USDA/ARS
National Germplasm Resources Laboratory
Report to PGOC, RTACs and CGCs
 2006

The National Germplasm Resources Laboratory (NGRL), located in the Plant Sciences Institute at the Henry A. Wallace Agricultural Research Center in Beltsville, MD, supports the acquisition, introduction, documentation, evaluation, and distribution of germplasm by the National Plant Germplasm System (NPGS) and other components of the U.S. National Genetic Resources Program (NGRP).  The Laboratory is comprised of the Germplasm Resources Information Network/Database Management Unit (GRIN/DBMU), the Plant Exchange Office (PEO) and the Plant Disease Research Unit (PDRU) whose functions and procedures are provided below. The Laboratory also facilitates the activities of the Crop Germplasm Committees that advise components of the NPGS on a variety of matters.

Plant Exploration and Exchange Program

The PEO supports the collection of germplasm for the NPGS through the management of a Plant Exploration and Exchange Grant Program.  Plant explorations involve field collection of germplasm not available in any germplasm collections, while plant exchanges are expeditions to arrange exchange of germplasm already conserved in foreign genebanks.  Annual guidelines for developing plant exploration and exchange proposals are prepared by the PEO and distributed to researchers.

An extensive review procedure is used to assess the relevance of the proposals to the NPGS needs and the likelihood that the proposed explorations or exchanges will accomplish their stated objectives.  Before submission, proposals are reviewed by the appropriate CGC or other crop experts. After submission to the PEO, proposals are reviewed by a subcommittee of the NPGS Plant Germplasm Operations Committee (PGOC).  The PEO then evaluates the proposals and the PGOC reviews and makes recommendations on funding to the ARS National Program Staff (NPS).

All foreign explorations supported by PEO comply with the provisions of the Convention on Biological Diversity on access and benefit sharing related to genetic resources. Prior informed consent to collect genetic resources is obtained from the appropriate host country authorities before the exploration takes place. The permission includes agreement on the benefits to the host country associated with access to genetic resources. The PEO is involved in most requests to foreign governments for permission for collecting and negotiates the terms of agreements when necessary. Foreign explorations are always conducted in cooperation with scientists from the host country and cooperation with the national genetic resources programs is strongly encouraged. Germplasm obtained on explorations is shared by the NPGS and the host country. 

(Attachments: FY 05 and 06 Plant Explorations and Exchanges)

Facilitation of Germplasm Exchange

The PEO assists NPGS personnel and other scientists in acquiring germplasm from scientists and private citizens, foreign national and international genebanks, domestic and foreign explorations, and special projects and agreements. The PEO also helps to expedite the distribution of germplasm from the NPGS to scientists and other genebanks.

PI Documentation

Since 1898, Plant Introduction (PI) numbers have been used as unique identifiers for accessions incorporated into the NPGS. In earlier times, PI numbers were automatically assigned to all material received by the Plant Introduction Office, a predecessor of the PEO. Currently, before PI numbers are assigned, NPGS curators first evaluate the passport data, and grow and observe new accessions to verify uniqueness and rationale for preservation in the NPGS. For this reason, curators usually assign a local identifying number to an accession until a decision is made to assign a PI number. When a decision is reached to assign a PI number to an accession, the curators are now requested to contact Mark Bohning for assignment of the next sequential number(s).        

In addition, ARS and the Crop Science Society of America (CSSA) have an agreement that all released cultivars, germplasm, parental lines, genetic stocks, and genetic mapping populations registered by the CSSA be preserved in the NPGS and assigned a PI number.

The NGRL also assigns PI numbers to plants that have received Plant Variety Protection (PVP) from the Plant Variety Protection Office.

International Collaboration to support conservation and exchange of plant genetic resources

PEO works with other US and international programs to support plant germplasm conservation and exchange worldwide.

During the past year, PEO continued to collaborate with the National Department of Genetic Resources and Biotechnology (DENAREF) of the National Institute of Agricultural Research (INIAP) in Ecuador, the Organization of Farmers and Indigenous Peoples of Cotacachi (UNORCAC), and the USDA/FAS on a P.L. 480 – funded project to support complementary (ex situ and on-farm) conservation and increased utilization of agro-biodiversity in native farming communities in Cotacachi, Ecuador.

The PEO also collaborated with USDA/FAS and USDA/ARS/OIRP to develop joint germplasm collection, conservation and maintenance programs in Jordan, Morocco, Tunisia, Peru, Bangladesh, Sri Lanka, Uzbekistan, Pakistan, Kazakhstan, Guyana, Georgia and Azerbaijan using US Food for Peace and other programs. 
           
Since 2002, PEO has been collaborating with the plant genetic resources programs of the eight Central Asia and the Caucasus countries: Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, Uzbekistan, Armenia, Georgia and Azerbaijan.  This program is organized by ICARDA (International Center for Research in the Dry Areas) and the focus is on development of national plant inventories, staff training, and plant exploration. 

PEO is collaborating with the International Center for Tropical Agriculture (CIAT) to develop Geographical Information System (GIS) technology to guide the collection of germplasm on plant explorations.  Projects are planned in Guatemala and Paraguay.

Ned Garvey (ngarvey@ars-grin.gov, (301) 504-7511)
Karen Williams (kwilliams@ars-grin.gov, (301) 504-5421)

The Germplasm Resources Information Network

The mission of the Database Management Unit (DBMU) is to develop and maintain information systems for the National Genetics Resources Program comprised of plants, animals, microbes, and invertebrates. We have completed the development of a new interface for the plant database and will continue to enhance that system when specific needs arise.  The first version of the National Animal Germplasm Program system has been completed and is currently being used in a production mode.  The DBMU has now begun developing a requirements document for version two.

Recent statistics for data in the plant database include:

            Over 80,000 taxonomic names (including synonyms)
             470,946 accessions representing 11,839 species and 1,916 genera
            1,543,563 inventory records
            1,235,671 germination records
            6,313,140 characteristics/evaluation records
            Over 106,000 Images

Germplasm accessions acquired by the National Plant Germplasm System (NPGS) since the effective date of the Convention on Biological Diversity continue to be flagged in the database with appropriate disclaimers and MTA’s.  These agreements are displayed with accession passport data and automatically printed on GRIN generated packing slips when accessions are distributed. During the past year, the DBMU continued to provide support to NPGS site personnel and assisted NPGS sites in loading passport data, evaluation data, distribution information and images into the database

GRIN was demonstrated at several Crop Germplasm Committees and commodity meetings along with scientists visiting NGRL throughout the year. The Directory of NPGS Personnel and Crop Germplasm Committees continues to be maintained on the GRIN Web page in a PDF format.

A GRIN site meeting will be held in September in Geneva, NY.  Many issues will be discussed about the GRIN site software and the public system.  Recommendations from that meeting will be incorporated into the system. 

In September of 2005 the NP301 began its second cycle and a stake holders meeting was held near Baltimore.  Two major issues regarding GRIN were identified including:

            1.) GRIN needs to handle molecular data being generated on NPGS accessions
            and needs to interact better with the plant genome databases

2.) The GRIN public web interface and software need to be rewritten in order to meet users needs

To address these issues a sub-committee of NPGS curators has been developed to advise us on how to incorporate molecular data into GRIN.  They have already laid out the structures that need to be added to GRIN and the DBMU has begun to create the new tables and software to manage and display the data to the user community.

A public interface committee has also been established and will consist of NPGS personnel to advise the DBMU on improving the public interface to GRIN.  The committee will solicit input from the CGCs and other stakeholders of the system.

The DBMU is also working with the international community to make the GRIN data available through a biodiversity portal which will allow users to search multiple databases at the same time.

The GRIN system was available 98% of the time on a 24 hour a day and 7 day a week schedule. Access to the database through the web pages continues at a brisk pace. Over the last year, there were 154,570 unique host computers that accessed the GRIN database. This accounted for 544,043 visits to the data.  We always encourage users to send any comments on the public interface by email to dbmu@ars-grin.gov .

The current version of pcGRIN will continue to be supported by the DBMU.  Any new pcGRIN software will be a version of the national GRIN system that can operate on a personal computer utilizing the same Database Management System and development tools to reduce maintenance costs.

Two Sun Microsystem computers were replaced in 2001, one that supports the web server and site users and one that is used specifically for the databases. The databases reside on a separate computer to provide additional security. We also purchased two additional small Sun Microsystems workstations that are used for database development and for testing new operating systems prior to release to the user community. Additionally, one terabyte of disk space was purchased to ensure adequate space is available for increases in characteristic, evaluation, and image data.

Security for the computer and databases are always being reviewed and monitored for intrusion by those who may attempt to corrupt web pages or to destroy data. The system is protected by a firewall and all data are backed up at onsite and offsite locations. We keep backups at several local offsite locations and one at Ft. Collins, CO, for long term storage.  The computer system has an Uninterruptible Power Supply for short term power outages and a diesel generator for long term power outages. The building is now locked with access permitted by either a building security person or a card key. The computers are in a locked room that is monitored for temperature on a 24 hour, 7 days a week schedule.

Crop Germplasm Committee Facilitation

Since January 1, 2005, over thirty of the 40 Crop Germplasm Committees (CGC) have met. An NGRL representative was present at most of the meetings to help facilitate their activities. Summaries of each meeting are prepared and distributed to appropriate National Program Leaders, NGRL staff and other NPGS personnel.  The committees continue to provide advice on all aspects of the NPGS including identifying gaps and duplications in the collections, germplasm maintenance and evaluation, quarantine issues and maintaining updated versions of the crop vulnerability reports.  The 10th biennial meeting of the CGC Chairs will be held in Ames, IA June 6-7, 2006.  This will be in conjunction with the Regional Technical Advisory Committees and the Plant Germplasm Operations Committee.  This meeting provides an opportunity for Chairs to hear presentations on the status of NPGS sites, plant germplasm exchange, international issues, preservation and utilization, the molecular characterization of accessions, interactions between curators and CGCs and plant quarantine issues.  It also allows the Chairs to meet and interact with each other, NPGS managers and curators, and invited guests from ARS, other government agencies, and non-government organizations.

Plant Disease Research Unit

Effective October 1, 2005, the responsibilities for the quarantine indexing and distribution of prohibited genera germplasm that were performed by the USDA-ARS, Plant Germplasm Quarantine Office (PGQO) in Beltsville MD were transferred to the USDA Animal and Plant Health Inspection Service-Plant Health Programs (APHIS-PHP).  Three scientists from PGQO and their support staff have established the Plant Disease Research Unit within NGRL (NGRL-PDRU).  The mission of NGRL-PDRU is to investigate pathogens and diseases of quarantine significance that occur in clonal plant germplasm that must enter the US through federal quarantine programs. The objectives are focused on determining the causal agents responsible for diseases that prevent germplasm from entering the country, and developing tools to effectively detect and eliminate them. These research efforts provide support to the APHIS quarantine program and help facilitate the safe introduction and international exchange of valuable plant germplasm.

NGRL-PDRU is glad to discuss potential collaborations with pathologists and stakeholders who have interest in clonally propagated, prohibited genera crops that are handled by the USDA quarantine program.

Contact Information:

Gary Kinard, gkinard@ars-grin.gov, 301-504-5951
Ruhui Li, rli@ars-grin.gov, 301-504-7653
Ray Mock, rmock@ars-grin.gov, 301-504-8624

 NPGS Plant Explorations/Exchanges Undertaken in FY 2005

NPGS Plant Explorations/Exchanges Planned for FY 2006