Location: Plant Germplasm Introduction and Testing Research
2025 Annual Report
Objectives
Objective 1: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority pulse, temperate forage legume, oilseed, vegetable, turf and forage grass, sugar, ornamental, and medicinal plant genetic resources and associated descriptive information.
Sub-objective 1.A: Acquire samples and associated passport information of priority plant genetic resources (including crop wild relatives) from the U.S. and/or other countries to fill current gaps in NPGS genetic resource collections.
Sub-objective 1.B: Classify, conserve, and distribute PGITRU plant genetic resources and their associated information.
Sub-objective 1.C: 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: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, then apply them to priority pulse, temperate forage legume, oilseed, vegetable, turf and forage grass, sugar, ornamental, and medicinal plant genetic resources to avoid backlogs in plant genetic resource and information management.
Sub-objective 2.A: Conduct research to identify storage and quality regeneration conditions ideal for priority crops and wild relatives.
Sub-objective 2.B: Evaluate germplasm accessions for priority agronomic and horticultural traits (e.g., nutritional) and biotic and abiotic stresses. Incorporate evaluation data into the GRIN-Global and/or other databases.
Sub-objective 2.C: In collaboration with university and industry partners, apply genotypic characterization techniques (e.g., next generation sequencing) and platforms (e.g., arrays) to selected crop accessions to estimate genetic diversity, relationships, and population structure, and identify gaps in the genetic coverage of the collection. Incorporate characterization data into the GRIN-Global and/or other (e.g., SciNet, NCBI, etc.) databases.
Sub-objective 2.D: With other NPGS genebanks and CGCs, develop, update, document, and implement best management practices and Crop Vulnerability Statements (CVS) for legume, oilseed, vegetable, turf and forage grass, sugar, ornamental, and medicinal genetic resource for which they are lacking.
Objective 3: Breed genetically-enhanced germplasm that broadens the diversity available for improving selected crops by incorporating superior traits from cultivars, landraces, and wild relatives into adapted genetic backgrounds and gene pools.
Sub-objective 3.A: Conduct collaborative crossing and selection programs to breed agronomically improved and disease-resistant germplasm.
Sub-objective 3.B: Through genomic and field evaluation data analyses, identify genetic markers associated with quality traits and resilience to biotic and abiotic stresses for application to crop genetic enhancement.
Sub-objective 3.C: Develop genetic mapping tools and resources for elucidating and validating the genetic basis of economically important traits for incorporation into genetic enhancement programs.
Approach
Conserve, regenerate, evaluate and distribute ~100,000 accessions of cool season food and forage legumes, grasses, common beans, oilseeds, vegetables, beets, ornamentals, medicinal crops and related and native wild species, and associated information according to 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. Try to address backlogs in regeneration and data entry into the Germplasm Resources Information Network (GRIN)-Global where these backlogs exist.
Conduct collaborative plant 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. 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 GRIN-Global and/or other databases. Conduct research on best methods to regenerate wild species in the collections, including germination and pollination requirements. 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.
With collaborators, create new crosses with genebank materials to create segregating material that will be of use to breeders. Create new bi-parental populations or diverse panels for use in identifying new genes controlling crop traits of interest. Validate and make markers linked to genes controlling useful crop traits easy to use by public breeders. Publish research results and release segregating or improved germplasm, and useful genetic markers, 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.
Progress Report
This progress report summarizes activities for local genebank programs that focus on conserving and promoting the use of large and diverse crop plant collections that are critical in underpinning global sustainable agricultural production. Germplasm must be acquired to be conserved and made available and this happens via donations, transfers, and collections. When receiving germplasm from genebank distributions stakeholders expect quality, which is achieved by assigning correct taxonomy and by careful record keeping. Despite optimized storage, germplasm loses quality over time and needs to be regenerated to make it available and precisely optimized growing conditions need to be developed to maintain genetic purity. Describing collections for important traits and making this information publicly available increases its utility. Genetic analysis tools help collection managers understand population structure to eliminate redundancy and identify possible gaps.
Collections are also often evaluated with specific breeding objectives aimed at developing improved germplasm. Molecular approaches are developed to accelerate plant breeding efforts for crops managed in the genebank. All these approaches increase access to the collections and traits therein and along with their associated information contribute critical tools to be used in sustainable agricultural production.
Supporting Sub-objective 1A and in an international collaborative effort, the Bean program team acquired wild bean seed species from 28 populations in southern New Mexico and Arizona, filling gaps in the existing collections. Seeds for accessions (i.e., entries in the collections) will be available for distribution and include 18 wild tepary beans with potential heat and drought tolerance. Every year improved material with expiring intellectual property rights is released to the National Plant Germplasm System (NPGS) and 78 accessions were incorporated and are now available. The Bureau of Land Management-led (BLM) native Seeds of Success program collected and transferred 82 new and unique accessions. In addition, 31 accessions are being held from collections made by both U.S. Fish and Wildlife Service and National Park Service.
For Sub-objective 1B, each of the curatorial programs continues to focus on correct taxonomic identification of collections. Misidentified, mislabeled, mixes and accessions only identified to the genus level restrict distribution and could cause delays in stakeholder research. Taxonomic confirmation is often done during seed regeneration using easily distinguishable traits, but also more recently has incorporated molecular approaches. From this year’s plantings, a larger subset of 55 accessions were correctly identified to the species level in the horticultural crops program in addition to a smaller number of forage legumes. The taxonomic records in our Germplasm Resource Information Network (GRIN)-Global database have also been updated. Distributions are also a component of Sub-Objective 1B and across all curatorial programs in FY 2024, 28,231 items (e.g., seed packets) of more than 20,685 accessions were distributed to stakeholders nationally and internationally, with significant distributions (6,817) to plant breeding organizations (126 unique requestors, both public and private).
Supporting Sub-objective 1C, genebank curatorial programs continue to focus on their core mission of long-term preservation by regenerating both seed and clonally propagated accessions using optimized and crop-specific practices. This fiscal year, 2,140 accessions were scheduled to be regenerated on three research farms in Pullman, Central Ferry, and Prosser, Washington.
In support of Sub-objective 2A, all curatorial programs continue to optimize approaches to germinate, establish and effectively increase germplasm, especially for wild relatives for which methods are often unknown and that are extremely difficult to maintain. This year the forage legume program undertook a large effort to regenerate a core subset of ~200 diverse annual medic accessions. These have never been grown on this scale and required new approaches including weed barriers to help in gathering of pods as they fall off at maturity and adjusted irrigation schedules as moisture retention under barrier could have prevented flowering and pod/seed recovery. The bean program is improving regeneration outcomes of older accessions by scarifying, pre-germinating, and transplanting germplasm with low vigor and germination rates. In addition, the program tested a winter nursery in Costa Rica with project collaborators for tepary beans which are difficult to regenerate in greenhouses. Using tissue culture protocols, the Horticultural Crops team performed virus elimination on 34 garlic accessions, increasing their longevity and making them available for disease-free distribution. Seed germination techniques were improved in the Food Legume program to boost germination numbers in wild accessions of annual chickpea, lentil, and lupin. In addition, this year, the Food Legume program has focused on prioritizing resources for increasing critical backups for its crop wild relative accessions which are extremely difficult to grow and to produce seeds.
For Sub-objective 2B, the Forage Legume Program focused on detailed characterization of ~200 diverse annual medic accessions as this was the first time this many accessions of this species were grown at one time. Working closely with Breeding Insight collaborators, the Field Book application was used to collect close to 20 phenological (e.g., flowering time), morphological (e.g., growth habit), and agronomic (e.g., seed yield) phenotypic descriptor traits. The Bean program is collaborating with other NPGS genebanks and the SeedLinked company on a community science project to leverage crowdsourcing the characterization of germplasm of multiple crops at diverse locations across the U.S. The Food Legume program evaluated 282 chickpea accessions for plant height and width, flowering time and color, yield and biomass, and pod count. Seed characteristics were also collected on these accessions via spectroscopy and included ash and protein. In addition, ten pea lines were evaluated for resistance to fungal disease resistance to Aphanomyces root rot. During regeneration, curatorial program personnel continued to collect additional characteristics using combinations of visual, hand measurements, applications (e.g., Field Book), unpiloted aerial systems (UAS), and autonomous rover to generate data. In addition, many digital images of plant leaves, leaflets, flowers, and fruit/pods that help in characterizing the collections were produced and were associated with accessions in GRIN-Global.
Progress on Sub-objective 2C included the agronomy program creating a safflower core collection that consists of 187 accessions representing 95% of the genetic variation found within 864 accessions using large numbers of molecular markers derived from sequencing approaches. The designation of accessions within the safflower core is now indicated in GRIN-Global and can be used when selecting germplasm. Raw sequence generated in this project is publicly available through National Center for Biotechnology Information (NCBI) website. In the Food Legume program, 12 breeder-friendly genetic markers developed to tell which lines carry Aphanomyces resistance and 12 genetic markers to tell which lines have higher levels of seed protein were used on a diversity panel of 200 lentil lines. Genetic trait associations were explored on seed mineral nutrients in a pea diversity panel of 482 lines with multiple markers associated with high levels of these minerals. In a collaborative popping bean grant, the program has sequenced 84 nuña (Peruvian popping bean) accessions as part of a larger panel, to understand the genetics of popping, reduced lectin, and other traits of interest. In the Horticultural Crops program, previous sequencing data allowed for the identification of genetic regions for species identification of in lettuce and relatives to be used in increasing the accuracy of taxonomic identifications in our collection.
For Sub-objective 3A, the Forage Legume program has developed nine populations resistant to alfalfa spring blackstem, which is a fungal disease with no adequate resistance in commercial cultivars. With continued support the program plans to screen this germplasm in a second round of recurrent selection prior to release. As part of a large collaborative and externally funded project, the Bean program created 24 putative crosses between photoperiod sensitive exotic lima bean lines with double nematode resistance or other traits of interest with broadly adapted commercial lines. The hybrids will be verified, advanced and shared with collaborators and the public. Another funded collaboration involving popping beans created families of crosses between Peruvian nuña beans which “pop” and temperate adapted cultivars. Seed generated was shared with collaborators for field-based selections in Washington, North Dakota, and Nebraska. In the food legume program, 350 chickpea accessions were increased in preparation to begin making crosses to improve protein and agronomic characteristics with the best lines which will be determined by genetic methods on the data being collected.
Supporting Sub-objective 3B, marker trait associations to identify genetic factors that influence the levels of key mineral elements (like boron, iron, calcium, etc.) in pea seeds grown over three years was completed. A panel of 482 genetically variable pea accessions were analyzed with many molecular markers which identified a subset that were significantly associated with mineral nutrient concentrations. Candidate genes linked to these markers were found to be involved in processes such as nutrient transport, metal binding, and stress responses, all of which affect mineral accumulation in seeds.
Accomplishments
1. Model legume plant species core collection becomes accessible from the NPGS. A limited number of seed of a diverse and irreplaceable core collection of barrel medic, a model legume, was transferred to the USDA ARS National Plant Germplasm System in Pullman, Washington, by French cooperators. All 192 individual lines in the core collection were field grown to address the primary goal of increased generation of seed. Additionally, and in collaboration with Breeding Insight, the replicated experimental design used, facilitated the detailed evaluation of the collection. Seed for the entries in the collection as well as all associated information will be available to stakeholders. Basic plant science researchers, many of them primary stakeholders of the USDA ARS National Plant Germplasm System collections, will have continued access to the core collection as well as improved information about the entries. Model plant species are critically important resources supporting new discoveries and indirectly benefiting U.S. agricultural communities.
2. Wild beans from southwestern U.S. may save the day. The world continues to lose agricultural plant diversity and efforts to collect and conserve this diversity need to be prioritized. This is especially true of wild relatives of cultivated crops that can provide traits not found in modern agricultural cultivars. An international collaborative team of plant science experts and explorers, including an ARS researcher in Pullman, Washington, collected 28 populations of wild beans (Phaseolus spp.) across arid regions of New Mexico and Arizona. The geographically and genetically diverse collections help fill gaps in the existing USDA ARS National Plant Germplasm System bean collection and add potential traits for heat and drought tolerance. New access to this seed and associated information expands the availability of unique germplasm and their traits that can be used in developing modern and resilient bean varieties accessible to U.S. producers and will improve rural livelihoods.
3. Community project with over 1,000 volunteer growers evaluating USDA genebank collections. The USDA ARS National Plant Germplasm Systems collections are diverse but often lack characterization and evaluation data, thus reducing its potential use by stakeholders. The first of its kind partnership was established by an ARS scientist in Pullman, Washington, with SeedLinked to leverage a digital platform and large geographically distributed grower networks for bean germplasm evaluations. This effort has produced extensive and publicly available data, which would have been impossible to generate in-house. This project demonstrated that crowdsourced, cost-effective, high-throughput evaluations are feasible and accurate for genebanks. The data associated with germplasm is crucial to aiding in sustaining a resilient and diverse agricultural system, capable of meeting demands for emerging markets and environmental stresses.
4. Finding valuable traits in your favorite agricultural plant collections. The nation’s agricultural production relies on modern cultivars, and it is the diversity conserved and made accessible in the agricultural plant collections of the USDA, ARS, National Plant Germplasm System that plant breeders and other plant scientists leverage for trait discovery and the creation of improved cultivars. In the past year, the Pullman-based genebank disseminated 20,685 unique entries for research purposes from its horticultural, edible pulses, beans, and forage grass and legume collections to public and private industry stakeholders around the world. Although the impact of germplasm distributed during the fiscal year may not be apparent for several years, much of it will play a role in many downstream applications. The germplasm distributed every year supports research and education at universities while private industry also heavily depends on access to the resources for their technical agricultural innovations. Many distributions in the past have produced agricultural success stories that saved industries, boosted rural economies, contributed to the U.S. economy, and enhanced the health of U.S. consumers.
Review Publications
Copp, C.R., DeShields, J.B., Kar, S., Clark, R.W., KC, A.N., Hallwachs, B.S., Bondada, B., Levin, A.D. 2025. Foliar starch accumulation precedes the cascade of grapevine red blotch disease symptoms. American Journal of Enology and Viticulture. 76. Article 0760001. https://doi.org/10.5344/ajev.2024.24045.
Jameel, S., Hameed, A., Shan, T., Coyne, C.J. 2024. Demystifying the nutritional and anti-nutritional genetic divergence of Pakistani chickpea (Cicer arietinum L.) genetic resource via multivariate approaches. Frontiers in Nutrition. 11. Article 1407096. https://doi.org/10.3389/fnut.2024.1407096.
Uhdre, R., Coyne, C.J., Bourland, B.M., Piaskowski, J., Zheng, P., Ganjyal, G., Zhang, Z., Mcgee, R.J., Main, D., Bandillo, N., Morales, M., Ma, Y., Chen, C., Franck, W., Thrash, A., Warburton, M.L. 2024. Association study of crude seed protein and fat concentration in a USDA pea diversity panel. The Plant Genome. 18(1). Article e20485. https://doi.org/10.1002/tpg2.20485.
Hallwachs, B.S., Martin, E., Hellier, B., Irish, B.M. 2025. Optimizing regeneration protocols for native Seeds of Success—collected milkvetch (Astragalus spp.) genetic resources. Native Plants Journal. 25(3):179-191. https://doi.org/10.3368/npj.25.3.179.
Nemchinov, L.G., Irish, B.M., Grinstead, S.C., Postnikova, O.A. 2025. Alfalfa transcriptomic responses to the field pathobiome. Plant Biology. https://doi.org/10.1111/plb.70021.
Medina, C., Zhao, D., Lin, M., Sapkota, M., Sandercock, A.M., Beil, C., Sheehan, M., Irish, B.M., Yu, L., Poudel, H., Claessens, A., Moore, V., Crawford, J., Hansen, J., Viands, D., Peel, M., Tilhou, N.W., Riday, H., Brummer, E., Xu, Z. 2025. Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers. Scientific Reports. 15. Article 1253. https://doi.org/10.1038/s41598-024-84262-x.
Nemchinov, L.G., Irish, B.M., Grinstead, S.C. 2024. First report of novel Medicago trirhavirus 1 infecting alfalfa in Washington State, USA. Plant Disease. https://doi.org/10.1094/PDIS-05-24-1132-PDN.
Chu, C.N., Cornwall, A.M., Tehseen, M., Preister, L.S., Boetel, M., Li, X., Dorn, K.M. 2025. Evaluation of 26 NPGS germplasm lines for sugar beet root maggot resistance, 2024. Arthropod Management Tests. https://doi.org/10.1093/amt/tsaf017.
Woolfolk, S.W., Jeffers, D., Hawkins, L.K., Uhdre, R., Ni, X., Warburton, M.L. 2025. Integrated approaches to maximizing fall armyworm resistance in maize. CABI Reviews. 20:1-13. https://doi.org/10.1079/cabireviews.2025.0013.
Warburton, M.L., Woolfolk, S.W., Smith, J.S., Hawkins, L.K., Castano-Duque, L.M., Lebar, M.D., Williams, W.P. 2023. Genes and genetic mechanisms contributing to fall armyworm resistance in maize. The Plant Genome. 16(2):e20311. https://doi.org/10.1002/tpg2.20311.
Kowenstrot, A.M., Cornwall, A.M., Warburton, M.L., Uhdre, R., Miles, C. 2025. Assessment of rhubarb cultivars grown in Alaska for commercial suitability and conservation. HortScience. 60(8):1333-1340. https://doi.org/10.21273/HORTSCI18674-25.