Location: Plant Germplasm Introduction and Testing Research
2022 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
In support of Objective 1, researchers in Pullman, Washington, worked to test and regenerate seed and send them to requesting researchers and educators from around the world. Although we were unable to collect wild onion relatives from South Carolina and Georgia, we were able to substantially meet the 2021 milestone for Sub-objective 1A, which had not been met last year. Please refer to the activities of the Seeds of Success (SOS) program below. To meet Sub-objectives 1B and 1C, the four curatorial programs working on these objectives include Horticultural Crops (Hort Crops); Phaseolus (Bean); Agronomy; and the Cool Season Food Legumes (CSFL) programs.
Hort Crops filled three garlic orders and 11 orders for rhubarb (65 order items). For the same time period we planted and harvested 320 A. sativum and other clonal Allium accessions, maintained plots of 60 accessions of Rheum, planted and/or harvested 100 inventories of miscellaneous accessions, planted and harvested 70 inventories of Lactuca sativa in the field, 20 inventories of Lactuca wild species in the greenhouse, and harvested 15 inventories and planted 17 inventories of Beta. The Bean program continued with regenerations focusing on Phaseolus vulgaris but also worked with P. lunatus, P. coccineus, and P. polystachios inventories. From October 2021 to September 2022, we planted 346 and harvested 239 Phaseolus inventories. All the P. polystachios collections made by a previous curator was put into cold storage. The seed was organized and counted, and the passport data organized and entered into Excel and loaded into the Germplasm Resource Information Network (GRIN)-Global database. In addition, we are continuing to improve the integrated pest management (IPM) program in the Phaseolus regeneration greenhouses.
The CSFL and Agronomy programs both met their goals of testing and regenerating seeds and filled all orders as they came in throughout 2022. In the Native Plants Program, associated with the Agronomy program, we continued to collaborate with Bureau of Land Management (BLM) to manage the U.S. native plant seeds collected by the SOS program from public lands. During this year’s effort project personnel dedicated time to quality assessing historical passport data and improvement of passport information data than can be queried and that are included in the GRIN-Global database. When undertaking this work, significant differences were encountered between historical records in GRIN-Global and BLM SOS database (BG-Base) records for unique identifier names and taxonomic identities. For the more than 20,000 SOS National Plant Germplasm System (NPGS) accession records, the team has focused on identifying these discrepancies, determining why they occurred and how to implement fixes. In addition, work continues to improve quantity and quality data for new incoming SOS collections during the process of accessioning. Passport information previously not included in GRIN-Global, like Ecoregion, Slope, Aspect, and Landowner, are being populated into the appropriate database fields now available in GRIN-Global. This increased information, currently available to NPGS curatorial staff, will aid in germplasm management decisions. The data will eventually be made public for stakeholders to aid in selecting germplasm for their research.
Many plants were generated from previously conducted seed germination optimization assays for native Astragalus (milkvetch) species accessions. The Native Plant Program used these plants, belonging to five accessions of five different species (A. bisulcatus, A. lonchocarpus, A. lentiginosus, A. drummondii and A. canadensis) to begin evaluating optimal regeneration protocols in 2021 and 2022. Evaluations focused on field establishment (fall 2020) of transplants at two sites located in Pullman and Prosser, Washington, and testing three different pollinator treatments. Pollinator treatments included caged honeybees, caged alfalfa leaf cutter bees, and an uncaged pollinator treatment. Notes were collected during the season on plant survival and harvested pods and seed is being cleaned to determine quality and assess what might be the best protocols for managing these native plant species. Little to no information exists on how best to manage these crop wild relatives Astragalus plant genetic resources.
In support of Objective 2, ARS researchers at Pullman, Washington, worked to characterize genebank materials genotypically and evaluate materials for important phenotypes, including disease resistance. In the Hort Crops program, we continued taking seed, flower, pod, leaf, and plant images along with herbarium samples for the "Miscellaneous" and Allium accessions. We wait until the increased seed has been put away before loading most of the images, but 313 preplant seed images were loaded into GRIN-Global. Program personnel started plants of many species of Lactuca that we have not previously grown for taxonomic confirmation using molecular markers. Personnel were also involved with a small group creating descriptor data ontologies for Onobrychis viciifolia. In the Bean program, a bean seed protein genomewide association studies (GWAS) trial was advanced and seed from the first year of evaluation for seed protein was measured; seed for the second year of evaluation was planted at Central Ferry, Washington, in a replicated field design and will be harvested and dried by this September. ARS researchers in this program also regenerated (planted, harvested, cleaned) all the material in the greenhouse for use this year’s trial. Finally, a near-infrared (NIR) calibration curve for bean seed protein was generated for the project.
In the CSFL program, seed mineral nutrient components were published for the lentil core collection in a scientific journal with collaborators. Wet lab and NIR calibration for this project was not yet completed due to lack personnel and resources but will be finished in the coming year. Genotyping by sequencing (GBS) was completed for the chickpea core single-plant collection from 300 accessions. In addition, whole genome sequencing was completed for 300 pea accessions and 136 lentil accessions. GRIN-Global software for storing single nucleotide polymorphism (SNP) data sets was developed in FY2022. We are in transition moving current GRIN resources for the pea SNP data set to a new public web interface for ease of public access. A Genomic Selection study on the pea core collection and two GWAS were published; one with the lentil core collection and one with the pea core collection, to identify disease (Fusarium root rot) and pest resistance genes in these species. In the process of creating the data for the GWAS, the lentil core collection was screened for reaction to Fusarium root rot and identified disease resistant accessions. Disease resistance data are now available to the public, and the results of the GWAS have been published. Although we were not able to characterize the fatty acid composition and oil content of 90 selected safflower germplasm accessions in this fiscal year, nor the year before, we were able to sequence 860 lines to produce a large dataset of 34,000 segregating SNPs. We will use this genotypic data for mapping studies when the phenotypic data are produced in the future.
In support of Sub-objectives 3A and 3B, researchers at Pullman, Washington, worked to update Crop Vulnerability Statements (CVS) and Operations Manuals. In the CSFL program, Standard Operating Protocols were completed on all tasks involving hazards using the Location Office Safety Template. In the Hort Crops program, the Leafy Vegetable Crop Vulnerability Statement (CVS) had been last updated in 2019. This Crop Germplasm Committee (CGC) has not met since the start of the COVID pandemic, and while the current CVS is not yet out of date, the program curator is contacting the CGC chair for updates. The operations manual on Lettuce Germplasm management is in progress and will be updated by the end of fiscal year 2022.
In support of Sub-objective 4B, researchers in Pullman, Washington, worked on a replicated trial of agronomic performance of a pea recombinant inbred line (RIL) population in Pullman and at other locations with collaborators. Seeds of the RIL populations were increased and are available for distribution to collaborators at other locations and within our unit. However, evaluation has not yet been done due to retirement of the previous research leader and faba bean breeder, who was to conduct the field work. Evaluations will proceed in 2023.
Accomplishments
1. Critical germplasm collections properly maintained and distributed. The USDA, ARS, National Plant Genetic Resources program holds the invaluable genetic diversity of over 200 crop species of importance to the United States. This diversity is key to creating new crop varieties for U.S. farmers with improved yield and resilience in the face of new climate and pest challenges. Curatorial programs in Pullman, Washington, all satisfactorily maintained their collections and met stakeholder requests for seeds in a timely fashion. 35,075 items were distributed from the genebank holdings including 23,859 within the United States and 10,504 to 45 countries globally. Of the 100,525 active accessions in the collections, representing 1,004 genera and 4,572 species, 75% of them are available for distribution, 71% of them are safely backed up at USDA facilities in Fort Collins, Colorado, and 20% are backed up at the Svalbard vault for long term safekeeping.
2. Genetic characterization data collected for key pea and lentil populations. New big data driven protocols for the efficient identification of genes of interest require very high numbers of genetic markers along all plant chromosomes. ARS researchers in Pullman, Washington, have completed sequencing of the pea and lentil core collections in addition to a substantial number of the pea and lentil crop wild relatives. This information was used to find SNP markers in dense coverage of the whole genome, which were used to discover genomic regions and gene candidates for resistance to aphids and useful agronomic traits in pea, and Fusarium root rot resistance in lentil. Gene discovery for improved nutritional content in pea and lentil are ongoing with these SNP markers as well. This data was made publicly available for use by collaborators and others in the pulse plant science research community for additional traits of economic importance.
Review Publications
Al Bari, M., Zheng, P., Viera, I., Worral, H., Szwiec, S., Ma, Y., Main, D., Coyne, C.J., McGee, R.J., Bandillo, N. 2021. Harnessing genetic diversity in the USDA Pea Germplasm Collection through genomic prediction. Frontiers in Genetics. 12. Article 707754. https://doi.org/10.3389/fgene.2021.707754.
Renzi, J.P., Coyne, C.J., Berger, J., von Wettberg, E., Nelson, M., Ureta, S., Hernandez, F., Smykal, P., Brus, J. 2022. How could the use of crop wild relatives in breeding increase the adaptation of crops to marginal environments? Frontiers in Plant Science. 13. Article 886162. https://doi.org/10.3389/fpls.2022.886162. [Corrigendum: Frontiers in Plant Science: 2022, 13, Article 1101822.]
Heineck, G.C., Altendorf, K.R., Coyne, C.J., Ma, Y., McGee, R.J., Porter, L.D. 2022. Phenotypic and genetic characterization of the lentil single plant-derived core collection for resistance to root rot caused by Fusarium avenaceum. Phytopathology. 112(9):1979-1987. https://doi.org/10.1094/PHYTO-12-21-0517-R.
Das, S., Porter, L.D., Ma, Y., Coyne, C.J., Chaves-Cordoba, B., Naidu, R.A. 2022. Resistance in lentil (Lens culinaris) genetic resources to the pea aphid (Acyrthosiphon pisum). Entomologia Experimentalis et Applicata. 170(8):755-769. https://doi.org/10.1111/eea.13202.
Nevada, S.S., Lupien, S.L., Watson, B., Okubara, P.A. 2021. Growth inhibition of Botrytis cinerea by native vineyard yeasts from Puget Sound, Washington State, USA. Journal of Biology and Nature. 13(1):42-53. https://www.ikprress.org/index.php/JOBAN/article/view/6534.
Wallace, L.T., Havey, M.J. 2021. Genetic analysis of mitochondrial sorting from the MSC3 mosaic mutant of cucumber. Journal of the American Society for Horticultural Science. 146(5):346-350. https://doi.org/10.21273/JASHS05075-21.
Yang, W., Guo, T., Luo, J., Zhang, R., Zhao, J., Warburton, M.L., Xiao, Y., Yan, J. 2022. Target-oriented prioritization: Targeted selection strategy by integrating organismal and molecular traits through predictive analytics in breeding. Genome Biology. 23. Article 80. https://doi.org/10.1186/s13059-022-02650-w.
Bertagna, F.B., Kuki, M.C., Neto, H.Z., Tessmann, D.J., Pinto, R.B., Scapim, C.A., Williams, W.P., Warburton, M.L. 2021. Association mapping and pathway analysis of ear rot disease caused by Aspergillus flavus in a panel of tropical maize germplasm. Crop Science. 61(6):4128-4138. https://doi.org/10.1002/csc2.20629.
