February 18, 2005

Maize Genome Sequencing Project: An NSF/DOE/USDA Joint Program

Under the auspices of the National Plant Genome Initiative (NPGI), the National Science Foundation (NSF), the U.S. Department of Energy (DOE), and the U.S. Department of Agriculture (USDA) announce their intention to support large-scale sequencing of the maize genome.  Previous funding has supported development of maize genome sequence resources, including physical and genetic maps, Expressed Sequence Tags (ESTs), sequences derived from gene-enriched genomic libraries, Bacterial Artificial Chromosome (BAC) sequences, and a community genome database. The objective of this program solicitation is to solicit proposals that build on these resources to develop a comprehensive sequence resource for the maize genome that will capture the majority of the sequence information in a timely and cost-effective manner.

Under the auspices of the National Plant Genome Initiative (NPGI), NSF, DOE, and USDA announce their intention to support large-scale sequencing of the maize genome.  This project represents one of the goals of the current 5-year plan for the NPGI (National Plant Genome Initiative 2005-2008: http://www.ostp.gov/NSTC/html/npgi2003/index.htm). 

The NPGI was established in 1998 to support research on plant genomics and to accelerate the acquisition and utilization of new knowledge and innovative approaches to the analysis of fundamental biological processes in plants.  The Initiative focuses on plants of economic importance and plant processes of potential economic value.  For the last 6 years, the NSF, USDA, and DOE have supported and coordinated the development of maize genome resources through the NPGI.  While sequencing of the maize genome has been a long-term goal from the beginning, its size and complexity have warranted a staged approach. 

Like many of the cereals, maize has a large genome, the 10 chromosomes together comprising about 2.5 Gigabases (Gb) of DNA.  The maize genome is therefore about the same size as the human genome and about 21 times larger than the Arabidopsis genome. The genome organization of maize is complex, with more than 88% of the DNA consisting of repetitive sequences, and about 12%, or about 300 Megabases (Mb), encoding genes.  In addition, the maize genome is highly polymorphic and individual lines can be highly variable in sequence and gene content. 

In July 2001, a community workshop was held in St. Louis, MO, to discuss sequencing the maize genome, and in particular, which maize genome should be sequenced, the technical approaches to, and possible outcomes of, such a project. A key recommendation of this workshop was that initial sequencing efforts focus on the inbred line B73, the source of DNA for the BAC libraries used to construct the physical map as well as many of the public ESTs.  The public B73 line is a good representative of commercially important germplasm and focusing on a single DNA source was recognized as a way to avoid complications arising from sequence polymorphisms. 

After the workshop, the first stage towards sequencing the maize genome was to develop a detailed picture of its landscape.  While the size and complexity were well known, the precise organization of the sequence components within the genome was largely uncharacterized.  As a result of coordinated research efforts, including physical mapping and sequencing of fractions of the genome enriched for genes, a picture has emerged of a maize genome that comprises islands of genes surrounded by a sea of repetitive sequence.  A substantial amount of sequence information has been gathered as well as information about the genic and repeat sequence content.  The second stage is to now use this information to develop a cost-effective strategy to sequence the maize genome and anchor the assembled sequence to the genome map. 

This Program Solicitation invites proposals to sequence the maize genome and to anchor the assembled sequence to the genome map.  It is expected that proposals will build on the available maize genome resources and will provide a detailed justification for each of the key strategies proposed.

Maize Genome Resources Substantial investments have already been made by the various agencies participating in the NPGI to develop a maize genome map and sequence resources, as well as a community database.  In keeping with the goals of the NPGI, all of these resources are freely available and in the public domain.  A complete catalog of these resources with links to the primary data is available at the maize community genomics database MaizeGDB (http://www.maizegdb.org), along with maize workshop reports, and a primer on what is known about the structure of the maize genome.   MaizeGDB also contains information about where to obtain seed, DNA, and libraries for the standard B73 line. Publicly available genome resources for maize include:

• Genetic and physical maps
• BAC libraries
• BAC-end sequences
• BAC sequences
• EST sequences
• Methyl-filtered and High C₀t genome sequences enriched for genes
• Whole genome shotgun sequences

In March 2004, an industrial consortium announced the public availability of over 3 million EST and 30,000 full-length cDNA sequences from a number of maize inbred lines.  More information about the sequences and terms of access can be found at http://www.maizeseq.org. 

The DOE Joint Genome Institute recently announced the plan to generate and release to GenBank one million whole genome shotgun sequence reads from B73 maize.  This valuable resource is being provided to facilitate rational development of maize genome sequencing and assembly strategies.  All reads and trace files are anticipated to be deposited in GenBank by the end of October 2004.

Key components of the maize genome sequencing project

The Maize Genetics Executive Committee, an elected body representing the broader maize community, has polled its membership about what the maize genome sequence resource should contain, and developed a definition of the "gold standard" for the maize genome sequence resource (see: http://www.maizegdb.org for the full report).  Proposals should address the key components listed below:

• The maize genome-sequencing project must provide the complete sequence and structures of all maize genes and their locations (in linear order) on both the genetic and physical maps of maize. 
• The gene space of B73 maize (gene sequences and adjacent regulatory regions) should be of finished quality according to currently acceptable standards (as per Bermuda/Ft. Lauderdale agreements). 
• If applicable, the sizes of gaps between the genes should be estimated and draft sequences of repetitive DNA between genes presented where possible. 
• The sequence must be fully integrated with the genetic and physical maps. 
• Annotation should include gene models, predicted exon/intron structure, incorporation of EST and full-length cDNA data, gene ontology, and relationship with homologs in other organisms, including but not limited to, the other sequenced plant genomes. 
• Annotation should be coordinated with existing maize community and comparative databases with the eventual goal of generating complete curation of the genomic sequences to a standard set by established model organism databases.  

Additional considerations

• International research collaborations are welcomed.  When applicable, proposed research activities should be coordinated with similar efforts in other countries to maximize efficiency and avoid unnecessary duplication of effort.  However, foreign participants should secure support for their component of the collaboration from their own national programs. 
• Private industry has already made significant investments in plant genome research. Innovative collaborations with industry are encouraged when they advance the goals of this project. Funds awarded under this solicitation may not be used to support industrial collaborators and release of data and information must comply with the requirements set out in this solicitation.  Requests for funding to pay for industrial fee-for-service sequencing are permitted. However, a draft of the sequencing contract must be provided with the proposal that includes specific information about what will be provided, and a timetable for sequence production.
• These projects offer an ideal opportunity to train young scientists at the interface of modern sequencing technologies and bioinformatics, and to promote increased participation by members of underrepresented groups. All proposals are expected to integrate research and education, taking advantage of opportunities unique to the project. Training and outreach activities should be integrated into the research plan commensurate with the scale and scope of the project.

Proposals are invited from U.S. academic institutions, U.S. non-profit research organizations, and consortia of U.S. organizations with appropriate research and educational facilities. A proposal from a multi-organizational consortium must be submitted by the lead U.S. organization as a single proposal. When a consortium submits a proposal, a single principal investigator must be designated as the project director and a single organization must accept overall management responsibility including the management of intellectual property that may result from the proposed research.  Proposals may also be submitted by qualified Federal Agencies, however, these proposals would be eligible for funding only by USDA and DOE.

PI Eligibility Limit: None Specified.

Limit on Number of Proposals: None Specified.

Potential proposers are strongly encouraged to carefully read the program solicitation prior to preparation of proposals and to contact a cognizant Program Director if there are any questions. Proposals that do not meet the guidelines may be returned without review.

Proposals must be submitted by FastLane (see "FastLane Requirements" section below) and must follow the guidelines described in the GPG. The following exceptions and additions apply to proposals submitted to this Solicitation:

Proposal Cover Sheet: In the NSF FastLane system, follow the instructions on proposal preparation. When completing the Cover Sheet, click on the GO button at "Program Announcement /Solicitation/ Program Description No."  Highlight “Plant Genome Research Project “ and click on the Select button. Your proposal will automatically be assigned to DBI--Plant Genome Research Project. Be sure to complete the remainder of the cover sheet information.  Please note that a maximum of 4 Co-PIs can be listed on the cover sheet. Additional Co-PIs and Senior Personnel should be included in the complete list provided in the Project Summary.

BIO Proposal Classification Form (PCF): Complete the BIO PCF, available on the NSF FastLane system. The PCF is an on-line coding system that allows the Principal Investigator to characterize his/her project when submitting proposals to the Directorate for Biological Sciences. Once a PI begins preparation of his/her proposal in the NSF FastLane system, selects any program within the Directorate for Biological Sciences as the first or only organizational unit to review the proposal, and saves the cover sheet, the PCF will be generated and available through the Form Preparation screen. Additional information about the BIO PCF is available in FastLane at http://www.fastlane.nsf.gov/a1/BioInstr.htm.

Project Summary (maximum 1 page): The project summary should consist of three separate parts in the following order:

(1) A list of senior personnel (PI, Co-PIs, key-collaborators) along with their home organizations.

(2) A summary of the scientific objectives and approaches.

(3) Expected broader impacts of the proposed research.

Both the scientific aspects and the anticipated broader impacts must be addressed or the proposal will be returned without review. Please read the Important Notice from the Director of NSF, which can be found at https://www.nsf.gov/pubs/2002/iin127/imptnot.pdf.

Project Description (maximum 20 pages) In addition to the standard description in the GPG, the guidelines below should be followed, noting that the page allowances listed are part of the overall 20-page maximum:

• Progress report (3 pages): Groups that have received prior funding to map or sequence the maize genome, or to develop maize informatics resources, should include the grant title and number, the funding agency, and a summary of exactly what has been released or developed (e.g. information about the status of a map, or bases sequenced and deposited in GenBank as finished sequence, the number of sequences which are in the process of being sequenced, sequence read lengths and quality scores).

• Research plan: Describe the goals of the project, scientific and technical approaches, including informatics and information management where appropriate, with expected outcomes. Descriptions must be sufficiently detailed to allow adequate review. 

  • DNA substrate and sequencing strategy: Include the source of the DNA (genomic DNA, BAC clones), the method of library preparation, and any other pertinent information. Describe the overall strategy to be used and how this will deliver the key components of the “gold standard” genome.

  • Sequence quality and quantity: The discussion of sequence quality and quantity should contain the following elements:

    • The overall approaches to be used (for example, whole genome shotgun, fosmids, BACs, selected genomic regions).
    • The type(s) of sequence to be generated (Phase I, Phase II, or Phase III).
    • For shotgun projects, the number of attempted sequence reads to be performed and anticipated read lengths (in bases of phred20, or equivalent, quality).
    • The anticipated amount of shotgun sequence to be delivered including such metrics as the number of successful sequence reads, total phred20 bases, paired end rate, where applicable, and fold coverage as appropriate.
    • Timetable for and location(s) of sequence production.
    • Steps to be taken to evaluate sequence quality, and the quality metrics to be used.
    • If appropriate, plans for assembly, finishing, and annotation, including how the sequence will be assembled onto the genome map, and how gaps will be captured or closed. 
      
      
  • Summary sequencing costs: Provide the following information in tabular form for each type of sequence to be generated.  Cost estimates should include direct costs for labor and materials:
    • Total number of attempted and successful sequencing reads budgeted
    • Anticipated sequence read length (in phred20 bases)
    • Anticipated paired end rate
    • Estimated cost of library preparation
    • Estimated cost per phred20 base
    • Estimated cost per finished base
• Plan to integrate research and education:  The proposal should include a thoughtful training/educational component that takes advantage of unique and specific opportunities the proposed project would provide.  The following items must be included: (1) a well designed plan to increase participation of members of under-represented groups that is specific to the proposed project, (2) an education plan for project trainees, and (3) a description of how these plans are integrated with the proposed research plan. A clear and realistic discussion of how the plan will be implemented should be included in the proposal. Simply describing general policies and ongoing efforts at the investigators' organizations will not be sufficient.                    

References Cited (no page limit): Follow the GPG guidelines for all references cited.  Indicate with an asterisk any cited publications that resulted from prior research funded by NSF for the PI, or Co-PI.

Biographical Sketches (2 pages each):  Biographical sketches following the GPG guidelines must be listed for the PI, Co-PIs and each of the Senior Personnel listed on the Project Summary page.                                                 

Proposal Budget: Provide yearly budgets and a summary budget for the duration of the proposed project. When subawards are involved, yearly and summary budgets are required for each subaward. A Budget Justification (maximum 3 pages per budget and subaward budget) should be provided.  A careful and realistic budget will add to the overall strength of a proposal. Funds for facility construction or renovation may not be requested. Funds to cover the cost of attendance of the PI and one co-PI (the informatics co-PI, where appropriate) at each year's annual awardee meeting in Arlington, VA should be requested.

Current and Pending Support: Current and Pending Support following the GPG guidelines must be listed for the PI, Co-PIs and each of the Senior Personnel listed on the Project Summary page.                                             

Facilities, Equipment and Other Resources: Provide a description of available facilities and priorities for its use. For projects requiring additional equipment, justify the need for these resources in the context of the work proposed.                     

Special Information and Supplementary Documentation:   Include the following materials, clearly labeled (A-1, A-2, etc.), and submit them under the “Supplementary Documents” section of FastLane:

(A-1) Sharing of Results and Management of Intellectual Property (maximum 5 pages): Describe the management of intellectual property rights related to the proposed project, including plans for sharing data, information, and materials resulting from the award. This plan must be specific about the nature of the results to be shared, the timing and means of release, and any constraints on release. The proposed plan must take into consideration the following conditions where applicable:

• Sequences must be released to GenBank according to the currently accepted community standard (Bermuda and Ft. Lauderdale agreements), following the current guidelines for quality assessment (see http://www.genome.gov/page.cfm?pageID=10506537). For large-insert clone projects, it is expected that DNA sequence assemblies of 2kb or greater will be deposited in GenBank within 24 hours of generation.  For whole genome shotgun projects, sequence traces are to be deposited to the NCBI Trace repository within one week of production, with whole genome assemblies deposited in GenBank as soon as possible after the assembled sequence has met the quality evaluation criteria stated in the Project Description.  Deposited data should be available to all for use without restriction.
• If the proposed project produces additional resources (libraries, software, etc.), these should be made available as soon as their quality is checked to satisfy the specifications approved prior to funding. The timing of release should be stated clearly in the proposal. The resources produced must be available to all segments of the scientific community, including industry and the international community. A reasonable charge is permissible for distribution, but the fee structure must be outlined clearly in the proposal. If accessibility differs between industry and the academic community, the differences must be clearly spelled out. If a Material Transfer Agreement is required for release of project outcomes, the terms must be described in detail.  
• When the project involves the use of proprietary data or materials from other sources, the data or materials resulting from research supported by this program must be readily available without any restrictions to the users (no reach-through rights). The terms of any usage agreements should be stated clearly in the proposal.
• Budgeting and planning for short-term and long-term distribution of the project outcomes must be described in the proposal. If a fee is to be charged for distribution of project outcomes, the details should be described clearly in the proposal. 
• In case of a multi-organizational proposal, the lead organization is responsible for coordinating and managing the intellectual property resulting from this award. Organizations participating in multi-organizational projects should formulate a coherent plan for the project prior to submission of the proposal.
• Please note that key project personnel may be required, prior to an award decision, to submit copies of any intellectual property agreements or material transfer agreements they have signed, or are planning to sign, that would impact the unrestricted and timely distribution of the outcomes of the research funded though this program.

(A-2) Management Plan (maximum 5 pages):  The management plan should include plans for internal means of communication, coordination of data and information management across the project, evaluation and assessment of progress, as well as allocation of funds and personnel.

• A statement should be provided agreeing to the formation of a "virtual" consortium with any other awardees should the proposal be recommended for funding.
• Each investigator's role should be described and a table summarizing the role of each investigator provided. The exact time commitment of each key project member should be indicated in the management plan, regardless of any request for his/her salary from NSF. A project timetable with yearly goals should be provided that includes benchmarks for the major anticipated outcomes and expected dates for their release.
• The relationship of the proposed activity to the other maize sequencing and bioinformatics projects, and how these activities will be coordinated, should be described.

(A-3) Sequencing Provider Profile (maximum 10 pages): Please provide the following information for all participating sequence providers:

• Total annual sequencing capacity.
• A list of ongoing projects with the capacity and time committed to each.
• The proportion of production sequencing dedicated to whole genome shotgun and BAC-based shotgun reads.
• The average length of production sequencing reads (in bases of phred20, or equivalent, quality) and the average usable read length.
• The amount of data deposited in a public database (bases deposited in a public nucleotide sequence database and reads deposited in a trace archive).  All of this sequence must be available to reviewers.
• The center’s total current monthly production capacity based on an average of the last six months of sequencing, including the number of attempted and successful reads, the number of base pairs per read of at least phred20 (or equivalent) quality, and the frequency of double ended reads, if appropriate.
• The internal metrics (e.g., reads per month, failed lanes, base pairs per lane) used to evaluate and manage progress.
• Sequence assembly experience at all scales (large-insert clones through whole genomes), including any draft genome assemblies deposited in public databases.
• Finishing process (if appropriate), from draft-level sequence or whole genome shotgun assemblies, including gap closing and building of contiguous finished sequence. 
• The amount of finished genomic sequence in finished base pairs produced in the last 12 months and how much of this has been deposited in a public database.  All of this sequence must be available to reviewers.
• Procedures used to check the quality of sequences and assemblies at each scale produced.

(A-4) Letters of collaboration: Letters from collaborators who are not requesting funds from the proposal must be attached, describing the nature of the collaboration and the source of their support.  General letters of support are not allowed.

Color Images (if applicable): Be advised that NSF cannot accommodate the printing of color images as part of proposal submission through the FastLane system, and submitted proposals that require the use of color or of very high resolution photographic images will necessitate additional steps.  Further instructions will be provided after the proposal has been received.

Any material not specifically requested or in excess of the page allowances will be discarded prior to review. It is the submitting organization's responsibility to ensure that the proposal is compliant with the guidelines. Non-compliant proposals may be returned without review.

Single Copy Documents:
Correspondence to the program not intended to be sent to reviewers such as the Conflict of Interest Document, a list of potential reviewers, or confidential materials, can be sent through the “Single Copy Document” section of FastLane. All other supplemental material intended for review should be uploaded into the “Supplementary Documents” section.

Conflict of Interest Document (no page limit): This document should be provided in table or spreadsheet form only, and should be sent as a single document through the Single Copy Document section of FastLane at the time of proposal submission. The document should consist of a list, in the form of a single alphabetized table, with the full names (Last name, first name, middle initial) of all people having a conflict of interest with any senior personnel (PI and Co-PIs) and any named personnel member whose salary is requested in the project budget. Conflicts to be identified are (1) Ph.D. thesis advisors or advisees, (2) collaborators or co-authors for the past 48 months, including postdoctoral advisors or advisees, and (3) any other individuals or organizations with which the investigator has financial ties (please specify type).  Members of current Advisory Committees who receive reimbursement for travel or honoraria should be included in this last category. 

NSF - No Limit.  Standard NSF policy regarding indirect cost rates should be applied to proposals submitted to this solicitation.

DOE and USDA - To accommodate differences in allowable indirect costs among participating agencies, proposers may be required at the time of award to submit a separate budget with indirect cost rates appropriate to DOE or USDA.

See Section II (Additional considerations) and Section V.A. (Proposal Budget).

February 18, 2005