Location: Plant Germplasm Introduction and Testing Research
2023 Annual Report
Objectives
Objective 1: Efficiently and effectively acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority legume, oilseed, vegetable, forage grass, sugar, ornamental, and medicinal genetic resources and associated information.
1A: Acquire samples of priority plant genetic resources (including crop wild relatives) from the U.S. and/or other countries to fill current gaps in NPGS collections of these priority crops.
1B: Conserve and distribute WRPIS plant genetic resources and their associated information.
1C: Regenerate accessions of priority plant genetic resources, emphasizing accessions with low germination, few seeds in storage, or those not yet backed-up at secondary sites.
Objective 2: Develop more effective genetic resource maintenance, evaluation, or characterization methods and apply them to priority legume, oilseed, vegetable, forage grass, sugar, ornamental, and medicinal genetic resources. Record and disseminate evaluation and characterization data via Germplasm Resources Information Network (GRIN)-Global and other data sources.
2A: With collaborators, apply next generation DNA sequence technology to genotype selected accessions of priority crops for assessing genetic diversity and analyzing genome-wide association among DNA sequence variants and traits of economic importance, emphasizing core subsets of priority genetic resources. Incorporate characterization data into the GRIN-Global and/or other databases.
2B: With collaborators, characterize with NIR spectroscopy the major nutritional component content of food legume genetic resources.
2C: Screen germplasm accessions, and/or candidates for accessions, for disease resistance. Identify disease agents by current taxonomic criteria. Disseminate research results in peer-review venues with citations in GRIN-Global.
2D: With collaborators, characterize the fatty acid composition and oil content of selected safflower germplasm accessions with gas chromatography.
Objective 3: With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for priority legume, oilseed, vegetable, forage grass, sugar, ornamental, and medicinal genetic resource and information management.
3A: Working with respective Crop Germplasm Committees and curators at other locations, update Crop Vulnerability Statements for Food Legumes, Pisum, Grass, Leafygreen Vegetables, Phaseolus Bean, Root and Bulb (allium) and sugarbeet.
3B: Update WRPIS Operations Manual on Germplasm Management and Research.
Objective 4: Develop selected populations of priority genetic resources which are genetically enhanced for potentially higher yields, tolerance to environmental extremes, host-plant resistance to diseases and pests, and/or increased nutritional quality.
4A: Identify markers associated with resilience to temperature extremes by conducting a genome wide association study of faba bean using SNP markers and field evaluation data.
4B: Develop a Pisum recombinant inbred population in order to elucidate the genetic basis of economically important traits.
Approach
Conserve, regenerate, evaluate and distribute approximately 98,000 accessions of cool season food and forage legumes, grasses, common beans, oilseeds, vegetables, beets, ornamentals, medicinal crops and related wild species, and associated information by following closely the National Plant Germplasm System Distribution Policy and the established protocols and procedures. Keep our active plant genetic resource collections in the seed storage facilities with adequate conditions for proper conservation of seed samples for short and medium term storage and for people entering the storage space to take samples for distribution and for viability tests. Monitor seed viability by periodic germination tests at variable intervals depending on the species. Ship high quality seed samples to National Laboratory for Germplasm Resources Preservation at Ft. Collins, Colorado and the Svalbard Global Seed Vault in Norway for long-term security back-up.
Conduct collaborative plant expedition/collection trips and germplasm exchange to acquire samples to fill gaps in NPGS collections, and to supply critically needed traits to support current and future breeding and research. Evaluate the phenotypic variation of economic traits of specialty crops independently or collaboratively. Use laboratory equipment to characterize major nutritional components of food crop germplasm such as using near infrared (NIR) spectroscopy to quantify the major nutritional component content of food legume genetic resources and gas chromatography to characterize the fatty acid composition and oil content of selected safflower germplasm accessions. Apply existing and newly developed genomic tools and technologies such as the Next Generation DNA sequencing to characterize genetic diversity, phylogenetic relationship and marker-trait association of priority crop collections. Upload characterization/evaluation data into the Germplasm Resources Information Network (GRIN)-Global and/or other databases. Survey production fields, identify pathogens causing emerging diseases with morphological-cultural and molecular techniques, investigate interactions among these host plants and their pathogens, and devise and apply pathogen management strategies to maintain the health of the assigned genetic resources.
Publish research results and release improved germplasm to the user community. Update the pertinent section of Operations Manual with reference to changes in collection holdings, management technologies and practices, diagnostic procedures, roles of personnel and any other relevant changes. Work with relevant crop germplasm committees to update the Crop Vulnerability Statements of the crops under our management.
Use both classical plant breeding methods and contemporary marker-assisted selection (MAS) to enhance the nutritional attributes and the resiliency to abiotic stress of faba bean.
Progress Report
This is the final report for project 2090-21000-032-000D. This project is being combined with the expiring project 2090-21000-026-000D in the future. This progress report summarizes all of the progress achieved for all of the objectives and sub-objectives of this expired project. For additional information, please review the new project report, 2090-21000-037-000D.
Supporting Sub-objective 1A, all genebank programs continue to acquire germplasm via plant explorations, donations, and transfers. The Cool Season Food Legume (CSFL) scientists in Pullman, Washington, connected with researchers in Morocco while attending the International Food Legume Research conference to plan plant exploration to collect faba bean landraces to fill gaps in the collection. In Morocco, approximately 90% of the varieties used in current production are landraces, which may harbor useful genes for disease resistance, heat tolerance and seedling vigor for weed suppression. A proposal was submitted and funded by the Plant Exchange Office for a collection trip. Important exchanges of pea and wild relative germplasm including 177 accessions were also incorporated from Russia, central Asia, and Europe. In the Phaseolus (Bean) program, seeds of wild kidney bean (P. polystachios) were collected from the southeastern States of Ohio, Georgia, and Tennessee in 2019, with regenerated seed increased and added to the collections in 2022. In the past 5 years curatorial programs have incorporated 271 expired Plant Variety Protected germplasm accessions. In that same 5-year period, a significant number of accessions (5,735) have been added to the Pullman-based collections that originated from the Bureau of Land Management (BLM)-led Seeds of Success (SOS) program. Many of the native species collected are crop wild relatives, wild utilized species, or play important roles in restoration. All germplasm acquired address efforts to increase needed genetic diversity by filling gaps in coverage in the collections and become readily available to stakeholder communities.
In support of Sub-objective 1B, over the five-year period (2018-2022) the curatorial programs distributed more than 200,000 items (e.g., seed packets, garlic cloves) of more than 57,475 accessions. These were delivered to stakeholders nationally and internationally, with significant distributions (more than 1,000) to plant breeding organizations (private and public). Some of the largest distributions came from requests to the CSFL program, where increased interest in alternative sources for protein from plants has soared. This program alone has distributed over 13,000 pea samples for evaluation and breeding to both national and international organizations who research plant-based protein sources. Access to plant genetic resources provides the traits, and often the underpinning, needed for new crops, new uses of crops, and improved existing crops.
Supporting Sub-objective 1C, genebank curatorial programs continue to focus on the core mission of long-term preservation by regenerating both seed and clonally propagated accessions using optimized and crop-specific best management practices. For the five-year period between 2018 through 2022, close to 8,000 accessions were regenerated in the five curatorial programs in greenhouses, screenhouses or on one of three research farms in Pullman, Central Ferry, and Prosser, Washington. All germplasm is queued for regeneration based on low seed stock and/or seed viabilities below critical thresholds, or because clonal stock needs replanting. Germplasm that is successfully increased is backed up in Ft. Collins, Colorado, as needed, and made available for distribution.
In support of Sub-objective 2A, ARS researchers at the CSFL program has created genomic resources for the pea, chickpea, lentil and faba bean crops. Over the five-year period the program has completed the genotyping of the pea, lentil, and chickpea core collections. Research in the CSFL program led to the description of significant quantitative trait loci associated with cold tolerance in chickpea, with the aim of giving producers in the pacific northwest an alternate fall-sown rotation crop. Additionally, research in the CSFL program led to the identification of Fusarium root rot disease resistance in lentil core germplasm using an association study. Disease resistance to this important soilborne disease can be bred into commercial cultivars to expand the toolset for sustainable production of lentil. In peas, research on sequencing germplasm has aided in the identification of loci for resistance to aphids and improved agronomic performance. Breeders can incorporate genes for insect resistance and agronomic performance into modern-day resilient pea cultivars. Finally, a detailed phenotypic characterization of the table beet collections was undertaken by the Horticultural crops program during the project cycle. Past efforts have focused on detailed characterization of sugar beets, with a gap in data for the table beet collection. Extensive descriptor data including plant growth habit and root phenotypes were collected. All data for these collections has been associated with individual accessions in Germplasm Resource Information Network (GRIN)-Global and can now be used in production and breeding.
For Sub-objective 2B, ARS researchers at the CSFL program completed an effort to determine seed protein concentrations for 3,500 pea and faba bean samples and the data was made available to the public via the GRIN-Global database. The Phaseolus (Bean) program also obtained wet lab analysis from commercial analytical services for protein (120 accessions) and fiber (60 accessions) content in common bean. This information was used to develop near infrared reflectance (NIR) calibration curves for rapid and non-destructive analysis of nutritional qualities. A replicated field study was established at Pullman, Washington, and Central Ferry, Washington, to identify DNA markers and genes associated with seed protein content in common bean. This evaluation and genotyping data were used in an association study to provide tools to improve efficiencies and genetic gains in corresponding crop breeding.
Supporting Sub-objective 2C, the Pathology research program completed a research project on optimized disease-free propagation methods in garlic. A clonally propagated crop, garlic is susceptible to several important diseases including the bulb rotting fungus Fusarium proliferatum. Research tested both bulbils and seed cloves as plant propagules in replicated trials and found that a reduced number of disease-free plants could be obtained from the bulbils. While bulbils take longer to produce mature bulbs, their use improves distribution of disease-free clonal plant genetic resources.
The following progress was achieved for Sub-objective 2D. The Agronomy program concluded an effort to characterize the seed fatty acid content and composition in 1,187 accessions in the safflower collection. This was a collaborative effort supported by a material transfer research agreement (MTRA) with the commercial company SeedTec. The percentage of oil content in seed ranged from just under 23% to a high of close to 39%. All the data collected as part of the collaboration has been entered into the GRIN-Global database and associated to specific accessions, increasing information for stakeholders to use when refining germplasm requests of this important oilseed crop.
Supporting Sub-objectives 3A and 3B, the genebank team made concerted efforts to revise crop vulnerability statements (CVS) and manuals of operating procedures (MOP) with up-to-date information. Specifically, CVS for Leafy Vegetables, Food Legumes, Pisum (pea), and Phaseolus (bean) were all updated. Operating procedures were also revised for Phaseolus, Lettuce and CSFL. These are “living” documents that need to be routinely reviewed and serve to retain institutional knowledge and detailed records during project personnel transitions.
In support of Sub-objective 4A, the research geneticist-led program provided advanced selections of large seeded faba bean (Vicia faba) breeding lines for replicated field evaluations of adaptation and yield to a private company breeder as a potential new crop for regional growers. ARS scientists in Pullman, Washington, provided two advanced breeding lines of faba bean with distinct differences in seed size and color to Pacific Northwest Farmer’s Cooperative. The germplasm was evaluated for potential introduction as a new grain crop for the northwest region of the United States.
Supporting Sub-objective 4B, researchers in the unit developed a pea recombinant inbred line (RIL) mapping population to study the genetic basis for agronomically-important crops. The parental lines used in the F1 cross have been used in pea reference genome sequencing. Seed was then advanced via inbreeding through the sixth generation by single seed descent. The seed of the RIL population has been increased and is available for distribution and evaluation. This unique population could play a significant role in determining genetic basis for many important traits in pea.
Accomplishments
Review Publications
Johnson, R., Love, S., Carver Jr., D.P., Irish, B.M. 2022. Using climate-driven adaptive evolution to guide seed sourcing for restoration in a diverse North American herb-shrub species. Restoration Ecology. 31(4). Article e13856. https://doi.org/10.1111/rec.13856.
Matova, P.M., Kamutando, C.N., Warburton, M.L., Williams, W.P., Magorokosho, C., Shimelis, H., Labuschagne, M., Day, R., Gowda, M. 2022. New techniques for breeding maize (Zea mays) varieties with fall armyworm resistance and market-preferred traits for sub-Saharan Africa. Plant Breeding. 142(1):1-11. https://doi.org/10.1111/pbr.13063.
Warburton, M.L., Jeffers, D., Smith, J.S., Scapim, C., Uhdre, R., Thrash, A., Williams, W.P. 2022. Comparative analysis of multiple GWAS results identifies metabolic pathways associated with resistance to A. flavus infection and aflatoxin accumulation in maize. Toxins. 14(11). Article 738. https://doi.org/10.3390/toxins14110738.
Huster, A., Wallace, L.T., Myers, J.R. 2021. Associated SNPs, heritabilities, trait correlations, and genomic breeding values for resistance in snap beans (Phaseolus vulgaris L.) to root rot caused by Fusarium solani (Mart.) f. sp. phaseoli (Burkholder). Frontiers in Plant Science. 12. Article 697615. https://doi.org/10.3389/fpls.2021.697615.
Weeden, N., Coyne, C.J., Lavin, M., McPhee, K. 2021. Distinguishing among Pisum accessions using a hypervariable intron within Mendel’s green/yellow cotyledon gene. Genetic Resources and Crop Evolution. 68:2591-2609. https://doi.org/10.1007/s10722-021-01152-1.
Volk, G.M., Byrne, P.F., Coyne, C.J., Flint Garcia, S.A., Reeves, P.A., Richards, C.M. 2021. Integrating genomic and phenomic approaches to support plant genetic resources conservation and use. Plants. 10(11). Article e2260. https://doi.org/10.3390/plants10112260.
Stalker, T.H., Warburton, M.L., Harlan, J.R. 2021. Harlan’s Crops and Man: People, plants and their domestication. 3rd edition. Madison, WI: Crop Science Society of America. 320 p.
