. Electronic Subscription to AFRI Announcements .............................................................................. 48

H. Definitions ........................................................................................................................................... 49

TABLE 1. Most Successful Universities and Colleges Receiving Federal Funds. ..................................... 51

TABLE 2. Lowest One Third of Universities and Colleges Receiving Federal Funds. ............................... 52

FIGURE 1. Flow Chart for Strengthening Grant Eligibility. ......................................................................... 54


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PART I FUNDING OPPORTUNITY DESCRIPTION

A. Legislative Authority and Background

Section 7406 of the Food, Conservation, and Energy Act of 2008 (FCEA) (Pub. L. 110-246) amendssection 2(b) of the Competitive, Special, and Facilities Research Grant Act (7 U.S.C. 450i(b)) to authorizethe Secretary of Agriculture to establish the Agriculture and Food Research Initiative (AFRI); acompetitive grant program to provide funding for fundamental and applied research, extension, andeducation to address food and agricultural sciences. Grants shall be awarded to address priorities inUnited States agriculture in the following areas:

1. Plant health and production and plant products;2. Animal health and production and animal products;3. Food safety, nutrition, and health;4. Renewable energy, natural resources, and environment;5. Agriculture systems and technology; and6. Agriculture economics and rural communities.

To the maximum extent practicable, the National Institute of Food and Agriculture (NIFA), in coordinationwith the Under Secretary for Research, Education, and Economics (REE), will make grants for highpriority research, education, and extension, taking into consideration, when available, the determinationsmade by the National Agricultural Research, Extension, Education, and Economics Advisory Board(NAREEEAB) pursuant to section 2(b)(10) of the Competitive, Special, and Facilities Research Grant Act(7 U.S.C. 450i(b)(10)), as amended. The authority to carry out this program has been delegated to NIFAthrough the Under Secretary for REE.

B. Purpose and Priorities

The purpose of AFRI is to support research, education, and extension as well integrated programs byawarding grants that address key problems of national, regional, and multi-state importance in sustainingall components of agriculture, including farm efficiency and profitability, ranching, renewable energy,

forestry (both urban and agroforestry), aquaculture, rural communities and entrepreneurship, humannutrition, food safety, biotechnology, and conventional breeding. Providing this support requires that AFRIadvance fundamental sciences as well as translational research and development in support of agriculture and coordinate opportunities to build on these discoveries. This will require that AFRI alsosupport education and extension that delivers science-based knowledge to people, allowing them tomake informed practical decisions. This AFRI RFA is announcing anticipated funding opportunities for fundamental research, applied research, education, extension, and integrated research, education, andextension projects.

NIFA may also solicit applications for AFRI funds through other announcements, including supplementalAFRI RFAs or RFAs issued in conjunction with other agencies. Such announcements will be made publicin the same manner as this announcement.

The programs described herein were developed within the context of the authorized purposes of USDAresearch, extension, and education. In addition, AFRI obtains input from Congress, the NAREEEAB, aswell as many university, scientific, and agricultural committees and organizations. NIFA developed astakeholders Web page ( www.nifa.usda.gov/business/reporting/stakeholder.html ) to documentstakeholder input that is considered when developing and updating Program Area Descriptions andPriorities each year.

BackgroundIn July, 2008, the National Institutes of Health (NIH), National Science Foundation (NSF), andDepartment of Energy (DOE) asked the National Research Councils Board on Life Sciences to convene

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a committee to examine the current state of biological research in the United States and recommend how best to capitalize on recent technological and scientific advances that have allowed biologists to integratebiological research findings, collect and interpret vastly increased amounts of data, and predict thebehavior of complex biological systems . The committee produced a report entitled New Biology for the21 st Century: Ensuring the United States Leads the Coming Revolution, and a set of recommendationsthat recognize that the most effective leveraging of investments would come from a coordinated,interagency effort to encourage the emergence of a New Biology that would enunciate and address broadand challenging societal problems.

The New Biology is already emerging, but it is as yet poorly recognized, inadequately supported, anddelivering only a fraction of its potential. The committee concludes that the most effective way to speedthe emergence of the New Biology is to challenge the scientific community to discover solutions to major societal problems and outlined four broad challenges in food, environment, energy, and health that couldbe tackled by the New Biology.

The four challenges are:1. Generate food plants to adapt and grow sustainably in changing environments 2. Understand and sustain ecosystem function and biodiversity in the face of rapid change3. Expand sustainable alternatives to fossil fuels4. Understand individual health

The committee chose to focus on these four areas of societal need because the benefits of achievingthese goals would be large, progress would be assessable, and both the scientific community and thepublic would find such goals inspirational. Each challenge will require technological and conceptualadvances that are not now at hand, across a disciplinary spectrum that is not now encompassed by thefield. In the committees view, one of the most exciting aspects of the New Biology initiative is thatsuccess in achieving the four goals chosen here as examples will propel advances in fundamentalunderstanding throughout the life sciences. Because biological systems have so many fundamentalsimilarities, the same technologies and sciences developed to address these four challenges will expandthe capabilities of all biologists.

USDA NIFA ApproachThe report New Biology for the 21 st Century bolsters the case for increasing the level and effectiveness

of USDAs agricultural research, education, and extension programs. These efforts have includedcreating NIFA and significantly increasing funding over previous levels for its research, education, andextension programs.

AFRI is one of NIFAs major programs through which to address critical societal issues such as those laidout in the New Biology for the 21 st Century report. USDA leadership has integrated the six AFRI priorityareas (outlined in Part I, A) with the four challenges and the approach laid out in the New Biology for the21 st Century Report to identify five primary challenge areas around which to structure the AFRI programand begin to focus the Departments investment in enabling an integrated approach to biologicalresearch, education, and extension. USDA science will support the following challenges:

1. Keep American agriculture competitive while ending world hunger 2. Improve nutrition and end child obesity

3. Improve food safety for all Americans4. Secure Americas energy future5. Mitigate and adapt to climate change

To address these challenges at a meaningful scale and to achieve outcomes of relevance to the societalchallenges, NIFA intends to release several AFRI RFAs. They will address each of the five challenges,enable transition and refocusing of grants made previously under AFRI, and provide pre- andpostdoctoral fellowship opportunities. These RFAs will solicit applications for larger awards for longer periods of time to enable greater collaboration among institutions and organizations and integration of basic and applied research with deliberate education and extension programs.

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In FY 2010, AFRI will solicit projects addressing the above challenges through five separate challengearea RFAs, each addressing one of the challenges. AFRI will also support research grants in the six AFRIpriority areas to continue building a foundation of knowledge critical for solving current and future societalchallenges. These six foundational programs are being announced in a single, separate RFA. In addition,funding opportunities for pre- and postdoctoral fellowship grants will be offered in a single, separate RFA.

The following table is provided to facilitate identification of appropriate funding opportunities for AFRIapplicants:

AFRI Priority Area FY 2010 AFRI RFAPlant Health and Production and Plant Products Climate Change

Foundational ProgramsGlobal Food SecuritySustainable Bioenergy

Animal Health and Production and AnimalProducts

Climate ChangeFood SafetyFoundational ProgramsGlobal Food Security

Food Safety, Nutrition, and Health Childhood Obesity PreventionFood SafetyFoundational Program

Renewable Energy, Natural Resources, andEnvironment

Climate ChangeFoundational ProgramsSustainable Bioenergy

Agriculture Systems and Technology Climate ChangeFood SafetyFoundational ProgramsSustainable Bioenergy

Agriculture Economics and Rural Communities Childhood Obesity PreventionClimate ChangeFood SafetyFoundational ProgramsSustainable Bioenergy

Foundational Program:This RFA focuses on building a foundation of knowledge critical for solving current and future societalchallenges. Project types supported by AFRI within this area include single-function Research Projectsand Food and Agricultural Science Enhancement (FASE) Grants.

Other sources of NIFA funding for work relevant to the Global Food Security challenge area are asfollows:

Increasing Scientific Data on the Fate, Transport, and Behavior of Engineered Nanomaterials inSelected Environmental and Biological Matrices (joint with the Environmental Protection Agency(EPA) and the National Science Foundation (NSF)) Total Program Funds: Approximately $4.2 million ($1.2 million from AFRI)Information is available at http://epa.gov/ncer/rfa/2010/2010_star_nano.html

Interagency Opportunities in Metabolic Engineering (joint with EPA, the National Institutes of Health (NIH), the Department of Defense (DOD), the Department of Energy (DOE), the NationalInstitute of Standards and Technology (NIST), NSF, and NASA)Total Program Funds: Approximately $9 million ($500,000 from AFRI)Information is available at www.nsf.gov/publications/pub_summ.jsp?ods_key=nsf08588

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C. Program Area Descriptions

NIFA offers a number of Program Areas that support Research, Education, Extension, and IntegratedProjects. Applicants are encouraged to review this entire RFA, other AFRI RFAs, as well as explore other programs offered by NIFA to find the most appropriate source of funding. This RFA can be accessedthrough the Agencys Web site: www.nifa.usda.gov/afri .

The following Foundational Program Areas provide a base from which applications for Research Projectsand FASE Grants may be developed. These descriptions provide boundaries on the scope of eachindividual Program Area within the scope of Program Area Priorities. AFRI encourages submission of innovative high-risk projects with potential for future high impact on agriculture, as well as innovativeapplications with potential for near-term use. The areas of science listed below will be supported in FY2010; however, the emphasis may change in FY 2011.

Projects addressing biological issues should focus on agriculturally-important organism(s) to accomplishthe project objectives. The use of other organisms as experimental model systems must be justifiedrelative to the goals of the appropriate program.

Note to multidisciplinary research teams: AFRI recognizes the value of research performed as a teameffort and recommends the following be taken into consideration when assembling a project team anddeveloping an application for funding. A competitive project will have objectives aligned with AFRIProgram Area Priorities and the appropriate person to complete the tasks proposed. A clear managementstrategy should be provided which identifies the contribution of each member of the team.

1. Plant Health and Production and Plant Products

Plant production and health plays a critical role in the sustainability and competitiveness of U.S.agriculture and, as a result, in the success and growth of the Nations economy. An increasedunderstanding of plant biology from the genome to the systems level provides the foundation for development of plant varieties with increased yield, reduced production cost, enhanced quality, andnew uses for food and industry. Similarly, the study of plant pests and diseases underpins thedevelopment of innovative approaches to increase effects of beneficial microbes, arthropods, andnematodes and limit harmful effects of new or re-emerging pathogens or pests.

In FY 2010, AFRI invites Research Project applications in the following programs in the Plant Healthand Production and Plant Products area:

a. Plant Sciences

Program Area Code A1101 Letter of Intent Deadline April 20, 2010 (5:00 p.m., ET); see Part IV, A (page 29) for instructionsApplication Deadline July 7, 2010 (5:00 p.m., ET)Total Program Funds Approximately $7.5 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project period of up to 5years will not be reviewed

National Program Leaders Drs. Liang-Shiou Lin (202-401-5045 or [email protected] ), ShingKwok (202-401-6060 or [email protected] ), and Ed Kaleikau (202-401-1931 or [email protected] )

BackgroundBasic plant sciences play a very important role in the sustainability and competitiveness of U.S.agriculture. There is a need for fundamental knowledge of plant biology to facilitate development of agricultural and forestry plants with improved or optimized performance. The lack of knowledge aboutbasic plant processes often limits the translation of genomic and genetic information in improvingagricultural plant and forest productivity, quality, and sustainability. Fundamental knowledge of basic

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plant sciences, along with other crop improvement techniques, will lead to practical applications, suchas enhancing the nutritional value of plant-based foods, increasing the productivity and fitness of agricultural plants and trees, better utilizing trees and agricultural plants for sustainable production of bioenergy, and developing agricultural plants that is sustainable to climate change. To meet this goal,proposals are requested to understand epigenetic mechanisms or gene regulatory networks thatregulate plant growth and development.

Program Area Priorities Applicants must address at least one of the following:1. Plants represent a premier experimental system for understanding epigenetic regulation and can

yield fundamental understanding of the impacts of epigenetic modifications on chromosomestructure and gene expression. Understanding epigenomes and related changes to plant growthand development will have broad impacts on plant health and production. Applications are limitedto epigenetic regulation of crop plants in: Water use efficiency or adaptation to drought Root or seed development Nutrient uptake, assimilation, and/or utilization

2. Light and hormones play critical roles in controlling plant growth and development. Understandinghow crop plants are able to coordinate the expression, assembly, and function of these regulatorynetworks will have broad impacts on plant productivity. Applications are limited to regulatorynetworks of crop plants in: Light or hormone signal transduction Photosynthesis or carbon sequestration

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. The program will not support research focusing solely on model organisms. If a model organism

is used in the study, the knowledge gained must be utilized for study of plants of agriculturalimportance in the submitted project, and such study should be a significant and integralcomponent within the experimental design.

b. Pest and Beneficial Insects in Plant Systems

Program Area Code A1111Letter of Intent Deadline April 22, 2010 (5:00 p.m., ET); see Part IV, A (page 29) for instructionsApplication Deadline June 10, 2010 (5:00 p.m., ET)Total Program Funds Approximately $6 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project periods of up to 5years will not be reviewedNational Program Leader Dr. Mary Purcell-Miramontes (202-401-5168 or [email protected] )

BackgroundInsects in agricultural systems have a critical role in affecting food security. Insects compete for agricultural crops and significantly reduce crop yields. Insects also contaminate stored food andvector plant diseases, which seriously damages crop quality. Conversely, insect pollinators are vitallyimportant to maintaining the worlds food supply. It is estimated that one-third of the agricultural cropsconsumed depend on pollinators. Recent studies indicate that pollinators are in serious decline world-wide. Numerous factors have been implicated in this phenomenon; e.g. , habitat destruction, drought,global warming, loss of floral resources, poor nutrition, invasive pests, diseases, and pesticideexposure. Other beneficial insects such as parasitoids and predators are also important. In severalsystems, insect pests are unable to establish or reach economically injurious levels due to the actionof these biological control agents. Similar factors that threaten pollinator species can also adversely

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affect predators and parasitoids. Fundamental and applied research is needed to enhancepopulations of beneficial insects as well.

Agricultural chemicals are still the primary means to control insect pests. Research has demonstratedadverse effects on public health, pollinators, and biological control agents. Environmentally safer alternatives are available in several systems. However, efficacy is often not optimal, and fundamentalknowledge is still lacking in biological processes which could lead to better usage of thesealternatives. In addition, the growing demand for organically-grown plants has increased needs for biological approaches to manage pests.

Program Area Priorities Applicants must address one or more of the following:1. Understand the environmental and biological processes that affect the abundance and spread of

agriculturally important insects. Organismal and molecular approaches are appropriate. Researchon Colony Collapse Disorder and native or managed bee pollinators is included in this priority.

2. Increase fundamental knowledge of plant-insect interactions affecting abundance and behavior of insects. Studies on signaling mechanisms or communication between insects or between insectsand plants are encouraged.

3. Elucidate genetic mechanisms used by insects to infest and develop in plants andcorrespondingly how plants respond to insects.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. This program is limited to the following plant systems: Horticultural and field crops, forests and

rangelands. Pest organisms are limited to insects and mites. Beneficial species include insectbiological control organisms ( e.g. , predators and parasitic wasps) native bees and honey bees.The following systems will not be supported in FY 2010: Livestock, transgenic crops, ornamentalplants, and turf grass. Organisms not supported include ticks, nematodes, termites, ants, storedproducts pests, nuisance pests, and insects that vector plant, animal and human diseases.

Projects that include an evaluation of management of pests are encouraged to include aneconomic component ( e.g. , how crop yields affected are or a cost-benefit analysis).

The application must include a section providing a justification for the system studied, in terms of economic or societal benefits (either in the short or long-term) to agriculture and/or ruralcommunities. Studies of model systems may be submitted to the program only if knowledgegained is applied to systems of economic or societal importance within the duration of thesubmitted project.

Applications pertaining to pollinator decline and Colony Collapse Disorder must justify how theresearch either builds upon or does not overlap with the goals of other funded research(Managed Bee CAP, area-wide project, etc .). Letters of support from Project Directors in other funded projects are strongly encouraged.

2. Animal Health and Production and Animal Products

Agriculturally important animal species, including equine and aquacultured species, play a crucial rolein the success and growth of the Nations economy. For example, the USDA Economic Research

Service (ERS) projects that cash receipts for livestock, poultry, and dairy alone will total $119 billion in2009 and accounts for 42 percent of total forecast U.S. agricultural receipts. Maintaining a strong,internationally-competitive animal agriculture industry and consumer access to safe and affordableanimal products, however, faces increasing challenges from animal diseases, reduced fertility inseveral animal species, suboptimal nutrition and growth, and non-tariff trade barriers.

In FY 2010, AFRI invites Research Project applications in the following programs in the Animal Healthand Production and Animal Products area:

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The program encourages applicants to take advantage of molecular approaches ( e.g. , functionalgenomics and proteomics) in order to accelerate the discovery of new targets for diagnostics,vaccines, and treatments. The program supports international efforts to analyze the current andfuture value of microarray data. Inclusion of microarray studies requires the addition of astatement addressing Minimum Information about Microarray Experiment (MIAME) compliance(see: http://www.mged.org ). Applicants must plan to release the results of their research to the

public in a timely manner. Inclusion of power analyses is required if a research project uses experimental animals. Failure todo so may result in a lower proposal ranking. Studies that propose to test and compare groupsmust justify the sample size chosen for each group. The main statistical considerations in samplesize calculation are the magnitude of the effect size ( e.g. , difference in proportions, means,survival times, etc .), standard deviation of the outcome, power and the significance level. Theseassumptions should be described in the rationale for the sample size. Studies that propose toestimate a population characteristic, such as the prevalence of disease, sensitivity and/or specificity of an assay should describe the allowable error margin around the estimate ( e.g. , 5percent) and desired confidence level ( e.g. , 95 percent) used to determine the sample size. Themost common problem is lack of adequate sample size, while use of more animals than isnecessary is also an important ethical concern.

b. Animal Health and Production: Animal Reproduction

Program Area Code A1211 Letter of Intent Deadline Letter of Intent NOT required for this Program AreaApplication Deadline May 4, 2010 (5:00 p.m., ET)Total Program Funds Approximately $4.0 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project period of up to 5years will not be reviewedNational Program Leaders Dr. Mark Mirando (202-401-4336 or [email protected] )

BackgroundPoor fertility is a major factor limiting the efficiency of animal production and, over the past severaldecades, fertility has declined significantly in several species of agricultural importance. This rate of decline has far outpaced the discovery of new information on the reproductive biology of theseanimals. Research is needed that expands our understanding of the basic biological mechanisms of reproduction in livestock, poultry, equine, and aquacultured species. This fundamental knowledge isrequisite to the development of new management strategies to mitigate poor fertility and increasereproductive efficiency in herds and flocks. Areas with major gaps in knowledge include thehypothalamic-pituitary axis; gonadal function, (endocrine as well as production, function, andpreservation of gametes); and embryonic and fetal development ( e.g. , interaction between theconceptus and its uterine environment).

Program Area Priorities Applicants must address at least one of the following:1. Function of the hypothalamic-pituitary-gonadal axis.2. Embryonic and fetal development, including interaction between the conceptus and its uterine

environment.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29 .) Applications from and collaborations with Minority Serving Institutions are strongly encouraged. Projects addressing uterine defense mechanisms are NOT suitable for this area. All model systems, especially the use of laboratory animals, cell cultures, etc., must be thoroughly

justified in terms of the program guidelines and relevance to U.S. animal agriculture. Thisprogram no longer accepts applications whose studies primarily utilize non-agricultural or non-aquacultured species as animal models.

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Applications that involve genomic or proteomic work ( e.g. , transcriptional/expression profiling,identification of single nucleotide polymorphisms, promoters or regulatory elements, or mapping/sequencing of genes involved in reproduction) must include substantial physiological or functional studies at the cellular, systemic, or whole animal level.

The program encourages applicants to take advantage of molecular approaches ( e.g. , functionalgenomics and proteomics) in order to accelerate the discovery of new targets for diagnostics,

vaccines, and treatments. The program supports international efforts to analyze the current andfuture value of microarray data. Inclusion of microarray studies requires the addition of astatement addressing Minimum Information about Microarray Experiment (MIAME) compliance(see: http://www.mged.org ). Applicants must plan to release the results of their research to thepublic in a timely manner.

Inclusion of power analyses is required if a research project uses experimental animals. Failure todo so may result in a lower proposal ranking. Studies that propose to test and compare groupsmust justify the sample size chosen for each group. The main statistical considerations in samplesize calculation are the magnitude of the effect size ( e.g. , difference in proportions, means,survival times, etc .), standard deviation of the outcome, power and the significance level. Theseassumptions should be described in the rationale for the sample size. Studies that propose toestimate a population characteristic, such as the prevalence of disease, sensitivity and/or specificity of an assay should describe the allowable error margin around the estimate ( e.g. , 5percent) and desired confidence level ( e.g. , 95 percent) used to determine the sample size. Themost common problem is lack of adequate sample size, while use of more animals than isnecessary is also an important ethical concern.

c. Animal Health and Production: Animal Health

Program Area Code A1221Letter of Intent Deadline Letter of Intent NOT required for this Program AreaApplication Deadline May 5, 2010 (5:00 p.m., ET)Total Program Funds Approximately $5.0 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project period of up to 5years will not be reviewedNational Program Leaders Drs. Peter Johnson (202-401-1896 or [email protected] ) andMargo Holland (202-401-5044 or [email protected] )

BackgroundOn a global basis, diseases of livestock (including horses) and poultry and aquacultured species aresignificant hindrances to sustainable animal production, as well as animal well-being. In addition tocontributing to animal suffering, diseases result in billions of dollars of economic losses in the U.S.annually, with global losses exceeding hundreds of billions of dollars. New and improved animaldisease prevention, control, and mitigation strategies are needed to address current losses andprepare for future threats. Current knowledge gaps in these areas, however, seriously impede amajor reduction in animal diseases that are already present in the U.S. Information gaps also

jeopardize food security and the future viability of animal industries by increasing animalsvulnerability to pathogens which may establish new niches or undergo genetic mutations to result innew and re-emerging diseases. Research is also needed to develop effective methods to detect and

control the potential spread of foreign diseases that are accidentally or intentionally introduced.

A growing number of current control strategies, such as antibiotics and pesticides, are becoming lesseffective due to increasing pathogen resistance. Use of these pharmaceutical products and pursuit of new ones will likely be further reduced due to societal concerns and high development costs.Similarly, current vaccines face the threat of further reduction of efficacy due to pathogen genetic driftand mutation. With fewer options expected in the future to prevent and control important animaldiseases, the need for new and improved tools is clear. By better understanding pathogenesis, host-pathogen interactions, immunology, epidemiology, and disease ecology, global animal health willimprove through the discovery and development of innovative tools and disease management

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protocols. This will also support a reduction in non-tariff trade barriers and continue to safeguard theproduction of high quality foods for consumers.

Program Area Priorities Applicants must address at least one of the following:Improved prevention, control and/or mitigation of the following diseases:1. Aquaculture : Visceral Toxicosis of Channel Catfish (limited to developing practical and

economical prevention or control tools/measures to reduce losses that can be used oncommercial farms within 2-5 years)

2. Beef cattle : Bovine Respiratory Disease Complex (limited to study of the synergy of major bacterial and viral agents implicated in BRDC to support improved prevention/control)

3. Broilers : Infectious Laryngotracheitis (limited to strategies for improved vaccines)4. Dairy cattle : Staphylococcus aureus or Streptococcus species mastitis (limited to host-pathogen

interactions to support improved prevention/control)5. Layers : E. coli peritonitis (limited to strategies for prevention/control)6. Swine : Porcine Reproductive and Respiratory Syndrome (limited to study of mechanisms of

heterologous protection to support improved vaccines)

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. The following areas are NOT suitable for this program: (1) disease surveillance as a principal

focus; (2) identification of candidate genes for disease resistance; and (3) proposals studyingplant-based vaccines

All model systems, especially the use of laboratory animals, cell cultures, etc., must be thoroughly justified in terms of the program guidelines and relevance to U.S. animal agriculture. Thisprogram no longer accepts applications whose studies primarily utilize non-agricultural or non-aquacultured species as animal models.

Applications that develop new or improved diagnostic tests are expected to include anappropriate validation plan. Failure to do so may result in a lower proposal ranking.

Applications that involve genomic or proteomic work ( e.g. , transcriptional/expression profiling,identification of single nucleotide polymorphisms, promoters or regulatory elements, or mapping/sequencing of genes involved in reproduction) must include substantial physiological or functional studies at the cellular, systemic, or whole animal level.

The program encourages applicants to take advantage of molecular approaches ( e.g. , functionalgenomics and proteomics) in order to accelerate the discovery of new targets for diagnostics,vaccines, and treatments. The program supports international efforts to analyze the current andfuture value of microarray data. Inclusion of microarray studies requires the addition of astatement addressing Minimum Information about Microarray Experiment (MIAME) compliance(see: http://www.mged.org ). Applicants must plan to release the results of their research to thepublic in a timely manner.

Inclusion of power analyses is required if a research project uses experimental animals. Failure todo so may result in a lower proposal ranking. Studies that propose to test and compare groupsmust justify the sample size chosen for each group. The main statistical considerations in samplesize calculation are the magnitude of the effect size ( e.g. , difference in proportions, means,survival times, etc .), standard deviation of the outcome, power and the significance level. Theseassumptions should be described in the rationale for the sample size. Studies that propose toestimate a population characteristic, such as the prevalence of disease, sensitivity and/or specificity of an assay should describe the allowable error margin around the estimate ( e.g. , 5percent) and desired confidence level ( e.g. , 95 percent) used to determine the sample size. Themost common problem is lack of adequate sample size, while use of more animals than isnecessary is also an important ethical concern.

Applications that address Porcine Reproductive and Respiratory Syndrome (PRRS) are requiredto briefly summarize in the Project Narrative how the proposed work fits within the framework of the community objectives established for the PRRS CAP: www.prrs.org (without being duplicativeof already funded projects).

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3. Food Safety, Nutrition, and Health

The maintenance of human health is significantly affected by the quantity and quality of foodconsumed and by foods that are contaminated with disease-causing microorganisms or toxins.Nutrition, obesity prevention, and food quality and safety are of paramount importance to theproducer, processor, distributor, and consumer. Data generated from these studies will be used for updating dietary recommendations, formulating national nutrition and food safety policy, andstimulating new product developments by the food industry.

In FY 2010 AFRI invites Research Project applications in the following programs in the Food Safety,Nutrition, and Health area:

a. Food-borne PathogenPlant Interactions

Program Area Code A1301Letter of Intent Deadline April 14, 2010 (5:00 p.m., ET); see Part IV, A (page 29) for instructionsApplication Deadline May 26, 2010 (5:00 p.m., ET)Total Program Funds Approximately $3.5 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project period of up to 5years will not be reviewedNational Program Leaders Drs. Jeanette Thurston (202-720-7166 or [email protected] )and Ann Lichens-Park (202-401-6460 or [email protected] )

BackgroundGaining an understanding of the mechanisms by which human pathogens attach, internalize, travel,survive, and multiply within a plant will greatly improve our ability to develop effective pathogencontrol and mitigation strategies. The research supported by this program will generate fundamentaland basic information pertaining to the physical and molecular mechanisms that enable humanpathogens to attach, internalize, grow and survive in fresh fruit, vegetables, and nuts. In addition, thisprogram will generate information on how plants, plant pathogens and plant-associated micro biota

interact with food-borne pathogens and if these associations affect the attachment and fate of humanpathogens on fresh crops.

Program Area Priorities Applicants must address the following:1. Studies must address physical and molecular mechanisms that allow food-borne pathogens

(bacteria, parasites, and/or viruses) to attach onto and internalize into fresh food crops, includingnuts. This research should include an assessment of how plant pathogens, plant micro biota andactivities of the plant itself enhance or limit food-borne pathogen attachment and internalization.Studies must include an assessment of a variety of environmental conditions (temperature,moisture, plant stress, etc.) to understand if they affect food-borne pathogen attachment andinternalization. The research team must include a microbiologist(s) that has experience with thefood-borne pathogen(s) under study and a plant scientist(s) with expertise in the food crop(s)under study.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. The study of multiple pathogens and inclusion of pathogens important to high risk populations is

highly encouraged. The study of multiple fresh fruits, vegetables or nuts is highly encouraged.

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b. Practical Approaches to Food Safety

Program Area Code A1311Letter of Intent Deadline May 12, 2010 (5:00 p.m., ET); see Part IV, A (page 29) for instructionsApplication Deadline August 4, 2010 (5:00 p.m., ET)Total Program Funds Approximately $2 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project period of up to 5years will not be reviewedNational Program Leaders Dr. Jeanette Thurston (202-720-7166 or [email protected] )

BackgroundThe FDA Center for Food Safety and Applied Nutrition (CFSAN) focuses specifically on programs,activities, and resources that promote food safety. In an effort to expand the scope of this program,NIFA and FDA are initiating a collaborative, interagency research program to support researchcovering specific food safety priorities.

Program Area Priorities Applicants must address the following:1. Studies must develop and validate on-farm and/or post-harvest processing sampling plans for

detection and enumeration of food-borne pathogens on produce and in environmental (soil,water, fomites, and manure) samples. The sampling plans must include criteria on how tointerpret the data from studies with a large number of samples with extremely low levels of pathogens and assist in validating the metrics used in Good Agricultural Practices (GAPs).Criteria for interpretation of data must be developed considering different food-borne pathogens(bacteria, viruses, and parasites) and take into consideration that there can be detection methoddifferences in specificity and sensitivity based on the targeted pathogen and sample matrix.These detection method variations can lead to different interpretations of samples wherepathogens are/are not detected. Also, the severity of disease produced by the detected pathogenshould be another factor considered in the criteria. Other factors (biological, environmental,climatic, etc) important in the interpretation of food-borne pathogen data should also be included.At least one food-borne bacterium, viral, and parasitic pathogen each must be included in theanalysis (a minimum of three pathogens). Methods used to validate the sampling plan and the

sampling plan itself must be statistically valid. In order to effectively develop and conduct a studythat addresses this priority, a statistician, microbiologist, risk analysis professional, andagricultural extension specialist must be part of the research team.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. Research aimed solely at development of a detection methodology will not be considered for

review. Inclusion of additional food-borne pathogens is highly encouraged, especially those important to

high-risk populations.

c. Reducing Food Allergies by Improving Food Quality

Program Area Code A1321Letter of Intent Deadline April 14, 2010 (5:00 p.m., ET); see Part IV, A (page 29) for instructionsApplication Deadline June 14, 2010 (5:00 p.m., ET)Total Program Funds Approximately $4.5 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project periods of up to 5years will not be reviewedNational Program Leaders Drs. Dionne Toombs (202-401-2138 or [email protected] ) andRam Rao (202-401-6010 or [email protected] )

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BackgroundFood allergy is a life-threatening reaction to foods by sections of populations. It is estimated that 150to 200 Americans die each year because of allergic reactions to food. Approximately 30,000Americans go to the emergency room each year to get treated for severe food allergies. Foodallergies affect about two percent of adults and four to eight percent of children in the United States,and the number of young people with food allergies has increased over the last decade, according toa recent report by the Centers for Disease Control and Prevention. Eight major foods or food groups

milk, eggs, fish, Crustacean shellfish, tree nuts, peanuts, wheat, and soybeans account for 90percent of food allergies. In addition, other food ingredients such as food additives and gluten cancause allergic/immune mediated reactions. At present, there is no known cure for food allergies. Foodprocessing has the potential for modifying the nature of the food allergen. There is a need, however,to understand the basic chemical and physical nature of the food allergens.

Chemical, physical, and biological processing methods continue to be at the core of the scienceneeded to improve the food quality and value. For this program, an understanding of the basicmechanisms involved in the interactions of molecules and their aggregates in the food ingredientsand food matrix in controlling the allergenicity and associated quality attributes of the foods isessential. Innovative physical, chemical, and biological processing methods to reduce/eliminateallergens in foods without compromising sensory and nutritional quality will be supported

Program Area Priorities Applicants must address at least one of the following:1. Characterization of unique biochemical and biophysical properties of food allergens enabling their

binding to IgE and how food processing might affect these unique characteristics2. Development of methods for qualitative and quantitative detection of allergens, including ex vivo

and in vivo models3. Physical, biological, and chemical processing methods that result in reduction or elimination of

allergens in foods, without affecting their sensory and nutritional/health qualities.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. This program funds applications in the post harvest food quality area only. Multi-disciplinary approaches are highly encouraged. Multidisciplinary proposals should include at

least 2 disciplines related to food science (chemistry, biochemistry/biology, physics, engineering,microbiology, biometry, sensory science, and nutrition).

4. Renewable Energy, Natural Resources, and Environment

The fundamental concept behind this area of programs is the application of ecological, economic, andsociological principles to agricultural production systems. The concept of agroecosystems or agricultural working lands can be applied within agriculture, rangeland, forested, or communitysystems at a range of spatial scales including the field, family, the farm level enterprise, thelandscape, watershed, institution, or community. Agriculture as managed systems involves humaninteractions and use of inputs. These production systems are influenced by and, in turn, influence the

natural systems surrounding them.

Human well-being is inextricably linked to the sustainable use and management of agroecosystems.The fundamental purpose of agriculture is to manage ecological structures, functions, and processesto favor human needs. The concept of sustainable agroecosystem management allows for achievingthe traditional agricultural goal of production while balancing the goals of conservation and protectionof natural resources, mitigation of environmental impacts, maintenance of ecosystem services, andrural community viability. One benefit of the agroecological approach is that it accommodates a broadrange of performance criteria in addition to increased production, such as ecological goods and

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services, sustainability, food security, energy resources, environmental quality, economic viability,and resource conservation. These criteria provide focus for the various programs.

In FY 2010, AFRI invites Research Project applications in the following programs in the RenewableEnergy, Natural Resources, and Environment area:

a. Microbial Communities in Soil

Program Area Code A1401Letter of Intent Deadline May 3, 2010 (5:00 p.m., ET); see Part IV, A (page 29) for instructions Application Deadline August 23, 2010 (5:00 p.m., ET)Total Program Funds Approximately $4.5 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project periods of up to 5years will not be reviewedNational Program Leaders Drs. Ann Lichens-Park (202-401-6460 or [email protected] ) andNancy Cavallaro (202-401-5176 or [email protected] )

BackgroundAgricultural soils are teeming with microorganisms. Soil microorganisms have significant impacts onnumerous agriculturally important processes, including plant production and protection, nutrientcycling and natural resource conservation. Sustainability of agricultural production systems arecritically dependent on the functioning of soil microorganisms. However, there are significant gaps inour knowledge of the microbes that live in the soil and how they function. Soil microbial communitiesare complex and the majority of soil microorganisms are currently unculturable. A more thoroughunderstanding is needed about the microbial species and communities in agricultural soils and howagricultural production and pest management approaches affect the diversity and functioning of thosesoil microorganisms. It is expected that improved understanding of microbial communities in soil willlead to 1) more effective biological control approaches to managing plant pests and diseases, and 2)improved methods of maintaining the healthy soils needed to maximize sustainable food production.

This program will support the discovery and characterization of soil microorganisms in agriculturaland forestry production systems. It will begin to characterize the communication systems betweenmicroorganisms and plants in the rhizosphere and it will build the foundations for a more extensivefuture effort to characterize one or a few model soil microbial communities.

Program Area Priorities Applicants must address at least one of the following:1. Genomic, metagenomic and molecular methods allow researchers to identify and begin to

characterize soil microorganisms in novel ways. This priority area will support discovery andclassification of agriculturally relevant soil microbial communities and their members. This priorityarea will support metagenomic approaches to characterizing soil microbial communitiescombined with sequencing of reference microbial strains which are components of the communityor communities under study. Proposals are expected to utilize both metagenomic and referencestrain sequencing approaches. The selection of reference strains must be well justified in terms of agricultural relevance. In addition, applicants are encouraged to select reference strains that areamenable to genetic approaches to elucidate gene function. Proposals should test a specific

hypothesis or hypotheses focused on how a specific biotic or abiotic factor or factors will alter thecomposition or functioning of the microbial community under study.2. The determination of molecular mechanisms of communication among bacterial and plant

members of rhizosphere communities. This priority area includes elucidation of communicationmechanisms associated with bacterial quorum sensing and/or signaling between plant roots andplant-associated microbes.

3. Proposals to develop and support a national workshop in the form of a Conference Grant to seekstakeholder input on the location(s) and characteristics of a model soil microbial community or communities which could be characterized in greater detail in an effort to better understand thecomposition and functioning of agriculturally important soil microbial communities. Proposals

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addressing this priority area should specifically indicate how the workshop will be publicized.Applicants should include a list of the types of stakeholders who would be included in theworkshop and the products that would result from the workshop ( e.g. , workshop proceedingsand/or white papers). It is anticipated that no more than one workshop proposal will be funded.The maximum award size for applications addressing this priority area will be $50,000 for oneyear.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. All soil environments and plants under study must be strongly justified in terms of agricultural

importance.

b. Agricultural Water Science

Program Area Code A1411 Letter of Intent Deadline Letter of Intent NOT required for this Program AreaApplication Deadline May 19, 2010 (5:00 p.m., ET)

Total Program Funds

Approximately $4.5 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project periods of up to 5years will not be reviewedNational Program Leader Dr. James P. Dobrowolski (202-401-5016 or

[email protected] )

BackgroundIn the United States, agriculture is responsible for approximately 40 percent of surface water withdrawals and nearly 70 percent of consumptive water use. Agriculture also is recognized as theleading cause of non-point source pollution in surface water and groundwater across the nation.Protecting water resources and increasing the efficiency of agricultural water use are critical to long-term sustainability of U.S. water resources and agricultural production. As part of USDAs AgriculturalWater Security initiative, the Agricultural Water Science program goals include improving risk-basedapproaches to both drought preparedness and irrigated agriculture with recycled water, twointerventions critical to sustainable water use for agricultural and energy production, the maintenanceof ecosystem services.

Program Area Priorities Applicants must address at least one of the following:1. Threshold values of drought indicators are drought triggers and tie the levels of drought severity

with appropriate responses to maintain agricultural production. Key to reducing drought impactson agriculture or determining drought aid and eligibility are readily understandable, scientificallysound drought triggers with temporal and spatial sensitivity and specificity. Develop the sciencebehind the most appropriate drought triggers and provide an understanding of the connectionbetween trigger levels and drought response decisions. NIFA is interested in the development of a trigger or triggers that have broad applicability across the states and territories of the U.S.

2. Recycled water from both municipal and return flow sources used exclusively or blended withsurface or groundwater for agricultural irrigation often retains constituents that could pose a riskof contamination for crops eaten fresh. Understand the potential and relevance for bioaccumulation of recycled water constituents applied at typical irrigation rates used exclusivelyor through blending with surface and groundwater sources.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. Applications addressing integrated research, education, and extension for water resources should

consider submission to the National Integrated Water Quality Program.

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5. Agriculture Systems and Technology

The scientific knowledge generated will lead to new and improved uses for agricultural and forestrybiomass in bioenergy and industrial applications and apply cutting edge technologies and tools, suchas nanotechnology, genomics, proteomics, and metabolic engineering, to ensure that agriculturalproduction in the U.S. remains competitive, innovative, and sustainable.

In FY 2010, AFRI invites Research Project applications in the following programs in the AgricultureSystems and Technology area:

a. Engineering Approaches for Improved or Alternative Management Systems to Safeguard Animal Welfare

Program Area Code A1501 Letter of Intent Deadline April 14, 2010 (5:00 p.m., ET); see Part IV, A (page 29) for instructionsApplication Deadline July 8, 2010 (5:00 p.m., ET)Total Program Funds Approximately $4.0 millionProposed Budgets exceeding $700,000 total (including indirect costs) for project periods of up to 5years will not be reviewedNational Program Leaders Drs. Margo Holland (202-401-5044 or [email protected] ),Richard Hegg (202-402-6550 or [email protected] ), and Peter Johnson (202-401-1896 or [email protected] )

BackgroundDefining and enhancing animal well-being throughout the food production cycle is a global challengefacing animal agriculture. Despite limited science-based knowledge to guide food animal well-being,societal demands have begun to encourage legislative bans or regulations on certain poultry andswine production systems and the development of certification programs in the United States. Abetter understanding of current food animal production systems and the development of newagricultural engineering standards for food animal management systems and their impact on animalwell-being is vital to remain competitive globally, avoid trade barriers, and maintain consumer trust inanimal agriculture. Improving valid scientific assessments of animal well being will enhance relianceon standards that reflect actual animal needs. The objective of this program is to increase theknowledge base and development of agricultural engineering approaches, as well as performancestandards for animal management systems with the goal of enhancing animal well being. Enhancedanimal well-being will be accomplished through improved well-being assessment (measures of cognition, physiology, motivation, behavior, and spacing requirements), improved and newmanagement/confinement production systems, and housing ( i.e. , improved feeding, watering,bedding practices and equipment design (pen/cage design, individual and population densities,ventilation).

Program Area Priorities Applicants must include the first priority in all applications and one of theremaining 2 priorities:

1. Objective, quantitative and qualitative measurement methods/standards for assessing animalwell-being by the development of valid, reliable, and reproducible systemic approaches thatinclude the animals physical condition, biological phenomena ( i.e. , reproduction, growth, andhealth), and cognitive well-being;

2. Comparisons between different confinement systems or development of alternative housingsystems that address engineering and performance standards for either poultry or swine housing;

3. Mitigation of environmental stresses that may adversely affect animal welfare (including behavior)such as heat, cold, and air quality in environments of poultry or swine.

Other Program Area Requirements:

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All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. Applications must include multidisciplinary teams with the appropriate combination of scientists

with expertise including, but not limited to, agricultural engineering, agricultural economics,veterinary medicine, animal science, animal behavior, animal welfare, animal productionefficiency, and occupational safety and health.

Inclusion of power analyses is required if a research project uses experimental animals. Failure todo so may result in a lower proposal ranking. Studies that propose to test and compare groupsmust justify the sample size chosen for each group. The main statistical considerations in samplesize calculation are the magnitude of the effect size ( e.g. , difference in proportions, means,survival times, etc .), standard deviation of the outcome, power and the significance level. Theseassumptions should be described in the rationale for the sample size. Studies that propose toestimate a population characteristic, such as the prevalence of disease, sensitivity and/or specificity of an assay should describe the allowable error margin around the estimate ( e.g. , +/- 5percent) and desired confidence level ( e.g. , 95 percent) used to determine the sample size. Themost common problem is lack of adequate sample size, while use of more animals than isnecessary is also an important ethical concern.

The project director will be required to attend annual investigator meetings associated with themost relevant Multistate Research Committee (such as NC 1029: Applied Animal Behavior andWelfare http://nimss.umd.edu/homepages/home.cfm?trackID=7016 ).

b. Nanoscale Science and Nanotechnology to Ensure Safe Food

Program Area Code A1511 Letter of Intent Deadline Letter of Intent NOT required for this Program AreaApplication Deadline May 14, 2010 (5:00 p.m., ET)Total Program Funds Approximately $3.5 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project periods of up to 5years will not be reviewedNational Program Leader Dr. Hongda Chen (202-401-6497 or [email protected] )

BackgroundNanoscale science and nanotechnology have been widely considered of great potential torevolutionize broad technologies and products for the societal benefits, including helping ensure andenhance the nations food safety system. The safety of our nation's food supply is of critical concernfor consumers, agriculture, food industry, the national economy, and the government. PresidentBarack Obamas announcement of the creation of the Food Safety Working Group (FSWG) is a clear indication of the importance of food safety. Although American consumers enjoy one of the safestfood supplies in the world, there are still multiple outbreaks and cases of food borne illness that occur each year and result in substantial economic losses. Nanotechnology holds the promise to further improve the safety of food imported into and produced in the United States when applied in thedevelopment, manufacture, production, and commercialization of foods, food and dietary ingredients,functional additives, and food contact substances such as food processing equipment and foodpackaging.

In the concerted effort with the major RFA on Improve Food Safety for All America, this program is tofocus on basic and applied research to establish a knowledge foundation of nanoscale science andnanotechnology that can aid future development and adaptation of effective food safety interventionapplications. Scientific challenges may include, but are not limited to, development and discovery of the principles of guided self assembled or engineered nanoparticles and nanostructures, surfacefunctionalization for molecular recognition and targeting ( e.g., second generation of nanoparticles),novel controlled release mechanisms, new nanomaterials and nano-biomaterials appropriate for foodsafety applications, and integrated and effective food safety systems. Furthermore, adequateattention must be given to develop scientific understanding of fate/transport and behavior of

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engineered nanomaterials in food, agriculture production, and the environment to ensure safe use of nanotechnology. Critically needed tools and methods to evaluate how food products have beenmodified for enhanced food safety using nanotechnology and how such modifications may impactsafety will be developed. The program will proactively address the basic need of food safety and safeapplications of food nanotechnology for the consumers. The success of this program will lay a solidfoundation that supports a comprehensive framework of responsible development and deployment of nanotechnology which include 1) detection of food borne pathogens or contaminants; 2) food safetyintervention technology; 3) consumer exposure of engineered nanoparticles; 4) hazardidentification/material characterization; and 5) risk/safety assessment of engineered nanoparticles.

Program Area Priorities Applicants must address the following:1. Development of knowledge and control of formation of novel nanoparticles, nanostructures and

systems that can effectively enhance food safety and biosecurity.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Institutions are strongly encouraged. Research sought that emphasizes developing a fundamental understanding of innovative

approaches based on nanostructures and nanoparticles that can effectively inactivate pathogenicmicroorganisms important in food safety.

Multidisciplinary team approach to include expertise in food safety, engineering, physics,chemistry, biological science, materials science, and toxicology as appropriate is highlyrecommended.

Basic information to aid risk assessment of the engineered nanoparticles to be developed in theresearch such as physical and chemical characteristics, biopersistence, stability in intended foodapplications, absorption, distribution, metabolism, and excretion (ADME) properties, and toxicityshould be considered as an integral and appropriate part of the research.

6. Agriculture Economics and Rural Communities

Success of U.S. agriculture and rural communities is increasingly dependent on maintaining andexpanding domestic and international markets. It is also dependent on the development of new products,production practices, and business and marketing tools and information that enhance efficiency, equityand the competitiveness of the producer. However, the new technology and increasing markets have notbenefitted all producers or rural communities. Primarily because of technological changes and associatedgrowth in corporate farming, the medium-sized farms are disappearing, with U.S. agriculture increasinglyreflecting a bimodal structure. Small and medium-sized farms are challenged by limited economicopportunities and increasing concerns about environmental quality. Although farming, including forestry,continues to be an important source of income, most of rural America is moving from agrarian to post-agrarian economies. Despite decades of intervention and billions of dollars in public investment, manyrural residents have a lower quality of life than many urban residents and rural poverty continues topersist as one of the most stubborn social problems. Some communities are facing economic decline andrural exodus, while other regions, especially coastal and mountainous areas, have experienced increasedeconomic growth and new resident influx.

In FY 2010, AFRI invites Research Project applications in the following programs in the AgricultureEconomics and Rural Communities area:

a. Prosperity of Small and Medium-Sized Farms and Rural Communities

Program Area Code A1601 Letter of Intent Deadline Letter of Intent NOT required for this Program AreaApplication Deadline July 14, 2010 (5:00 p.m., ET)

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Total Program Funds Approximately $7.0 millionProposed Budgets exceeding $500,000 total (including indirect costs) for project periods of up to 5years will not be reviewedNational Program Leader Dr. Suresh Sureshwaran (202-720-7536 or [email protected] )

BackgroundDuring the last 30 years, dramatic social, economic, and technological changes have occurred inmany rural areas in the United States. Technological changes have expanded rural economies intolarger regional markets. Therefore, in the future, the prosperity of many small and medium-sizedfarms and rural communities are going to be more closely dependent on the economic developmentand employment opportunities in the region. For example, many small and medium-sized farms willbecome increasingly dependent on regional food systems or part-time employment opportunities innon-agricultural enterprises. Therefore the purpose of this program is to promote a multifacetedapproach to address the challenges encountered by small and medium-sized farms and the ruralcommunities utilizing regional perspectives.

In the recent years, the challenges encountered by small and medium-sized farms have beenmagnified by adverse economic conditions, especially in credit markets; tremendous demographicshifts, illustrated by a new generation of farmers with very little farm experience; new opportunitiesand regulations in local, regional and global markets; increased competition from vertically integratedagribusinesses; new national programs and priorities, including increased emphasis on biofuelproduction and climate change; and the increasing competition for farm land for non-agricultural uses.New research is needed to examine the entire production, processing, and marketing systems toenhance the long-term viability, competitiveness, and efficiency of small and medium-sized farms(including social, biological and other components, if necessary) and the rural economy. The smalland medium-sized farms may include dairy, livestock, forestry, crop and other commodity operations.While small and medium-sized farms with less than $500,000 in annual sales account for less than 25percent of the value of all agricultural products sold in the U.S., the long-term viability of these farmsis critical to the prosperity of rural people and places as these farms account for approximately 92percent of all farms in the U.S.

Rural economic development is hampered by the lack of trained workforce, entrepreneurship skills,public services, and sufficient market size for the provision of some goods and services. Ruralpoverty remains as one of the most difficult social problems facing legislators and other public policymakers. In addition, population gain driven by migration and industrial development has changed thelandscape, creating new challenges and opportunities in rural design. Because of differences inphysical, economic, cultural, environmental, social and other factors, technological advances inagriculture and economic growth in rural areas have not benefited all rural people.

The Prosperity of Small and Medium-Sized Farms and Rural Communities Program seeks togenerate knowledge that will: (i) increase the value of agricultural products sold per farm by small andmedium-sized farms through the adoption of environmentally sustainable, economically viable bestmanagement practices; (ii) increase the accessibility and decrease the costs of inputs, includingcredit, to small and medium-sized farms; (iii) enhance sustainability of small and medium-sized farmsand rural communities through appropriate entrepreneurship and small business development; (iv)

enhance the efficiency and equity of public and private investment in agriculture and ruralcommunities; and (v) develop common methods and practices for decision making about optimallandscape design to promote sustainable rural development and in turn, reduce rural poverty.

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of integration on producers, prices, etc; the effects of market failures and externalities on consumersand producers; and the impacts of food chain clusters on independent producers, markets, etc. Tomaintain and expand international market opportunities for U.S. agribusiness, more research isneeded on rapid changes in consumer demand for agricultural products, the impacts of expandingagricultural markets on domestic producers and consumers, the benefits and costs of regulation, andalternative market solutions; the influence of existing and new policy and technology, etc. In anincreasingly interdependent world economy, economic development of the United States isdependent on the impacts of changes in world production and demand on U.S. production andconsumption of agricultural commodities; and on other global issues.

The Economics of Markets and Development Program seeks to generate knowledge that will: (1)maintain and develop domestic and international markets and enhance economic efficiency andequity in U.S. agribusiness sector; (2) assist with new product development and insertion in the valuechain for value-added plant, animal and bio-based products; and (3) enhance understanding of market failure and help develop strategies to reduce externalities.

Program Area Priorities Applicants must address at least one of the following:1. Enhance understanding of the changes in agricultural input- and output-market structure and

conduct, and in turn, its effectiveness in the development of competitive markets at home andabroad.

2. Develop new models and theories to enhance understanding of changes in domestic and foreignconsumer tastes and preferences to help promote the development of new agricultural geneticmaterials, and agribusiness products and technology.

3. Enhance understanding of causes and impacts of market failure and develop strategies toincorporate the externalities in agricultural resource and product markets.

Other Program Area Requirements: All applications must adhere to the requirements beginning in Part IV (page 29). Applications from and collaborations with Minority Serving Ins

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