Cereals Comparative Genomics Initiative

*A Research Partnership among the United States Scientific Community,
International Agricultural Research Centers, and National Agricultural
Research Systems in Developing Countries*

Request For Proposals

January 2003

A program managed by the Plant Biotechnology Center

Kansas State University

Manhattan, Kansas

**Cereals Comparative Genomics Initiative**

**Request For Proposals**

**I. PROGRAM OVERVIEW**

**Program Purpose:** This program seeks to bring the science of genomics
to bear on serious constraints to sustainable productivity growth in the
cereals, the staple food of most of the poor in the developing world.
Priority will be placed on addressing cereal production problems
relevant to sub-Saharan Africa and/or previously neglected minor cereal
crops. The application of science will be through partnerships between
scientific research and education institutions in the United States of
America, the Future Harvest Centers of the Consultative Group for
International Agricultural Research (CGIAR) and national programs in
developing countries. These partnerships aim to leverage the large
investments made by the US public sector in basic research on cereals
genomics and the large investments made by the international community
in developing agricultural research and delivery capacity in developing
countries. An important feature of this partnership will be to further
the education of scientists from developing countries at the graduate,
post-graduate and post-doctoral levels.

**Program Scope:** Potential research subjects include all cultivated
cereals and their wild relatives. Projects will generate and utilize
knowledge of genetic diversity within species to dissect the genetic and
functional basis of traits contributing to sustainable increases in
productivity and/or quality. Preference will be given to projects that
address production constraints in sub-Saharan Africa and South Asia,
develop new tools applicable across cereal species, address complex
traits and traditionally intractable problems, and/or contribute to the
improvement of cereals that historically have received little research
attention (e.g. the millets and tef). In addition to research on cereals
genomics, resources will be directed towards creating the capacity to
store, manipulate, analyze and share functional genomic information
among the cereals. Genome sequencing projects are beyond the scope of
this program.

**Subject Areas:** (1) Genetic diversity analysis for cross species
comparisons within the cereals and their relatives and gene discovery
related to high priority traits; (2) Understanding and manipulating the
genetic basis for tolerance to major environmental constraints such as
drought, heat, and adaptation to nutrient-poor soils; (3) Understanding
and manipulating the genetic basis for broad-spectrum resistance to
major diseases and insect pests; (4) Enhancement of productivity and
nutritional value; (5) Generation of bioinformatics tools necessary for
progress in the previously mentioned subject areas.

**Capacity Building:** A second order objective of this program is to
strengthen the genomics research and application capacity of scientists
in developing countries. Therefore, preference will be given to project
proposals that include advanced education and training opportunities for
scientists from developing countries. This can be, for example, as
opportunity for graduate or post-doctoral study in a US institution,
shared graduate programs among US institutions, Future Harvest Centers
and Universities in developing countries, or post-doctoral/visiting
fellow programs in the Future Harvest Centers.

**Eligible Institutions:** The lead principal investigator(s) (co-PIs)
must be from a non-profit institution of higher education and/or
research based in the United States of America or a Future Harvest
Center of the CGIAR. At least one co-PI must be based in a developing
country and be employed by a non-profit national or international
institution of higher education and/or research. Scientists from the
private sector may participate if their company accepts the intellectual
property access requirements of the program.

**Partnerships**: As this program seeks to foster linkages between US
research and educational institutions, the Future Harvest Centers and
national programs in developing countries, each project proposal must
include at least one institution from the United States and one
institution from a developing country, with a Future Harvest Center
partner encouraged. A partnership between a US-based institution and a
Future Harvest Center may embed collaboration with national agricultural
institution(s) via pre-existing agreements and/or collaborations between
the Center and the national institution(s). This relationship should be
explicitly stated and documented in the project proposal.

Scientific Oversight: Programmatic focus, scientific quality, technology
generation and information transfer will monitored by a panel of
scientists with an established and highly regarded record of experience
in the areas of genomics and crop improvement with relevance to
developing countries. This panel will meet at least once per year and
will establish the mechanisms for evaluating the preproposals and the
full proposals. A coordinating staff will support these
responsibilities.

**Size of Awards:** Proposals will be evaluated as two groups.
Relatively small projects requesting up to \$100,000 per year for one or
two years and larger projects requesting between \$100,000 and \$300,000
per year for up to three years.

**Grant Awards Process:** The selection of awards will be a two-step
process. The first step will be submission of a preproposal (see
instructions in the following section). The preproposal must be directed
to one of the five subject areas specified above. They must be submitted
no later than April 1, 2003. The preproposals will be evaluated
following a procedure established by the Scientific Oversight Committee
(SOC). The preproposal review will either be by the SOC itself or by a
review team selected by the SOC. The second step will be submission of
full proposals. PIs of preproposals selected to develop full proposals
will be notified by May 15, 2003. The number of preproposals selected
for full proposal development will be such that the anticipated award
rate will be approximately 50%. However, the award rate will ultimately
be determined by the final amount of funding available to the program.
Full proposals will be due August 15, 2003. Proposals will be subjected
to external peer review, and the reviews will be submitted to the SOC
for determination of awards. Co-PIs may be asked to meet electronically
with the SOC at its discretion. Winning awards will be announced by
November 1, 2003. Projects are expected to begin on January 1, 2004.

**Time Frame and Funding:** Projects may be funded for up to three
years. Funding for this program will be made annually by USAID to the
International Rice Research Institute and managed at the outset by
Kansas State University. Funding from US Federal agencies normally
cannot be assured for more than one fiscal year. **Therefore, although
grants may be awarded for multiple years, funding can only be assured on
an annual basis.** Continued funding will be contingent on sufficient
funds being made available from USAID and on satisfactory progress.

**Intellectual Property:** It is intended that products and information
from this program will be made freely available to not-for-profit
entities in developing countries for research and for technology
(including varietal) development purposes. Products from this program
should also be made freely available to not-for-profit organizations in
developed countries for research purposes. Any protection and/or
licensing of intellectual property created in part from support from
this program should facilitate the freedom of access described earlier
in this paragraph.

**II. Preparation and Submission of Preproposals:**

> Participation:

PIs: No PI can serve as a lead PI on more than 1 preproposal, nor appear
as a collaborator on more than 4 preproposals. After the first round of
competition, a PI may appear on no more than two funded projects at any
one time.

> Format:
>
> Paper size: 8 ½ x 11 inch or A4; 12 pt font size; 1 inch (2.54 cm)
> margins.
>
> Cover Page:
>
> Title
>
> Lead PI and Collaborating Scientists
>
> Participating Institutions
>
> Submission Date
>
> Executive Summary (limit of 300 words)
>
> Summary of Objectives, Activities, and Expected Outputs: 3 Pages
>
> Letters of Intent from partners indicating their willingness to
> participate in the proposal
>
> One page c.v. for each PI and co-PI
>
> Indicative Budget (Broken down by Institution):

Salaries (show appropriate benefits as a separate line)

> Supplies and Services
>
> Travel
>
> Training (tuition, living expenses, etc.)
>
> Equipment
>
> Indirect Costs (Limited to 19%)
>
> In-Kind Contribution

**Evaluation:**

Preproposals will be evaluated for their: relevance to one or more of
the Program subject areas as described in Section I of this document;
evidence that significant problems of relevance to cereal production in
developing countries, especially sub-Saharan Africa, will be addressed;
evidence that expected outputs will contribute to, or help develop tools
that will contribute to, cereals improvement; evidence of meaningful
partnerships. The panel ultimately charged with evaluating full
proposals will evaluate pre-proposals.

**Preproposal Submission Instructions:**

Preproposals should be submitted to R. S. Zeigler as an e-mail
attachment (<rzeigler@ksu.edu>) or by mail (Dr. Robert S. Zeigler,
Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center,
Kansas State University, Manhattan, KS 66506-5502, USA), no later than 1
April, 2003. **Total email message size must not exceed 3MB.**

**III. PREPARATION AND SUBMISSION OF FULL PROPOSALS**

PIs for preproposals selected to advance to full proposal development
will be notified by May 15, 2003.

**Format:** Paper size: 8 ½ x 11 inch or A4; 12 pt font size; 1 inch
(2.54 cm) margins.

**Proposal Contents:**

> Cover Page
>
> Table of Contents
>
> Executive Summary (300 word maximum) suitable for a non-scientific
> audience
>
> Scientific Summary (300 word maximum)
>
> Main Text (12 pages):
>
> Objectives and Intended Specific Outcomes
>
> Introduction and Rationale
>
> Approach and Methods
>
> Partners
>
> Management Plan
>
> Critical Assumptions and Contingency plans
>
> Timeline and Milestones
>
> Budget (broken down as in preproposal)
>
> Global Budget (annual and summary)
>
> Budget by Partner (annual and summary)
>
> Budget Notes and Rationale
>
> Appendices
>
> Description of Partners (demonstrating their capacity to undertake to
> the project and a rationale for the proposed partnership)
>
> CVs of PI and Collaborating Scientists (maximum two pages each
> including five most recent relevant publications)
>
> Letters of Intent from Partner Institution specifying resource,
> in-kind etc. commitments, if appropriate
>
> Intellectual Property Statements from each partner

**Evaluation Criteria:**

Preproposals that advance to full proposal development will already have
met the minimum standard requirements of relevance, appropriateness,
scope and partnership as covered in Section I of this document. Full
proposal evaluations will weight these factors as shown below

> Applicability of outputs to solving production constraints in
> developing
>
> countries, especially sub-Saharan African and South Asia, and
> applicability
>
> beyond one specific crop 30%
>
> Feasibility (potential to achieve proposed objectives and outcomes)
> 30%

Scientific merit and originality 20%

> Capacity building of national programs 10%
>
> Strength of, and rationale for, proposed partnerships 10%

**Full Proposal Submission Instructions:**

> Proposals should be submitted to R. S. Zeigler as an e-mail attachment
> (<rzeigler@ksu.edu>), or by mail (Dr. Robert S. Zeigler, Department of
> Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State
> University, Manhattan, KS 66506-5502, USA), by August 15, 2003.
> **Total email message size must not exceed 3MB.**