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Bylaws (Updated)

View the Policies and Procedures in PDF format (PDF; 134Kb)

POLICIES AND PROCEDURES

     ·         Article I. Goal Statement

·         Article II. Structure and Roles of Committees

o        Section 2.01 Basic Structure

o        Section 2.02 Executive Committee

o        Section 2.03 Administrative Office (AO)

·         Article III. Request for Plans of Work (RFP) and Review Process

·         Article IV. Annual Research Forum

o        Section 4.01 Site Selection

o        Section 4.02 Development of Agenda

o        Section 4.03 Report of Proceedings

·         Article V. Strategic Plan and Program Assessment

o        Section 5.01 Strategic Plan Development

o        Section 5.02 Annual Reports

o        Section 5.03 Assessments

·         Article VI. Amendments to Procedures

o        Section 6.01 Format of Recommended Change

o        Section 6.02 Submission Dates

o        Section 6.03 Dissemination of Change

o        Section 6.04 Approval of Amendment

January 19, 2010

Article I. Goal Statement

The goal of the National Sclerotinia Initiative is to conduct a coordinated research strategy to minimize the devastating effects of Sclerotinia sclerotiorum (white mold) on soybeans, canola, sunflowers, dry edible beans, and the pulse crop group consisting of dry peas, lentils, and chickpeas.

 

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Article II. Structure and Roles of Committees

Section 2.01   Basic Structure

The Sclerotinia Initiative will consist of an Executive Committee (EC) and an Administrative Office (AO). The EC is considered a permanent committee to work in concert with the AO.  Other special temporary committees to help with a special need can be formed as necessary.   They could include an Annual Meeting Committee, Technical Advisory Committee, Site Review Committee, ad hoc committees, etc.  

Section 2.02    Executive Committee

02(a)                  Purpose:

The purpose of the Executive Committee is to provide overall guidance and oversight to the AO for the purposes of establishment of research priorities, selection of research projects and execution of the National Sclerotinia Initiative.

02(b)                  Committee Composition

                 (i)     Number of Members

The EC will consist of eight members as indicated in the table below:

 

Crop

Total Members

Affiliated Group

Totals

 

Sunflowers

1

National Sunflower Association

1

 

Dry Beans

1

U.S. Dry Bean Council

1

 

Dry Peas & Lentils

1

USA Dry Pea & Lentil Council

1

 

Canola

1

US Canola Association

1

 

Soybeans

1

American Soybean Association

1

 

USDA ARS

1

USDA-ARS Fargo - admin

1

 

USDA ARS

1

USDA-ARS NPS

 

1

 

USDA ARS

1

USDA-ARS Area Office

1

 

Totals

8

 

8

 

 

               (ii)     Length of Term

Members shall serve no specified length of term.   Changes will be made at the discretion of each organization.  A Committee member may select an alternative to represent the organization, including USDA-ARS, in case of member absences, etc.

              (iii)     Administration

The member from USDA-ARS in Fargo will serve as administrator of the National Sclerotinia Initiative. That individual will serve as fund holder/administrator of the appropriated funds.   

             (iv)     Addition of Members

Inclusion of additional commodity organizations as part of the Initiative will be based on available funding and upon approval of the EC. Each commodity group participating in the Initiative will have one representative on the EC.  A 2/3 vote of the EC will be required for addition of members.

02(c)                   Meeting Protocol

                 (i)     Quorum

A quorum shall consist of more than 50% of the current members.  This also pertains to voting by electronic media.

               (ii)     Voting

Each member of the committee will have one vote. Voting outcome shall be determined by a simple majority of votes cast. 

              (iii)     Meetings

The EC will hold a formal meeting during the January annual research forum meeting of the Initiative.  Additional meetings may be called as necessary.  Teleconference meetings are acceptable.   

02(d)                  Responsibilities

·       Provide direction and guidance to the Initiative.

·       Review and approve research area program descriptions and research priorities.

·       Review and approve the process to request pre-plans of work (RFP).

·       Review and approve the agenda and location of the annual research forum.

·       Review and approve the National Sclerotinia Initiative recommended budget.

·       Review and approve the structure and composition of the SC and other committees as needed.

·       Approve the Procedures and Amendments to the Procedures.

 

Section 2.03   Administrative Office (AO)

03(a)                  Purpose

The purpose of the AO is to act as the administrative and communication headquarters for the National Sclerotinia Initiative under the direction of the EC.  The USDA-ARS Fargo member serves as administrator.  Responsibilities include:

  • Organize EC meetings, conference calls, etc.
  • Record and distribute minutes.
  • Organize Initiative annual research forums.
  • Act as liaison between Initiative and USDA-ARS.
  • Manage the Initiative’s website, email & address lists, newsletters, press releases, etc.
  • Publish annual reports, status reports, and financial summaries.
  • Develop and update Initiative Strategic Plan.
  • Develop a process to conduct an assessment of research accomplishments conducted under the Initiative Strategic Plan and report the assessment to the EC and other appropriate individuals.
  • Organize calls for pre-plans of work, facilitate review process and distribute funding to selected projects.
  • Serve as resource management/accountability center.

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Article III. Request for Plans of Work (RFP) and Review Process

 

The National Sclerotinia Initiative’s goal is to conduct a coordinated research strategy to minimize the devastating effects of Sclerotinia on soybeans, canola, sunflowers, dry edible beans, and the pulse crop group consisting of dry peas, lentils, and chickpeas.  The Initiative provides funds to United States scientists to conduct research targeted at Sclerotinia management within the above listed crops in one of the following research focus areas:

 

a) Crop Germplasm Resources and Genetics

b) Pathogen Biology and Development

c) Pathogen and Host Genomics

d) Pathogen Epidemiology and Disease Management (including crop production practices & biological/chemical control)

 

Scientists from other countries (e.g. Canada) or working on other than the above named crops may participate in the Initiative via formal collaboration with U.S. investigators as listed above.

 

In October of each year calls for “Plans of Work” to address needs within each research focus area are requested from interested scientists.  Final Plans of Work are submitted to the Sclerotinia Initiative AO by mid-December.  Plans of Work are accepted for review only if they strictly adhere to submission procedures established by the Sclerotinia Initiative AO and approved by the Sclerotinia Initiative SC.  No Plan of Work will be accepted for review if it is submitted after the approved deadline or if the format for submission is not followed.  Plans of Work are then reviewed by Scientific Review Panels in January/February to determine their scientific merit.  Results are forwarded to the Sclerotinia Initiative AO which convenes a meeting of the Sclerotinia Initiative SC in February/March for final funding and implementation decisions.

 

In addition to the Scientific Review Panels, each of the five affiliated commodity groups within the SC will independently review each plan of work during the January/February time frame.  These separate reviews will be used to insure that commodity and grower research priorities are recognized and properly evaluated.  These panels will provide ranked results to their particular SC representative who will bring results to the February/March final funding and implementation meeting.  Each affiliated commodity group is free to conduct these reviews in the manner that best suits the organization.  Affiliated Group Review Panels will provide a written summary of their review results, including critique of the plans of work, to the AO during the February/March final funding and implementation meeting.

 

Prior to the calls for Plans of work the Sclerotinia Initiative SC will identify priority research needs per research focus area based on action items identified from the Sclerotinia Initiative Strategic Plan.  These needs will be articulated in the call for Plans of Work and will also be provided independently to the scientific and affiliated group review panels.

 

Calls for Plans of Work will be distributed to current and former Initiative researchers and non-funded researchers who previously submitted Plans.  Notices will also be sent to the following:

a)       National Sclerotinia Initiative list server
b)       Agricultural Experiment Station Directors
c)       Cooperative Extensions Directors
d)       1890 Institutions
e)       1994 Land Grant Institutions
f)         The National Sclerotinia Initiative Website

 

Selection of Peer Reviewers for Scientific Review Panels:

Peer reviewers are scientists and/or technical experts possessing the knowledge to make critical decisions on the scientific merit and adequacy of the submitted Plans of Work.  A panel chair will be selected by the Sclerotinia Initiative AO at that office’s discretion.  Potential peer reviewers will be solicited by the Sclerotinia Initiative AO in coordination with the panel chair.   Review panel members will then be selected from a pool of individuals without collaborative/cooperative interests in the Sclerotinia Initiative.  Peer reviewers will provide objective reviews based on the set of criteria established below.  Each will sign a confidentiality agreement to protect potentially sensitive information included in Plans of Work.  Review panel chairs will be disclosed, but review panel members will not be disclosed to the EC or researchers.

 

The panel chair and all reviewers will be reimbursed for expenses (travel, lodging, meals, etc.) related to serving on a review panel. 

 

Scientific Review Panel Operation:

Review panels will consist of a Chair and up to four additional reviewers.  A member of the Sclerotinia Initiative AO may attend to provide administrative and policy support of the process.  A minimum of one review panel will meet each year to make decisions on the scientific merit and adequacy of submitted Plans of Work.  Review panels will convene to discuss and rank Plans of Work in each of the four Sclerotinia Initiative Research Focus Areas. The number of review panels to be convened will be based on total number of submitted Plans of Work.  If necessary, review panels can be combined as follows: a) Pathogen Epidemiology and Disease Management & Pathogen Biology and Development; b) Crop Germplasm Resources and Genetics & Pathogen and Host Genomics.  Combined review panels will include individuals identified as experts for both research areas.  Three weeks (minimum) prior to review panel meetings submitted Plans of Work will be sent to each panel member.  The Chair will assign individual projects to various panel members to lead discussions during the review panel meeting.  Each panelist, including the Chair, will individually score all plans of work being reviewed during the meeting (the representative from the Sclerotinia Initiative AO will not score projects or participate in scientific merit related discussions if attending the reviews).   Preliminary scoring should be completed prior to arrival at the review panel meeting to facilitate discussions.  Final scores from each panelist will be obtained following discussions on each Plan of Work.  The Chair will moderate the review panel meeting and is responsible for maintaining order during the meeting.  The Chair conveys all review panel decisions to the Sclerotinia Initiative AO.

 

Scientific Review Criteria:

Each submitted Plan of Work will be evaluated using the three criteria listed below.  Panelists are requested to provide written comments/criteria relevant to each Plan of Work being reviewed.

 

A) Scientific Merit, Conceptual Adequacy & Innovation - is the work well conceived? Is the planned work novel?  Does it include an innovative approach to answering the objectives? Are the methods and procedures appropriate? Are hypotheses and objectives clearly delineated? Is the work feasible as defined? What is the probability that the described research will be completed within stated time frames? Does the work duplicate existing or previously conducted research? 

 

B) Institutional Qualifications - are the researchers qualified to conduct the proposed study? Are researchers aware of current literature on the proposed area of study?  Are available facilities, instrumentation, equipment, personnel, and existing funding adequate to provide proper augmentative support of the proposed study?  Is the amount of requested dollars adequate, excessive, or too low to complete the study? 

 

C) Relevance and/or Progress - does the proposed study address the prioritized needs of the Initiative based on guidance provided by the Sclerotinia Initiative SC?  Does the study directly relate to action items determined from the Initiative Strategic Plan?  Will the work lead to development of new knowledge or new technology to manage the disease?  Is reasonable progress being made if the Plan of Work is a continuation of a previously funded study?  (Plans of Work funded for three consecutive years must show quantitative progress before additional funding will be considered.  Examples of progress include: improved germplasm under selection, germplasm release, publications, patents, etc.)

 

D) Anticipated Progress/Outcome – What is the probable likelihood for success of the planned research over the next 12 months?  Beyond 12 months?

 

Review panel members will score each of the four criteria under the following categories:  high, medium, low.  Points will be assigned to match the ratings with high = 6; medium = 4; low = 2; The four scores are added together to obtain a final panelist recommendation.  Review panelist recommendations are then averaged together to obtain a final recommendation score to be provided to the Sclerotinia Initiative EC.   Consensus scores among the review panel are not required.

 

Final Reviewer Recommendations are:

 

A) High - Highest priority for funding (average scores of 4.8 – 6.0)

 

B) Medium - Funding recommended on a case by case basis if available (average scores 3.3 – 4.7)

 

C) Low – No funding recommended (average scores 2 – 3.2)

 

Final Funding Decisions:

Scientific Review Panel scores and summaries of review critiques are forwarded to the Sclerotinia Initiative AO at the close of the review panel meetings.  The Sclerotinia Initiative EC will then meet to discuss the results of the Scientific and Affiliated Group Review Panels and to finalize Plan of Work funding decisions, including allocation of available dollars.  Final funding decisions are based on research priorities previously established and communicated by the EC and the total available dollars provided to the Sclerotinia Initiative within a fiscal year (October through September).   There is no prescribed formula for commodity-based funding.  The Sclerotinia Initiative EC will follow Scientific Review Panel recommendations as closely as possible, but retains the authority to move a project up or down on the priority list based on feedback received from Affiliated Commodity Group Review Panels.  It is preferred that no Plan of Work be funded if it has received a unanimous score of low (2.0) from the Scientific Review Panel.  The EC will retain the right to not fund a project regardless of the score.  Once the EC approves the budget allocation, the AO shall send written notification to all researchers who submitted a Plan of Work.  The AO will make every effort to explain the reasons for disapproval of the plans.  Feedback will be based on written comments received from the Scientific Review Panels and the Affiliated Group Review Panels. The AO also reserves the right to veto EC funding recommendations based on past funding experience of the applicant or other extenuating circumstances specific to an application submission.  The AO cannot redirect funds to another applicant without SC approval.

 

Funding Mechanisms:

Currently, the USDA-ARS Sunflower Research Unit of the Red River Valley Agricultural Research Center, Fargo, ND is the fund holder for the Sclerotinia Initiative.  Funds will be distributed to cooperators for 12 month periods beginning in July of each year.

 

Scientists who submit a Plan of Work selected by the Sclerotinia Initiative EC to participate in the Initiative will receive funds in one of two ways:

 

A)     USDA-ARS scientists (or scientists from a cooperating Federal agency) will receive funds via a direct fund transfer from the Sunflower Research Unit.

B)     Scientists from cooperating institutions (universities, state government agencies, private industry, foreign government research laboratories, etc.) will receive funds via the establishment of a Specific Cooperative Agreement with the Sunflower Research Unit.  The Center Director of the Red River Valley Agricultural Research Center, who currently serves as the ARS administrator of the Sclerotinia Initiative, will serve as the ADODR of all agreements.

 

Funds received from the Sclerotinia Initiative will be used only to support research approved by the Sclerotinia Initiative EC.  No funds will be provided for Principal Investigator and cooperating scientists employed as full time employees of ARS or a cooperating institution.  Cooperating institutions include state agencies, research or educational institutions, and for-profit or nonprofit organizations.  Postdoctoral associates, graduate students, undergraduate students, and technical support staff are not considered Principal Investigators.  Specific Cooperative Agreements have limitations on what funds can be used for.   In general, funds cannot be used for purchase of non-expendable equipment of greater than $5,000 in value.  Non-expendable equipment is defined as equipment that will not normally be used up or consumed in service.  Sclerotinia Initiative funds will be approved for travel only to Sclerotinia related meetings and workshops, and for Sclerotinia research activities. 

 

All funded projects will provide periodic progress reports and an annual report to the ARS Initiative administrator.

 

**Final approval of all decisions related to fund distribution and establishment of specific cooperative agreements is the responsibility of USDA-ARS.

 

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Article IV. Annual Research Forum.

Section 4.01              Site Selection

Members of the EC may nominate sites and receive recommendations from the AO. The EC shall select a site by vote. Site selection should take place early enough to facilitate contracts and reservations for facility providers.

Section 4.02  Development of Agenda

The EC in conjunction with the AO shall draft the agenda. The agenda shall be approved by December 15 prior to the annual meeting. The meeting should be held in January of each year.

Section 4.03  Report of Proceedings

The AO shall publish a proceedings document including the abstracts of the presentations, status reports from current research and other pertinent information.

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Article V.  Strategic Plan and Program Assessment

 

Section 5.01              Strategic Plan Development

The AO shall lead development of a 5-year Strategic Plan that outlines the research objectives and priorities of the Initiative as outlined in Section 3.  The plan will be finalized and approved by members of the EC and forwarded to the ARS National Program Staff.  This plan will be reviewed and updated as appropriate.  A completely new and revised Strategic Plan will be developed every 5 years.  The Strategic Plan will be used to guide selection of the research funded by the Initiative.  The plan will include performance measures, anticipated products and milestones, and potential benefits.  Within the plan action items of critical importance will be developed by each participating commodity group.  These items will be reviewed per each participating commodity annually (led by commodity organization leader on EC) and updated as appropriate.

 

Section 5.02  Annual Reports

 

An annual report addressing each element of the Strategic Plan will be developed in November and December of each year.  The AO will request accomplishment statements from each funded project that directly relate their research to the Plan.  The AO and other individuals as requested will compile the reports which will be posted on the Sclerotinia Initiative website and presented during the annual meeting.

 

Section 5.03  Assessments

Every 5 years the AO will convene a panel of experts to review the accomplishments of the Initiative as related to the elements of the Strategic Plan.  The panel will provide a written assessment of progress which will be presented to the EC.  This assessment will be posted on the Sclerotinia Initiative website and presented during the Annual Meeting.  Future research direction/needs of the Initiative will be modified as suggested by the assessment.

 

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Article VI. Amendments to Procedures

Section 6.01  Format of Recommended Change

Amendments shall be submitted in electronic and written format to the AO. Any member of the SC can submit amendments to these procedures.

Section 6.02  Submission Dates

To be timely, a change should be submitted at least 30 days prior to a scheduled meeting of the SC. Untimely submissions may be reviewed but will not be acted upon by the board until the next scheduled SC meeting.

The SC can meet for the purposes of considering an amendment if a majority of the SC agrees. The meeting should still allow 30 days for purposes of dissemination and consideration of the change.

Section 6.03  Dissemination of Change

The change must be disseminated by electronic and written means to all members of the SC.

Section 6.04  Approval of Amendment

Amendments must receive a two thirds majority vote to be approved.

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Strategic Plan (Updated)

View the Strategic Plan in a PDF Format (PDF; 207Kb)

 

STRATEGIC PLAN

Goal 1: Develop novel germplasm and varieties with field resistance to Sclerotinia sclerotiorum

·         PM 1.1:  Identify new sources of resistance in plant germplasm.

·         PM 1.2: Transfer new sources of resistance genes into useful plant germplasm via interspecific hybridization and other means.

        ·         PM 1.3: Genetic analysis and discovery of quantitative trait loci (QTL) that confer resistance to Sclerotinia

·         PM 1.4: Pyramid white mold resistance in plant germplasm.

·         PM 1.5:  Use marker-assisted selection for enhanced resistance to white mold.

·         PM 1.6:  Develop plant germplasm with improved resistance using biotechnology and other novel genetic methods.

·         PM 1.7: Release plant germplasm/ cultivars with improved resistance. Elite cultivars or germplasm with improved resistance to S. sclerotiorum for commercial production with enhance crop productivity and profitability.

 

Goal 2:  Understand Sclerotinia sclerotiorum biology and development

·         PM 2.1: Characterize migration/population structure and ecological variability of genotypes.

·         PM 2.2: Characterize virulence/aggressiveness within the population, identify isolates for use in screening, and monitor durability of host resistance.

·         PM 2.3: Identify factors involved in myceliogenic and carpogenic germination of sclerotia.

·         PM 2.4: Develop genetic markers and molecular tools to study pathogen biology.

 

Goal 3:  Improve ability to discover and characterize gene sequences associated with crop resistance to Sclerotinia sclerotiorum

·         PM 3.1:  Develop DNA markers for QTL identification and marker assisted selection.

·         PM 3.2:  Develop a physical map of genomic regions with clusters of pathogen resistance genes in major crops.

·         PM 3.3: Identification of the function of candidate genes involved in Sclerotinia resistance

·         PM 3.4:  Identify mechanisms of Sclerotinia resistance in model and crop plants.

·         PM 3.5:  Develop bioinformatics resources to facilitate public use of genomic information.

 

Goal 4:  Broaden knowledge of Sclerotinia sclerotiorum epidemiology and improve disease management strategies.

·         PM 4.1:  Optimize fungicide application programs. 

·         PM 4.2:  Develop bio-control alternatives for disease management.

·         PM 4.3:  Develop quantitative models that describe environmental and host-crop interactions on epidemic development.

·         PM 4.4:  Optimize cultural practices for disease management.

 

·         Cross Reference for Performance Measures

 

·         Collaborators & Organizations

Executive Summary
Vision Statement: An integrated research approach is needed to guide the effective development of diagnostic technologies, disease management systems, genomic resources, and crop germplasm exhibiting durable resistance to Sclerotinia sclerotiorum. Strategic deployment and use of these resources will help sustain the competitiveness of U.S. canola, pea, lentil, chickpea, common bean, soybean, and sunflower producers in domestic and global markets.

 

Process & Development of the Sclerotinia Initiative Strategic Plan 2008-2012: On January 20-22, 2008, approximately 80 scientists and related stakeholders with knowledge of the fungal disease, Sclerotinia sclerotiorum (white mold) participated in an annual workshop hosted by the United States Department of Agriculture’s Agricultural Research Service (ARS) in Minneapolis, MN. ARS, the National Sunflower Association, the U.S. Canola Association, the USA Dry Pea and Lentil Council, the U.S. Dry Bean Council, and the American Soybean Association co-organized this program. The participants reviewed the current status of research targeted at improved understanding and management of white mold in canola, dry edible beans, peas & lentils, soybean, and sunflower; and received an independent peer assessment of the research performance of the USDA ARS National Sclerotinia Research Initiative (NSI) over the past five years. The panel of experts was chaired by Dr. Billy E. Caldwell.

 

The assessment panel findings included the following. The NSI addressed performance measure 2.2.3 (Expand, maintain, and protect our genetic resource base, increase our knowledge of genes, genomes, and biological processes, and provide economically and environmentally sound technologies that will improve the production efficiency, health, and value of the Nation’s crops) under Goal 2 (Enhancing the competitiveness and sustainability of rural and farm economies) of the USDA, ARS Strategic Plan for 2006 to 2011. The NSI contributes to that Goal through ARS National Research Programs NP 301 (Plant Genetic Resources, Genomics & Genetic Improvement), NP 302 (Plant Biological and Molecular Processes) and NP 303 (Plant Diseases). This initiative is implemented as an integrated research approach to guide the effective development of diagnostic technologies, disease management systems, genomic resources, and germplasm enhancement for seven crop commodities (canola, dry bean, pea, lentil, chickpea, soybean and sunflower). Currently, the NSI is supported by 73 ARS projects and specific cooperative agreements with 17 Universities and Agricultural Experiment Stations (AES) in 13 U.S. states, plus one AES in Canada.

 

The panel’s review was based on the NSI Research Accomplishment Report (2007) developed from statements submitted by project investigators, by ARS leadership, which focused on the overall impacts of projects within the Initiative. The panel’s assessment of the NSI was meant to be an overarching review rather than a project by project review. Reviews of ARS projects are conducted by the Office of Scientific Quality Review. In addition to the accomplishment report, panelists were able to draw on other resources, including publications, databases and a brief overview of the research areas within relevant ARS national programs by USDA-ARS leadership including:

 

Dr. Lawrence Chandler, Area Director, Midwest Area, Peoria IL, and

Dr. William Kemp, Agricultural Administrator, Northern Crops Research Laboratory, Fargo ND

 

Research accomplishments were assessed against commitments (performance measures) identified in the NSI Strategic Plan 2004 to 2008. Our recommendations are outlined under each of the following Goals:

  • Develop novel germplasm and varieties with field resistance to Sclerotinia sclerotiorum
  • Improve understanding of Sclerotinia sclerotiorum biology and development
  • Improve ability to discover and characterize gene sequences associated with crop resistance to Sclerotinia sclerotiorum
  • Broaden knowledge of S. sclerotiorum epidemiology & improve disease management strategies

Based on the assessment report, a new 5-year strategic plan was developed by a writing team with stakeholder input that outlined four strategic goals with related overarching research objectives. This plan provided program and scientific focus to ensure that the Sclerotinia sclerotiorum research community working in canola, dry edible beans, peas & lentils, soybean & sunflower under the auspices of ARS and the National Sclerotinia Research Initiative attained planned results in an effective & timely manner.

 

The following individuals contributed to the development of this Strategic Plan:

 

Goal 1:     Phil Miklas, USDA ARS, Prosser WA

              George Graef, University of Nebraska, Lincoln NE

              Jim Myers, Oregon State University, Corvallis OR

              Brent Hulke, USDA ARS, Fargo ND

 

Goal 2:     Berlin Nelson, ND State University, Fargo ND

              Henrick Stoltz, University of Oregon, Corvallis OR

              Weidon Chen, USDA ARS, Pullman WA

              Jim Steadman, University of Nebraska, Lincoln NE

 

Goal 3:     Steven Clough, USDA ARS, Urbana IL

              Jeff Rollins, University of Florida, Gainesville FL

             Tobin Peever, Washington State University, Pullman WA

              Kevin McPhee, USDA ARS, Pullman WA

 

Goal 4:     Howard Swartz, The Ohio State University, Columbus OH

              Luis Del Rio, ND State University, Fargo ND

              Tom Gulya, USDA ARS, Fargo ND 

 

This strategic plan encompasses the breadth of research disciplines necessary to better understand the disease and to provide significant management options for the affected producers across the U.S. To achieve the strategic goals and research objectives, this plan emphasizes achievements that hinge on teamwork throughout the Sclerotinia research community. All actions and results will be attained in a manner that is both inclusive and open to public scrutiny.

 

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Introduction
Sclerotinia sclerotiorum is a plant pathogenic fungus that causes important diseases known as white mold, Sclerotinia stem rot, wilt or stalk rot, or Sclerotinia head rot on a wide variety of broadleaf crops.  It is commonly found damaging dry edible beans, sunflowers, soybean, canola, peas, and lentils. There are many other crops that are susceptible such as alfalfa, potato, peanut, mustard, safflower, flax, borage, crambe, buckwheat, chickpea, lupine, faba bean and numerous vegetables such as lettuce and carrots. Some of these crops are rarely damaged by the fungus, while others are quite susceptible.   This pathogen is known to infect about 400 species of plants.   Numerous weeds such as marsh elder, lambsquarters, pigweed, Canada thistle, sow thistle, and wild mustard are also hosts and can play a role in disease cycles.

 

Sclerotinia causes serious economic loss by negatively impacting crop quality and yields. The collective annual losses for the five crops participating in the ARS National Sclerotinia Research Initiative have been as high as $482 million.  Specifically, annual losses for each of the crops have been as high as $100 million for sunflowers; $300 million for soybean; $46 for dry edible beans; $24 million for canola; and $12 million for pulse crops. The disease is a serious threat to the future of the confection sunflower, where quality is a significant concern. Diseased seeds cannot always be separated in cleaning and processing resulting in bitter tasting seeds which are rejected by consumers.

 

The primary survival (overwintering) structure of S. sclerotiorum is the sclerotium. A sclerotium is a

hard resting structure consisting of a light colored interior portion called a medulla and an exterior black protective covering called the rind.   The rind contains melanin pigments which are highly resistant to degradation, while the medulla consists of fungal cells rich in beta glucans and proteins. The shape and size of sclerotia depend on the host and where they are produced in or on infected plants. The Sclerotinia disease cycle begins when sclerotia are germinate after overwintering in soil. Sclerotia may undergo carpogenic germination which results in the production of a small mushroom called an apothecium and ascospores which are ejected into the environment. The pathogen produces oxalic acid and numerous enzymes that break down and degrade plant tissue. Disease development is favored by moisture and moderate temperatures of 15 to 25 C.

 

Another method of germination is myceliogenic, where sclerotium produce mycelium. This is common in the disease cycle in Sclerotinia wilt of sunflower. Most other Sclerotinia or white mold diseases of dry edible beans, soybean, canola and sunflower head rot are initiated by carpogenic germination and infection of above ground plant parts by ascospores.   The primary methods for field infestation are: 1) incoming crops or weeds infected by ascospores or sclerotia from adjacent infested fields; 2) via surface irrigation water or rain water; and 3) contaminated seed. Few studies have quantified sclerotia survival in the field. Microbial degradation is the principal reason for a decline in populations of sclerotia. Many fungi, bacteria and other soil organisms parasitize or utilize sclerotia as carbon sources. Crop rotations allow the natural microbial population to degrade sclerotia. Two important fungal parasites involved in the natural degradation of sclerotia are Coniothyrium minitans and Sporidesmium sclerotivorum. Both may become biocontrol agents for sclerotia.

 

The effect of tillage on survival of sclerotia is poorly understood. Fungicides have been used with some success in dry edible bean and canola. Crop rotation continues to be used for certain crops such as sunflower where inoculum densities in the soil play a major role in disease development. Host resistance has been an elusive goal of many control programs. Most Sclerotinia diseases are not controlled by host resistance. However, moderate levels of host resistance in dry edible beans and soybean have been used in integrated control programs.

 

The National Strategic Plan for the Sclerotinia Initiative 2008-2012 provides the research community with a foundation for a comprehensive and integrated research approach toward these problems. The performance measures outlined in this plan are relevant to the current needs of US agriculture. The plan defines the actions that will be taken to solve these problems, describes what is promised or will be produced, assigns accountability for the work to be accomplished, and provides a mechanism for peer review and assessment of research progress.

 

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Strategic Plan for Sclerotinia Research
Crop Germplasm Resources & Genetics

Goal 1: Develop novel germplasm and varieties with field resistance to Sclerotinia sclerotiorum

PM 1.1:  Identify new sources of resistance in plant germplasm. 

Commercially available canola, pea, lentil, chickpea, common bean, soybean and sunflower cultivars are not resistant to S. sclerotiorum, although some differences in susceptibility exist. USDA and International Germplasm Collections will be fully evaluated for genes that mediate effective resistance to S. sclerotiorum.

 

Anticipated Products

  • Accessions of USDA canola collections for B. napus, B. rapa, B. carinata, and B. juncea with resistance to S. sclerotiorum are identified and used in breeding programs.
  • Accessions of USDA and world pea germplasm collections including wild species including Pisum elatius, P. humile, P. fulvum with resistance to S. sclerotiorum are made available to the user community as breeding lines.
  • Accessions of USDA and world collections of lentil germplasm (L. culinaris) including wild species such as Lens orientalis and L. odemensis with resistance to S. sclerotiorum are characterized and used by breeding programs.  
  • Accessions of USDA and world collections of chickpea germplasm including wild species with resistance to S. sclerotiorum are characterized and used by breeding programs.  
  • Accessions of 20+ annual Helianthus taxa in USDA and world sunflower germplasm collections with stalk rot and head rot resistance in are characterized and used in breeding programs
  • Exploration trips to obtain seeds of wild species currently not available in USDA germplasm collections
  • Improved germplasm screening methods and greenhouse S. sclerotiorum inoculation procedures with validation in field trials.

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PM 1.2: Transfer new sources of resistance genes into useful plant germplasm via interspecific hybridization and other means.

Wild species of cultivated crops often exhibit resistance genes that are not found in unadapted germplasm. Inter-specific crosses between wild relatives or their amphidiploids and cultivated species are often constrained by genetic incompatibilities or other problems resulting in non viable progeny. Sophisticated strategies will be developed and deployed to utilize beneficial genetic variation for Sclerotinia resistance from unadapted and wild species in modern variety production.

 

Anticipated Products:

  • Common bean breeding lines and inbred backcross lines derived from interspecific crosses of common and runner beans that exhibit white mold resistance.
  • Three interspecific Phaseolus RIL populations for QTL conditioning resistance with major effect and stable expression across environments.
  • White mold resistant selections of unadapted pea evaluated for agronomic traits.
  • Lentil germplasm with partial resistance to S. sclerotiorum and suitable agronomic traits for adaptation and end-use. Promising selections with resistance to S. sclerotiorum have been increased and are available for release as improved cultivars.
  • Chickpea lines with tolerance to the collar rot phase of the disease identified and used extensively in chickpea breeding programs.
  • Improved resistance sources in soybean used to incorporate confirmed resistance QTL into elite germplasm. Near-isogenic lines for specific QTL and candidate genes are used to understand mechanisms related to specific QTL resistance genes, genotype x genotype and genotype x environment interactions.
  • Sunflower germplasm with resistance genes from wild Helianthus perennial species H. maximiliani and H. nuttallii (head rot), and perennial accessions of H. schweinitzii, H. californicus, and H. verticillatus (stem rot). Interspecific amphiploid hybrids for resistance to head and stem rot. Backcross populations to incorporate more resistance genes into HA 410 and HA 441 with chromosome number 2n=34.  

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PM 1.3:  Genetic analysis and discovery of quantitative trait loci (QTL) that confer resistance to Sclerotinia

Knowledge of the genetics of resistance to S. sclerotiorum is essential to formulation of effective screening strategies for disease resistance. Genetic maps of the genome are needed to facilitate breeding efficiency and genetic associations are necessary to understand the nature and the number of genes involved in resistance. Information gained from genetic analyses will lead to the identification and positioning of closely linked molecular markers on genetic maps for disease resistance genes, and the discovery of relevant QTLs..   

 

Anticipated Products:

  • Highly inbred PI 255956 x Wolven Pole mapping population with validated QTLs in interspecific backcross-inbred populations with scarlet runner bean (P. coccineus)
  • RIL populations for QTL analysis to generate a high density genetic map of the pea genome and for map based cloning of genes for resistance to S. sclerotiorum.
  • Highly inbred lentil mapping populations (RILs) phenotypic association with QTLs for resistance to S. sclerotiorum. A high density genetic map of the lentil genome and verification of closely linked molecular markers associated with resistance to S. sclerotiorum.
  • Integrated linkage maps of QTL from ICA Bunsi in a pinto bean background.

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PM 1.4: Pyramid white mold resistance in plant germplasm.

Resistance QTL may occur on multiple linkage groups and some are associated with regions containing other fungal resistance genes or resistance gene analogs. Parental lines seldom contain all the identified favorable QTL alleles for reaction to Sclerotinia. Therefore, QTL from multiple sources must be combined into single lines to enhance overall resistance.

 

Anticipated Products:

  • Recurrent selection common bean populations segregating for >10 QTL for white mold resistance, and advanced testing in the National White Mold Nursery
  • At least one released soybean breeding line with pyramided resistance QTL for resistance and agronomic traits. Initiate crosses to incorporate enhanced resistance into elite cultivars. Sclerotinia resistance evaluation in regional disease nurseries. Initiate crosses to combine complimentary QTL from the best multi-QTL lines identified to date

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PM 1.5:  Use marker-assisted selection for enhanced resistance to white mold.

A MAS system for selection for specific traits requires identification of germplasm with contrasting phenotypes, identification of markers closely associated with QTLs, and high-throughput phenotyping technologies to facilitate rapid/cost effective screening of large populations. Translational genetics will be needed to determine which of the marked genes for disease resistance are most important for use in breeding enhanced germplasm and cultivars. Such knowledge will help plant breeder’s better handle the complexity of gene recombination in breeding populations. Otherwise, independent segregation of alleles may make it too daunting to select progeny with the desired trait or combination of traits.

 

Anticipated Products:

  • High resolution genetic map in common bean for the G122 X Pinto bean RIL population and new populations to achieve higher levels of resistance in pinto bean and snap bean.
  • Disease reaction date from multiple field environments and greenhouse tests for advanced common bean RIL populations possessing different combinations of QTL for resistance
  • MA’s capability for the most important QTL derived from ICA Bunsi.
  • Marker-assisted selection protocol for resistance to SWM in peas. Markers converted to easily assayed sequence characterized amplified regions (SCARs) for more efficient
    genotyping and use in marker-assisted selection.  
  • Valid markers for effectiveness in a MAS protocol for resistance to SWM in lentils. Markers converted to sequence characterized amplified region (SCAR) markers for more efficient genotyping.
  • DNA markers associated with resistance used to identify soybean germplasm QTL. Breeding populations for trait phenotyping. Knowledge of interaction among genotypes (both plant and pathogen) and environmental factors for resistance to Sclerotinia in soybean.
  • DNA markers in sunflower for Sclerotinia head rot and stalk rot resistance. Identify QTL controlling stalk rot and/or head rot resistance from different sources. Field verification of field resistance.       

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PM 1.6:  Develop plant germplasm with improved resistance using biotechnology and other novel genetic methods.

Novel methods of developing Sclerotinia resistant germplasm include mutagenesis and transformation. Accumulation of endogenous plant genes to enhance Sclerotinia resistance, introduction of genes from unrelated plants or other sources may provide complementary and useful approaches for effective control of white mold in crop species.  

 

Anticipated Products:

  • Develop doubled haploid canola lines for resistance, and test the best lines in multiple environments
  • Advanced generations of common bean lines transformed gf-2.8 for oxalate oxidase expression; inheritance studies and field evaluation of the putative transgenic lines.
  • An inventory of candidate disease resistance genes, promoters, and constructs for transformation into pea germplasm. Efficacy of oxalate oxidase and other defense related genes for control of SWM in peas. Pea germplasm transformed with anti-fungal genes and tested for efficacy for reducing SWM damage
  • An inventory of candidate disease resistance genes, promoters, and constructs for transformation into lentil germplasm. Efficacy of oxalate oxidase and other defense related genes for control of SWM in peas. Lentil germplasm transformed with anti-fungal genes and tested for efficacy for reducing SWM damage
  • Release of Perlka-resistant soybean lines as a management tool for S. sclerotiorum and regional testing of resistant lines. Field and controlled-environment tests on transgenic soybeans containing an antifungal peptide. Knowledge of nematicidal effects of Perlka on soybean cyst nematode

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PM 1.7: Release plant germplasm/cultivars with improved resistance.  Elite cultivars or germplasm with improved resistance to S. sclerotiorum for commercial production with enhance crop productivity and profitability.

 

Anticipated Products:

  • Resistant canola lines with the best agronomic attributes released for commercial production. 
  • Agronomic resistant pea, lentil and chickpea lines released for commercial production. 
  • Resistant lines with the best agronomic attributes (high yield, adequate seed size, etc.) for use in improving common bean, pinto bean and related market classes
  • Testing programs for disease reaction in new common bean varieties in CO, ID, MN, ND, NE, and WA
  • Release at least one soybean germplasm or cultivar with improved yield and resistance to Sclerotinia stem rot, BSR, SCN, and Phytophthora. Determine resistance gene interactions.
  • Inbred confection sunflower lines with genetic resistance from HA 441, RHA 439, and RHA 440, for Sclerotinia head rot and for Sclerotinia stalk rot resistance. BC1F6-derived BC1F7 germplasm lines will be testcrossed and the resultant hybrid seed with desired traits will be released for commercial use.

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Pathogen Biology & Mechanisms of Disease Resistance
Goal 2:  Understand Sclerotinia sclerotiorum biology and development

Sclerotinia sclerotiorum has an unusually large host range of over 400 plant species in numerous families. The pathogen is found in diverse environments from southern to northern climates and in different agricultural systems under both dry land and irrigated conditions. Although found primarily as a pathogen in the field, it can also be a problem under storage conditions for some crops. The success of this pathogen and its demonstrated ability to adapt to a wide range of conditions can be largely attributed to its aggressive mode of pathogenesis and to the production of specialized multicellular developmental structures for survival and dispersal. There are many aspects of the biology of this biology that are not understood. An improved knowledge of population structure, ecological types, virulence diversity, germination factors, pathogenicity factors, and improved molecular methods for studying the biology, would aid in the development of controls for the numerous diseases caused by this fungus.

 

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PM 2.1: Characterize migration/population structure and ecological variability of genotypes. 

Clonal and sexual processes are involved in expressing genetic variability in S. sclerotiorum, but the true genotype structure of the population within North America is not well characterized. More detailed characterization of pathogen genotype collections from a wide variety of economic and wild hosts is necessary. Identifying ecological types within populations will provide an understanding of how disease develops in agro-ecosystems and provide insight into pathogen survival. Information is needed on ecotypes associated with certain hosts and agro-ecosystems, and there is limited knowledge on the virulence range of isolates.  

 

Anticipated Products:

  • Standardized genotypic characterization of the pathogen on wild species and cultivated crops
  • Defined environmental requirements for pathogen biotype germination and disease development.
  • Documented significance of gene-flow or outcrossing in population variability
  • Evidence of ecological types in the population and biotypes with fungicide resistance
  • Geographical inventory of populations across the US and multistate approach to associate gene activity in Sclerotinia with specific phenotypic characteristics of isolates.

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PM 2.2: Characterize virulence/aggressiveness within the population, identify isolates for use in screening, and monitor durability of host resistance.  

Differences in virulence exist within the pathogen population, but the extent of the variation and how it relates to pathogen genotype and host range is poorly understood. Physiological characteristics may be important to disease development and pathogenesis. Standard methods will be developed to describe virulence/ aggressiveness in the pathogen. Host specificity and the range of virulence/aggressiveness of collections from different hosts and environments will be tested to determine impact on partial resistance.

 

Anticipated Products: 

  • Documented variability in virulence/aggressiveness of isolates from widely different geographic areas on a range of hosts.
  • Knowledge of pathogen virulence/aggressiveness on sources of partial resistance in various crops.
  • Determine environmental parameters that affect virulence/aggressiveness of isolates.
  • Theory on the influence a virulent isolate x partially resistant host interaction may be a factor in the virulence on other hosts.
  • Identification of crop germplasm with partial resistance to a variety of virulent isolates
  • Criteria for testing virulence/aggressiveness on specific hosts.

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PM 2.3: Identify factors involved in myceliogenic and carpogenic germination of

sclerotia.

Germination of sclerotia is a critical event in disease development. Certain environmental factors are involved in the germination process, but the biological mechanisms are not precisely understood. The role of soil microorganisms, other than mycoparasites, in the sclerotiasphere also will be determined on the germination process to aid in the prediction of disease and identify points in the cycle where germination can be disrupted.

 

Anticipated Products:

  • Determined host factors that foster myceliogenic germination of sclerotia.
  • Evidence on effects of the microbial population (other than mycoparasites) in the sclerotiasphere on germination and dormancy
  • Identification of host factors that may enhance myceliogenic germination.
  • Identification of microbes that enhance or inhibit/retard germination of sclerotia in the soil.
  • Identification of microbes that inhibit/retard mycelial growth.

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PM 2.4: Develop genetic markers and molecular tools to study pathogen biology.  Identification of isolates and genotyping pathogen populations requires an array of molecular markers such as microsatellites, SNPs and ALFPs. High density genetic maps of the pathogen genome will be developed with DNA markers for isolate discrimination, alignment of DNA fragments, and localization of QTL for Sclerotinia resistance.

 

Anticipated Products:

  • Reporter gene constructs with inducible promoters, organelle specific targets; insertional mutant libraries
  • Standard molecular protocols to genotype isolates.
  • Transformed isolates for host/pathogen interactions, pathogen/microbe interactions and resistance.             

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PM 2.5:  Develop EST libraries from stains of the pathogen. 

A publicly-funded Sclerotinia sclerotiorum whole genome sequencing project has produced a draft sequence of the nuclear and mitochondrial genomes at an 8X sequence depth, and has provided a computer-based annotation of the coding sequences within the genome. Gene discovery in Sclerotinia will be accelerated by significant amounts of sequence data from transcribed genes to achieve high confidence in the annotation. Expressed sequence tags (ESTs) are the most effective means of collecting gene sequence information. cDNA libraries from S. sclerotiorum-infected crops at a variety of physiological and developmental stages of Sclerotinia. These include: sclerotial initials, polygalacturonic acid-grown mycelia, neutral pH-shifted mycelia, differentiating apothecia, low pH vegetative mycelia, agar grown mycelia, and infection cushions.

 

Anticipated Products:                 

  • cDNA libraries from about 20,000 ESTs from fungal tissue grown in culture under different growth conditions and stresses.
  • Useful cDNA libraries to identify infection-related genes from both host and pathogen.
  • Independent sequence information derived from the Sclerotinia genome sequencing project as well as from various plant sequencing projects to facilitate differentiation of host and fungal genes.
  • Full length, normalized cDNA libraries to ensure a high rate of gene discovery.

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PM 2.6:  Use transcriptomics to identify candidate genes involved in Sclerotinia

pathogenicity. 

Development of microarrays from Sclerotinia would allow high through-put screening based on pathogen gene expression during pathogen attack and will provide further clues as to key factors for pathogenicity and defense. Universal mechanisms exist in organisms to inactivate target genes with interfering RNA molecules to prevent them from being translated into functional proteins. RNAi approaches in Sclerotinia will be standardized and widely available.

 

Anticipated Products:

  • Large collections (>10,000) of ATMT for use in phenotypic screens.
  • Transcriptome profiling approaches for a variety of gene targets and high through put functional analyses
  • Promoters useful for expressing RNAi constructs during infection (e.g., plant-inducible promoters).
  • Inventory of genes involved in pathogenesis recovered from ATMT random mutagenesis.
  • Discovery of candidate gene function using a systems biology approach to gene silencing.

          
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Crop Genome Analysis and Genomic Tools
Goal 3:  Improve ability to discover and characterize gene sequences associated with crop resistance to Sclerotinia sclerotiorum

 

PM 3.1:  Develop DNA markers for QTL identification and marker assisted selection.

Breeding for Sclerotinia resistance is of paramount importance to achieving yield potential of may agricultural crops.  However, phenotypes for protection traits often are governed by multiple genes which may include alleles of the same gene. The probability of selecting a desired genotype from a breeding population is reduced significantly by the number of alleles involved in expression of a phenotype. Development and use of DNA markers, maps, and arrays that target alleles associated with trait expression will improve selection efficiency and expedite delivery of enhanced germplasm and cultivars for commercial production. Advances in genome ‘resequencing’ and ‘fine-mapping’ technologies will enable whole genomic analysis of progeny from segregating populations.

 

Anticipated Products:

  • Affordable high-throughput genotyping and phenotyping technology for high-resolution quantitative trait loci (QTL) detection
  • High density genetic map of DNA markers for genes associated with genetic resistance to Sclerotinia and other pathogens
  • Ability to determine the biological basis for host-pathogen interactions               

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PM 3.2:  Develop a physical map of genomic regions with clusters of pathogen resistance genes in major crops. 

Clusters of disease resistance genes often are found on various linkage groups in soybean. Similar regions rich in resistance genes are anticipated in the genomic organization of canola, common bean, pea, lentils, chickpea and sunflower. Construction of physical maps of these genomic regions will provide a wealth of information that facilitates the discovery of additional DNA markers, location of expressed genes associated with Sclerotinia resistance, and the potential for whole genome sequencing in breeding populations and germplasm collections

 

Anticipated Products:

  • Extensive cDNA libraries developed from host tissue at different stages of infection
  • DNA markers from BAC-ends to facilitate anchoring DNA fragments to the genetic map for Sclerotinia resistance genes
  • A physical map of genomic regions containing Sclerotinia resistance genes
  • High through-put resequencing capacity and haplotype maps for genomic regions containing Sclerotinia resistance genes
  • Discovery of candidate gene sequences associated with Sclerotinia resistance

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PM 3.3:  Identification of the function of candidate genes involved in Sclerotinia

resistance. 

Identifying key genes that mediate defense against Sclerotinia sclerotiorum involves the association of a putative gene sequence with a measurable phenotype. Such knowledge facilitates strategies for genetic manipulations that could enhance protection to the pathogen, including the development of DNA markers that are exclusive to specific alleles. Gene microarrays containing thousands of gene representatives will be used to survey pathogen-challenged tissue for changes in gene expression patterns. In addition, gene function will be determined by exploiting universal mechanisms in organisms that inactivate target genes using interfering RNA molecules or other gene silencing techniques.

 

Anticipated Products: 

  • Microarrays representing high numbers of genes are currently available for soybean, canola, chick pea, common bean, lentil, pea, and sunflower.
  • Sequenced cDNA libraries from infected host tissue of the 7 major crops susceptible to Sclerotinia (canola, chick pea, common bean, lentil, pea, soybean, sunflower), each based on ca. 100,000 new ESTs
  • Identification of candidate genes for Sclerotinia resistance..
  • Functional RNAi systems that target gene sequences associated with Sclerotinia resistance in crops
  • Useful promoters for expressing RNAi constructs during infection (e.g., disease-inducible promoters) with improved transformation efficiency
  • Known function of candidate genes using high throughput methods such as virus induced gene silencing (VIGS) to implement a systems biology approach for refining targets for gene silencing. 

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PM 3.4:  Identify mechanisms of Sclerotinia resistance in model and crop plants.

Genetic and molecular tools are most proficient for the model plant Arabidopsis thaliana. S. sclerotiorum causes lethal rot on all ecotypes tested to date. However, sensitivity to the virulence factor oxalate varies and the rate of disease progress may differ among ecotypes. Traits related to Sclerotinia infection can be used effectively to identify and characterize genes that confer partial resistance. Arabidopsis offers additional resources that are related to resistance or defense genes and an easy genetic system to functionally
validate the roles of any given gene. Arabidopsis genetics can provide a means to identify genes that mediate oxalate toxicity and thus susceptibility to the pathogen.

 

Anticipated Products:

  • Yeast screens that reveal Arabidopsis thaliana ecotypes and well-characterized defense-related mutants for oxalate sensitivity and defense against Sclerotinia
  • Molecular markers and maps of regions containing Sclerotinia defense-related genes
  • Transgenic incorporation of genes into crops and determine their effectiveness against Sclerotinia.

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PM 3.5:  Develop bioinformatics resources to facilitate public use of genomic information.

Genetic information is being generated at a very rapid pace. The amount of data is so great that the traditional journal-based system for accessing this data is becoming ineffective, especially in providing plant breeders and fungal biologists with easy, logical access to sequence and genomic data in a format that they can readily assimilate. Data will be available in web-accessible, user friendly formats.

 

Anticipated Products:

  • A mechanism in place to allow continuing communication between the fungal molecular and plant breeding communities
  • Curation of a robust communication system between the fungal molecular and plant breeding communities that targets genomic approaches to important pathogenic and virulence traits                 

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Disease Management & Pathogen Epidemiology

Goal 4:  Broaden knowledge of Sclerotinia sclerotiorum epidemiology and improve disease management strategies.

 

PM 4.1:  Optimize fungicide application programs. 

Efforts will identify fungicides (mixes), concentrations and application methods that provide best control of Sclerotinia in canola, soybean, common bean, pea, lentil, chickpea and sunflower.  

 

Anticipated Products:

  • A region-wide collection of S. sclerotiorum isolates to establish a baseline of fungicide sensitivity
  • Identification of the efficacy of new chemistries
  • Updated management guides for growers on use of fungicides for disease management
  • New spraying technologies that enhance canopy penetration, like electrostatic and air-assisted blast

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PM 4.2:  Develop bio-control alternatives for disease management.

Initial activities will focus in the evaluation of already available commercial bio-control agents, like Coniothyrium minitans. Additional surveys and screening exercises will identify new antagonists of S. sclerotiorum and optimal application

 

Anticipated Products:

  • Grower recommendations for the use of commercially available sclerotial antagonists as control agents.
  • Inventory of other commercially available microbial biocontrol agents
  • Evidence of the efficacy of Sporidesmium sclerotivorum as a potential new biocontrol agent
  • Updated management guides for growers on use of biofungicides for disease management

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PM 4.3:  Develop quantitative models that describe environmental and host-crop interactions on epidemic development.

Early warning systems based on pathogen epidemiology are needed to facilitate effective disease management measures for S. sclerotiorum in canola, dry bean, sunflower, soybean, and pulse crops. The association between the disease and yield or crop quality loss will be determined to establish disease management criteria and decision models for commercial production systems.

 

Anticipated Products:

  • Models with predictive capability that could be used in a disease warning system in canola based on the association between weather variables and epiphytotics of S. sclerotiorum  
  • Validated predictive models in other crops.
  • Yield loss models based on time of infection and inoculum concentration
  • Use of threshold levels obtained in yield loss experiments in disease management programs

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PM 4.4:  Optimize cultural practices for disease management.

The impact of common cultural practices on disease development will be evaluated through field experiments emphasizing crop rotation schemes, variety/hybrid selection, planting dates, etc. The use of precision agriculture technology will allow growers to treat hot spots with fungicides instead of broadcast them in entire fields.

 

AnticiVariety selection criteria based on the amount of sclerotia produced in planting dates and densities

  • Integrate information into disease management packages that are available to growers
  • Epidemiological information on disease development (spatial distribution, remote sensing, etc.) that could be used to support a precision agriculture program for canola, sunflower, dry bean, soybean, and pulses.
  • Validated epidemiological data and integration into disease management packets that include a precision technology strategy 

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Appendices
Cross Reference for Performance Measures

Crop Germplasm Resources & Genetics

Goal 1: Develop novel germplasm and varieties with field resistance to Sclerotinia sclerotiorum

 

  • PM 1.1:  Identify new sources of resistance in plant germplasm
    • PM 1.1.1:  Identify new sources of resistance in Brassica germplasm
    • PM 1.1.2:  Improve methods to identify resistant canola germplasm 
    • PM 1.3.1:  Identify sources of resistance in pea germplasm and wild species.
    • PM 1.4.1:  Identify sources of resistance in lentil germplasm and wild species.
    • PM 1.5.1:  Identify sources of resistance in chickpea germplasm and wild species
    • PM 1.7.1:  Develop inoculation methods for field and greenhouse to assess head rot and stalk rot resistance in sunflower
    • PM 1.7.3:  Evaluate cultivated sunflower germplasm for head & stalk rot resistance
    • PM 1.7.5:  Evaluate wild Helianthus germplasm for head rot and stalk rot resistance

  • PM 1.2: Transfer new sources of resistance genes into useful plant germplasm via interspecific hybridization and other means. 

    • PM 1.2.2:  Transfer resistance from scarlet runner bean to dry and snap bean via interspecific hybridization
    • PM 1.2.6:  Characterize and transfer resistance from Bunsi into pinto bean and other susceptible market classes
    • PM 1.3.2:  Transfer resistance to improved pea varieties through crossing & selection
    • PM 1.4.2:  Transfer resistance to improved lentil varieties through crossing & selection
    • PM 1.5.2:  Transfer resistance to chickpea through hybridization and selection.
    • PM 1.7.4:  Transfer resistance from cultivated to oilseed and confection sunflower germplasm. 
  • PM 1.7.6: Transfer resistance from wild Helianthus into adapted sunflower germplasm.

    • PM 1.3:  Genetic analysis and discovery of quantitative trait loci (QTL) that confer resistance to Sclerotini
    • PM 1.1.4:  Identify quantitative trait loci (QTL) that confer resistance to Sclerotinia in canola. 
    • PM 1.2.1:  Genetic analysis for resistance in scarlet runner bean
    • PM 1.2.3:  Determine durability and genetics of resistance among interspecific dry bean breeding lines.  
    • PM 1.3.3:  Develop mapping populations for inheritance and to genomic analysis of resistance genes in pea.
    • PM 1.4.3:  Develop mapping populations for inheritance of resistance and genomic analysis of resistance genes in lentil.

  • PM 1.4: Pyramid white mold resistance in plant germplasm
    • PM 1.2.4: Pyramid white mold resistance in dry bean.
    • PM 1.6.2: Combine resistance genes from different sources of Glycine. 
    • PM 1.6.4: Pyramid QTL for resistance genes in soybean germplasm. 
  • PM 1.5:  Use marker-assisted selection for enhanced resistance to white mold
  • PM 1.2.5:  Use marker-assisted selection for dry bean resistance to white mold.
    • PM 1.3.4:  Use DNA markers for resistance genes in pea for marker-assisted selection.  
    • PM 1.4.4: Use DNA markers for resistance genes in lentil for MAS
    • PM 1.6.3:  Use DNA markers for resistance genes in soybean for MAS
    • PM 1.7.2:  Use MAS approaches for Sclerotinia resistance in sunflower

  • PM 1.6:  Develop plant germplasm with improved resistance using biotechnology and other novel genetic methods

    • PM 1.1.3:  Develop canola germplasm with improved resistance using novel methods.
    • PM 1.2.8: Transform beans with Germin oxalate oxidase gene.
    • PM 1.3.5:  Introduce resistance or anti-fungal genes in pea germplasm by genetic modification.
    • PM 1.4.5:  Introduce resistance or anti-fungal genes in lentil germplasm by genetic modification.
    • PM 1.6.5:  Evaluate transgenic approaches for control of S sclerotiorum in soybean.

  • PM 1.7: Release plant germplasm/cultivars with improved resistance

    • PM 1.1.5: Release canola germplasm/cultivars with improved resistance
    • PM 1.2.9: Determine genotype x environment effects on performance of resistant dry bean germplasm.
    • PM 1.6.1: Release soybean germplasm and cultivars with resistance to Sclerotinia stem rot

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Pathogen Biology & Mechanisms of Disease Resistance

Goal 2:  Understanding Sclerotinia sclerotiorum biology and development

 

  • PM 2.1: Characterize migration/population structure and ecological variability of Genotypes

    • PM 2.0.1: Characterize migration/population structure and ecological variability of genotypes.   

  • PM 2.2: Characterize virulence/aggressiveness within the population, identify isolates for
    use in screening, and monitor durability of host resistance

    • PM 2.0.2: Characterize virulence/aggressiveness within the population, identify isolates for use in screening, and monitor durability of host resistance

  • PM 2.3: Identify factors involved in myceliogenic and carpogenic germination of Sclerotia

    • PM 2.0.3: Identify factors for myceliogenic & carpogenic germination of sclerotia

  • PM 2.4: Develop genetic markers and molecular tools to study pathogen biology

    • PM 2.0.4: Develop genetic markers and other molecular tools to study the biology of the pathogen. 

  • PM 2.5:  Develop EST libraries from stains of the pathogen

    • PM 3.0.6:  Develop EST libraries from stains of the pathogen. 

  • PM 2.6:  Use transcriptomics to identify candidate genes involved in Sclerotinia pathogenicity

    • PM 3.0.7:  Use transcriptomics to identify candidate genes involved in Sclerotinia pathogenicity. .
    • PM 3.0.8:  Target candidate genes by RNAi to screen for pathogenicity and virulence.  

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Crop Genome Analysis & Genomic Tools

Goal 3:  Improve ability to discover and characterize gene sequences associated with crop resistance to Sclerotinia sclerotiorum

 

  • PM 3.1:  Develop DNA markers for QTL identification and marker assisted selection

 

    • PM 1.2.7:   Identify candidate genes contributing to resistance. 
    • PM 3.0.3:  Develop new DNA markers for QTL identification and marker assisted selection.

  • PM 3.2:  Develop a physical map of genomic regions with clusters of pathogen resistance genes in major crops

    • PM 3.0.1:  Use transcriptomics to identify candidate genes involved in Sclerotinia resistance
    • PM 3.0.5:  Target candidate genes by RNAi to screen for susceptibility and resistance

  • PM 3.3:  Identification of the function of candidate genes involved in Sclerotinia Resistance

    • PM 3.0.4:  Accumulate genome sequence information from major crops susceptible to Sclerotinia.

  • PM 3.4:  Identify mechanisms of Sclerotinia resistance in model and crop plants

    • PM 3.0.2:  Identify mechanisms/genes of resistance in the model plant Arabidopsis.

  • PM 3.5:  Develop bioinformatics resources to facilitate public use of genomic information

    • PM 3.0.9:  Develop bioinformatics resources to provide genomic information to the scientific community.  

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Disease Management & Pathogen Epidemiology

Goal 4:  Broaden knowledge of Sclerotinia sclerotiorum epidemiology and improve disease management strategies.

  • PM 4.1:  Optimize fungicide application programs

    • PM 4.0.1:  Optimize fungicide application programs. 
    • PM 4.0.2:  Optimize fungicide delivery systems. 

  • PM 4.2:  Develop bio-control alternatives for disease management

    • PM 4.0.3:  Develop bio-control alternatives for disease management.
    • PM 4.0.4:  Develop non-fungicidal chemical alternatives for disease management. 

  • PM 4.3:  Develop quantitative models that describe environmental and host-crop interactions on epidemic development

    • PM 4.0.5:  Develop quantitative models that describe the role of weather variables on epidemic development.
    • PM 4.0.6:  Develop quantitative models that describe the relationship between S. sclerotiorum and yield for sunflower, canola, dry bean, and pulse crops.

  • PM 4.4:  Optimize cultural practices for disease management

    • PM 4.0.7:  Optimize cultural practices for disease management.
    • PM 4.0.8:  Optimize disease management at field level by combining IPM practices with precision agriculture technologies.

Index - (Goal#).(Commodity#) where, 1= canola; 2 = common bean; 3 = pea; 4 = lentil; 5 = chickpea; 6 = soybean; 7 = sunflower; 0 = all

 

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Collaborators & Organizations

Advisory Committee

Rick Bennett

Larry Chandler

Barry Coleman

Tim Courneya

Tom Grebb

  

William P. Kemp

Larry Kleingartner

Tim McGreevy

Stephen R. Muench

Beth C. W. Nelson

  

Todd Scholz

Dale Thorenson

Greg Varner

Brady Vick

Rich Wilson

 

AgriBusiness

Jesse Barthel

Bob Green

Daryn McBeth

Mike Bodewitz

Sonia Hallier

Ottmar Philipp

Joe Caroline

Mike Hutter

Keith Reinholt

  

 

Christopher Clark

Jim Johnson

Robert R. Sutter

Jon Dockter

Tom Johnson

John Swanson

Pat Duhigg

Clinton Jurke

Kris Versdahl

Timothy Eschbach

  

Ron Klinge

Alan S. Wicks

Igor Falak

Mike Krueger

Chunren Wu

Radisa Gjuric

Jean Q. Liu

David Goulet

Tom Borgen

 

Universities/Institutions

North Dakota State University

South Dakota State University

University of Minnesota, St. Paul

University of Nebraska, Lincoln

Michigan State University

 

 

 

 

Cornell University

University of Idaho

Ohio State University

Oregon State University

University of Florida

 

 

 

 University of Georgia

University of Illinois

University of Wisconsin

USDA-ARS

RRV Ag Research Center

 

Agricultural Organizations

National Sunflower Association of Canada

USA Pea & Lentil Council

Northern Canola Growers

 

 

Northarvest Bean Growers

Association

Central Bean Company

National Sunflower Association

 

 

United Soybean Board

Minnesota Canola Council

U.S. Canola Association

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Strategic Milestones and Accomplishment Report

Meeting Strategic Milestones of the National Sclerotinia Research Initiative for 2012

View the Strategic Milestones and Accomplishment Report 2012 in PDF format (PDF; 379 Kb)

 

Meeting Strategic Milestones of the National Sclerotinia Research Initiative for 2011

View the Strategic Milestones and Accomplishment Report 2011 (v3) in PDF format (PDF; 377Kb)

 

Meeting Strategic Milestones of the National Sclerotinia Research Initiative for 2010

View the Strategic Milestones and Accomplishment Report (v4) in PDF format (PDF; 335Kb)

 

 

 

     
Last Modified: 05/06/2013