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United States Department of Agriculture

Agricultural Research Service

Research Project: PLANT GENETIC RESOURCE AND INFORMATION MANAGEMENT
2011 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 fourth progress report of Project 3625-21000-053-00D, initiated 04/14/2008. Many activities are seasonal and overlap fiscal years. Cold, wet spring weather challenged planting; unlike the 2009 windows of opportunity which allowed reasonable progress. To date, no severe storm damage has occurred. From August 1, 2010 to July 31, 2011, 779 regeneration attempts were made for accessions of maize, vegetables, ornamentals and other crops; 1170 were harvested (2010 plantings); about 3.6% of collection holdings were tested for viability, a sharp decline due to shrinking student labor resources; 2388 accessions were backed up at the ARS National Center for Genetic Resources Preservation (NCGRP) in Ft. Collins, CO and 1,936 deposited for backup at Svalbard, Norway. Nearly 17,720 crop data descriptors were loaded to the GRIN (Germplasm Resources Information Network) system, and 1,482 plant/seed images captured. Cryogenic storage protocols for Fraxinus (ash) buds were developed with the NCGRP in 2011. The ability to store buds for future use is critical if ash trees threatened by the Emerald Ash Borer cannot be maintained in the field. The USDA Plant Hardiness Zone Map is complete; a Specific Cooperative Agreement (SCA) was extended a year ago to facilitate publication and dissemination. Necessary documentation was provided to procurement personnel who have been asked to expedite the process to authorize publication. Evaluation data are being collected for 2011 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 second year of collaborative Daucus characterization and taxonomic identification is underway. All available maize inbreds (about 2750) were evaluated phenotypically in 2010 by teams in Ames, IA, Raleigh, NC, Columbia, MO, and Ithaca, NY. The Ames staff grew them again in 2011 due to 2010 storm losses. Tissue captured from 2010 samples was genetically characterized via SNP analysis by the ARS lab in Ithaca, NY. FY11 seed requests were the highest on record, with 33,498 items of 16,401 unique accessions distributed to 900 requestors; 28% were requested by internationals and 72% by domestic requestors. Maize comprised 44% of all orders; lines with recently expired plant variety protection certificates are popular. Vegetables comprised about 25% of all distributions. Large numbers of sunflower, other oilseeds, spinach, and melons, and woody ornamentals used in the NC7 Regional Trials were distributed. The development of GRIN-Global to replace GRIN (Germplasm Resource Information Network) is near completion. Designed to provide a genebank information management system for the U.S. and all world genebanks, the project is a partnership among the Global Crop Diversity Trust, USDA-ARS, and Bioversity. Version 0.9 was released to testers in spring 2011. A training session for international system administrators was held in Ames in November, 2010, and a prototype public-facing website demonstrated to stakeholders at the Plant and Animal Genomes XIX meeting in January 2011.


4.Accomplishments
1. GRIN-Global system development. Released V0.9 as a result of the leadership by our Unit's development staff in collaboration with the Database Management Unit in Beltsville, MD, the Global Crop Bioversity Trust, Bioversity International, and the testing efforts of international researchers who attended multiple training sessions held in the U.S. This system will provide the international plant genetic resource community with a database-neutral system to manage germplasm information and genebank activities that functions on networked or stand-alone PCs, with freely available source code, and no recurring licensing costs.

2. New plant genetic resources. Acquisition of over 450 new accessions of plant germplasm offer expanded opportunities for utilization and investigation. Because access to plant genetic resources is limited, well-targeted acquisition strategies offer avenues to expand diversity for crop improvement and utilization to support agricultural success.

3. Modeling changes in maize seed viability over time. Promising research resulted from a collaborative project between ARS and Iowa State University scientists in Ames, IA, that modeled maize seed deterioration, as a new Bayesian statistical approach greatly increased computational efficiency in model development. Curators need strategies that provide guidance on how frequently viability tests should be conducted; too frequent testing wastes valuable resources, while testing too seldom risks loss of valuable germplasm. The impact of this research will expand as the model is extended to the dynamics of other species over time, simplify creation of an efficient software package, and improve the effectiveness and efficiency of plant genetic resource conservation.

4. Value of Prunella vulgaris to combat HIV-infection. Strategies to combat HIV-infectivity are valuable, and investigations in drug development costly. Research findings conducted collaboratively (scientists with ARS in Ames, University of Iowa, Iowa State University and funded partially by the National Insitutes of Health) on ARS germplasm indicated that aqueous extracts of Prunella vulgaris inhibited HIV-1 infectivity in cell culture and suggested that inhibition occurs primarily by interference of early, post-virion binding events. The ability of aqueous extracts to inhibit early events within the HIV life cycle suggests that these extracts, or purified constituents responsible for the antiviral activity, are promising microbicides and/or antivirals against HIV-1. Quality-controlled Prunella extract products may provide a low-cost addition to anti-HIV-1 treatment options.

5. Prunella reproductive system research. Very little is known about the reproductive systems of Prunella, an ornamental plant that also has value for medicinal use. (Promising research results indicate anti-inflammatory and anti-viral properties.) Our investigations reveal that the breeding system in Prunella vulgaris is more complex than previously thought, and both self- and cross-fertilization occurs depending on flower structure and other factors. The results can help direct more in-depth studies of its breeding system and suggest strategies for effective genetic conservation and crop improvement. This is important in order to consistently provide a source of germplasm for crop development in order for it to be economically viable.

6. Validity of methods to determine presence of maize seed-borne diseases. International exchange of maize germplasm, including commercial-seed commerce, is governed by phytosanitary laws designed to prevent introduction of disease. Comparisons of nine PCR primer sets designed to detect Pantoea stewartii, a causal organism of Stewart's wilt disease of maize, indicated that these markers could not reliably differentiate between P. stewartii and related species isolated from maize seed. Therefore the PCR diagnostic method should not be adopted for use in determining whether seed meets standards to determine whether phytosanitary certificates can be issued and seed exported. Valid ELISA methods currently used should be retained.

7. Resistance to white mold of sunflower. Losses due to Sclerotinia, also known as white mold, are a serious challenge for sunflower producers. Greenhouse disease-resistance evaluations progressed with screening of additional perennial sunflower (Helianthus) species. All the perennial species showed remarkable resistance. Several H. salicifolius accessions had >90% survival and seven had 100% survival. Helianthus salicifolius is a diploid perennial species, with the potential for easier crossing compatibility with cultivated sunflower (H. annuus). These findings support development of Sclerotinia-resistant cultivars.

8. Maize inbred phenotyping and genotyping. Over 2500 maize inbred lines were provided by the Agricultural Research Service collection in Ames, IA and phenotyped by ARS scientists in Ames, Columbia, MO, Ithaca, NY, and Raleigh, NC. Tissue was captured for genotyping. By making the phenotype data available in the Germplasm Resource Information Network (GRIN) database, researchers will be able to better target germplasm for research and trait discovery objectives.

9. Camelina genetic diversity. Camelina is a relatively new crop, currently grown chiefly in the northwestern U.S. for its oil for biofuel (jet fuel), and its meal is valued for animal feed. Little was known about the diversity of our camelina collection for seed and oil quality traits, necessary for effective collection use. Agricultural Research Service scientists in Ames, IA and Peoria, IL, with collaborators at Iowa State University and North Dakota State University, assessed the ARS camelina collection for seed- and oil-quality traits and fatty acid composition, identifying accessions with high yield and high oil content, and determined variability for these traits. These results will be used by researchers involved in camelina crop improvement for biofuel use.

10. Pennycress germination requirements. Another new crop, pennycress (Thlaspi arvense), has been identified for its value for biodiesel production. Agronomic development research that supports successful production of pennycress seed is necessary in order to determine optimal production areas and grower protocols for planting to ensure consistently good plant populations. Effects of temperature gradients on germination of pennycress accessions were evaluated and suitable temperature ranges identified. Breeders involved in developing pennycress varieties will now have access to knowledge on an accession's ability to contribute tolerance to low temperature emergence conditions. Because this crop is a winter annual, it is an important trait for commercial success.

11. Daucus taxonomic revision. Taxonomic classification of Daucus carota and its relatives is in need of revision. In FY10 and FY11, significant segments of the carrot collection were evaluated and characterized by Agricultural Research Service scientists in Ames, IA as part of a major effort to improve Daucus systematics. Thorough systematic revisions will support more effective germplasm utilization.


Review Publications
Kovach, D.A., Widrlechner, M.P., Brenner, D.M. 2010. Variation in Seed Dormancy in Echinochloa and the Development of a Standard Protocol for Germination Testing. Seed Science and Technology. 38:559-571.

Widrlechner, M.P., Thompson, J.R., Kapler, E.J., Kordecki, K., Dixon, P.M., Gates, G. 2009. A Test of Four Models to Predict the Risk of Naturalization of Non-native Woody Plants in the Chicago Region. Journal of Environmental Horticulture. 27(4):241-250.

Oh, C., Price, J., Brindley, M., Widrlechner, M.P., Qu, L., Mccoy, J., Murphy, P., Hauck, C., Maury, W. 2011. Inhibition of HIV-1 infection by aqueous extracts of Prunella vulgaris L. Virology Journal. 8:118.

Qu, L., Widrlechner, M.P. 2011. Variation in the Breeding System of Prunella vulgaris L. HortScience. 46(5):688-692.

Last Modified: 10/30/2014
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