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United States Department of Agriculture

Agricultural Research Service

Research Project: PLANT GENETIC RESOURCE AND INFORMATION MANAGEMENT

Location: North Central Regional Plant Introduction Station, Ames, Iowa

2009 Annual Report


1a.Objectives (from AD-416)
The long-term objectives of this project are to acquire, conserve, evaluate, characterize, document and distribute high-quality plant genetic resource (PGR) collections and associated information for research applications to support sustainable agricultural productivity. Objective 1: Strategically expand the genetic diversity in genebank collections and improve associated information for priority maize, oilseed, vegetable, pseudocereal, forage, woody ornamental, medicinal, bioenergy, and other specialty and industrial crop genetic resources. Objective 2: Conserve and regenerate priority maize, oilseed, vegetable, pseudocereal, forage, woody ornamental, medicinal, bioenergy, and other specialty and industrial crop genetic resources efficiently and effectively, and distribute pathogen-tested samples and associated information worldwide. Objective 3: Strategically characterize (“genotype”) and evaluate (“phenotype”) priority Zea (maize and wild relatives), Daucus, Helianthus, Coriandrum, Echinacea, Hypericum, and Melilotus genetic resources for molecular markers, morphological descriptors, taxonomic verification, and key agronomic or horticultural traits, such as maize starch content for bioenergy production. Objective 4: Develop superior information management software for optimally supporting the needs of genetic resource curators, researchers, breeders, and other users.


1b.Approach (from AD-416)
To accomplish these objectives, USDA-ARS and ISU staff of the North Central Regional Plant Introduction Station (NCRPIS) work collaboratively with the National Germplasm Research Laboratory (NGRL) to acquire and document germplasm in the Germplasm Resource Information Network (GRIN) database, the National Center for Genetic Resource Preservation (NCGRP), and a wide array of researchers and genebank personnel in the U.S. and abroad. Expected outcomes from research and service activities include available, high-quality plant germplasm for distribution; documentation and transfer of evaluation and characterization information that enables targeting of PGR to meet research objectives; improved information management tools to support curatorial, research and other germplasm user-community needs.


3.Progress Report
This is the second progress report of Project 3625-21000-053-00D, initiated on 04/14/2008. Many of the activities are seasonal and overlap fiscal years. Cold, wet spring weather delayed or hurt much of the vegetable plantings, and some of the oilseeds, particularly sunflowers. Since October 1, 2008, 815 accessions of maize, vegetables, ornamentals and other crops were planted for regeneration; 1146 accessions have been harvested; about 4% of collection holdings were tested for viability; 4092 accessions from all crops were backed up at the National Center for Genetic Resources Preservation in Ft. Collins, CO or at Svalbard, Norway; over 20,900 crop data descriptors were loaded to the Germplasm Resources Information Network (GRIN) system, and 364 plant or seed structure images were captured.

Cryogenic storage protocols for Fraxinus (ash) buds have been tested and are being refined in collaboration with the NCGRP. The ability to store buds for future use may be critical if ash trees threatened by the Emerald Ash Borer cannot be maintained in the field.

The USDA Plant Hardiness Zone Map is complete. The review team has finalized three map versions, a 15 year data set, 30 year data set, and a difference map. An SCA has been established to facilitate publication and dissemination of these products.

Evaluation data is being collected for 2009 increases and observation plantings. Wild Helianthus is being evaluated for resistance to Sclerotinia rot – 250 accessions were tested in the greenhouse and 25 advanced to field trials at two locations. A field was established for collaborative Daucus characterization and taxonomic identification (in progress).

Record numbers of seed requests are anticipated for a fourth consecutive year. For the period October 1, 2008 to July 26, 2009: 25,985 germplasm items were distributed of 12,279 unique accessions to 991 recipients; 77% of the germplasm was requested by U.S. and 23% by international researchers. Maize comprised nearly two-thirds of U.S. orders, and over half of all orders; lines with recently expired plant variety protection certifications are popular. Large numbers of sunflower, other oilseeds, spinach, and melons, and woody ornamentals used in the NC7 Regional Trials were distributed.

The development of the replacement for the GRIN system, GRIN-Global, has been in progress for 18 months, or half of the project's term. Designed to provide a genebank information management system for the US and any genebank in the world, the project is a partnership between the Global Crop Diversity Trust, USDA-ARS, and Bioversity to provide for genebank information management needs. To date, the development team has built a three–tiered system architecture, migrated database content from Oracle to MySQL and to SQL Server, developed a public-facing website for communication of features and functionalities with stakeholders, obtained their input, developed a unique new 'Google-like' search engine, and produced beta versions of the system that are being tested by a group of key users.


4.Accomplishments
1. USDA Plant Hardiness Zone Map. The PRISM team at Oregon State University, supported by an SCA from this project, with input from a technical review team led by the Unit's Horticulturist, completed development of new USDA Plant Hardiness Zone Maps. Climatic conditions vary to some degree each year, but climatic fluctuations over the past 20-30 years resulted in a need for development of a new U.S. hardiness zone map that more accurately categorized plant hardiness zones, with the best possible algorithm to extrapolate climate data among weather stations in order to reflect local variation. The new maps are designed to be accessible via the internet with very fine-scale (800 meter) resolution. Release of these maps will aid the nursery industry's efforts to provide appropriate plants for specific areas on a finer scale, and will also aid consumer confidence. Official public release of these maps will occur, once technical details regarding the hosting of a high-volume website are resolved.

2. Development of GRIN-Global, Successor to GRIN (Germplasm Resources Information Network). During the past 18 months, much progress has been made in developing a genebank information management system (IM) that will replace the U.S. GRIN system and provide a system for any of the world's genebanks that require IM tools to manage information associated with their collections. The USDA-ARS, the Global Crop Diversity Trust, and Bioversity International formed a partnership toward this end. To date, the development team has built a three–tiered system architecture, migrated the database from Oracle to MySQL and to SQL Server, developed a public-facing website for communication of features and functionalities with stakeholders, obtained their input, developed a unique new 'google-like' search engine, and produced beta versions of the system that are being tested by a group of key users. When complete, the modular system can be readily implemented by any genebank, the source code will be freely distributed, and the world's genebank information records will be more secure.

3. Transfer of Plant Germplasm and Associated Information. Access to unique, well-characterized plant genetic resources is key for successful cultivar development, crop improvement, utilization and economic development. For the period October 1, 2008 to July 26, 2009: 25,985 germplasm items were distributed of 12,279 unique accessions to 991 recipients; 77% of the germplasm was requested by US and 23% by international researchers. Maize comprised nearly two-thirds of distributions to U.S. requestors, and over half of all orders; lines with recently expired plant variety protection certifications are popular. Large numbers of sunflower, other oilseeds, spinach, and melons, and woody ornamentals used in the NC7 Regional Trials, were distributed. The impact of these distributions is realized through the applications, inventions and research accomplished by the resource requestors; impact may be realized via development of improved disease or resistance, agronomics, compositional, or aesthetic traits.

4. Identification of a New Wild Cucumis Species. Six accessions of wild Cucumis (melon) from Zambia were described and identified as a new species, Cucumis zambianus, based on molecular and phenotypic data. This work resulted from collaboration with scientists from Iowa State University, St. Louis University, our USDA-ARS research unit, and the U.S. National Arboretum. Correct taxonomic identification is key to providing useful genetic resources for researchers, and enabling them to build upon previous efforts.


5.Significant Activities that Support Special Target Populations
Management Unit personnel mentored American Indian Student interns interested in plant science and bioinformatics for the fourth summer. These students worked with the maize collection, the MaizeGDB (genome database), and medicinal plant research. This effort is supported by an outreach component of an NSF grant "Plant Gemetics and Genomics Outreach to Native Americans", by ARS, and by the George Washington Carver Intern Program managed by Iowa State University's Minorities in Agriculture, Natural Resources and Related Studies (MANRRS) program personnel.


6.Technology Transfer

Number of New Germplasm Releases1
Number of Web Sites Managed1
Number of Other Technology Transfer1

Review Publications
Block, C.C., Shepherd, L.M. 2008. Long-term survival and seed transmission of Acidovorax avenae ssp. citrulli in melon and watermelon seed. Plant Health Progress. Available: http://www.plantmanagementnetwork.org/sub/php/brief/2008/melon/.

Brindley, M.A., Widrlechner, M.P., Mccoy, J., Murphy, P., Hauck, C., Rizshsky, L., Nikolau, B., Maury, W. 2009. Inhibition of lentivirus replication by aqueous extracts of Prunella vulgaris. Virology Journal. 6:8.

Widrlechner, M.P., Smith, W.R. 2008. Rubus, blackberries and raspberries. In: Smith, W.R., editor. Trees and Shrubs of Minnesota. Minneapolis, Minnesota: University of Minnesota Press. p. 440-551.

Lopez, P.A., Widrlechner, M.P., Simon, P.W., Rai, S., Boylston, T.D., Isbell, T., Bailey, T.B., Gardner, C.A., Wilson, L.A. 2008. Assessing phenotypic, biochemical, and molecular diversity in coriander (Coriandrum sativum L.) germplasm. Genetic Resources and Crop Evolution. 55:247-275.

Wu, L., Dixon, P.M., Nikolau, B.J., Kraus, G.A., Widrlechner, M.P., Wurtele, E. 2009. Metabolic Profiling of Echinacea Genotypes and a Test of Alternative Taxonomic Treatments. Planta Medica. 75:178-183.

Maury, W., Price, J., Brindley, M., Oh, C., Neighbors, J., Wiemer, D., Wills, N., Carpenter, S., Hauck, C., Murphy, P., Widrlechner, M.P., Delate, K., Kumar, G., Kraus, G.A., Rizshsky, L., Nikolau, B. 2009. Identification of Light-independent Inhibition of Human Immunodeficiency Virus-1 Infection through Bioguided Fractionation of Hypericum perforatum. Virology Journal. 6:101. doi:10.1186/1743-422X-6-101. Available: http://www.virologyj.com/content/pdf/1743-422X-6-101.pdf.

Cruz, V.V., Rife, C.L., Nason, J.D., Brummer, E.C., Gardner, C.A. 2008. Measuring the effectiveness of isolation of Brassica napus l. accessions during caged germplasm regeneration. Plant Genetic Resources Newsletter. 154:14-19.

Last Modified: 10/1/2014
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