Research Project: Management of Priority Legume, Oilseed, Vegetable, Forage Grass, Sugar, Ornamental, and Medicinal Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing Research

2020 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
Considerable progress was made on all four objectives, which address Problem Statement 2A (Plant and microbial genetic resource and information management) of Component 2 (Plant and microbial genetic resource and information management) of the National Program 301, Plant Genetic Resources, Genomics, and Genetic Improvement (2018-2022). In support of Objective 1, approximately 1,403 new accessions were added to our collection, most of which were crop wild relatives collected by the Seeds of Success (SOS) project. SOS is a national native seed collection program led by the Bureau of Land Management in partnership with a variety of non-federal organizations and federal agencies including USDA. Wild pea accessions recently collected by the Crop Diversity Trust and donated to USDA were added. As of July 2020 there were 100,485 accessions belonging to 4,614 species. Most of these newly introduced resources are available to researchers and breeders. During the past year we distributed a total of 46,474 packets of seed samples to 1,125 requestors across all 50 states and 42 foreign countries. The plant exploration proposal to collect faba bean landraces to fill the gaps in our collection was selected for funding by the Plant Exchange Office. The faba bean curator/horticulturalist communicated with their collaborators in Morocco and arranged a plant collecting trip with drive routes mapped to growers’ fields for seed collecting at harvest time. However, with COVID19 travel restrictions, the plant exploration trip has been postponed. For Objective 2, a total of 2,346 inventories of diverse plant germplasm were regenerated in the field or in greenhouses. Quality fresh seed samples of 1,568 inventories were shipped to the National Laboratory for Genetic Resource Preservation (NLGRP), Fort Collins, Colorado, and to the Svalbard Global Seed Vault, Svalbard, Norway, respectively, for secured backup. A total of 2,604 digital images, including 2,565 seed images, of 2,020 accessions were uploaded into the Germplasm Information Network (GRIN) - Global database that is accessible via the internet by researchers, educators and the general public worldwide. All ongoing germplasm regeneration, seed increase, characterization, and evaluation research experiments are progressing well, and evaluation data are being collected. Molecular characterization of the lentil core collection was completed in 2020 and a manuscript published. In support of Objective 3, germplasm curators have been working with members serving in various Crop Germplasm Committees on updating crop vulnerability statements. Crop vulnerability statements were completed for safflower and new crops. Updating the Unit operations procedures is in progress. Subset standard operating procedures were completed for Near-Infrared seed quality testing and Food Legume seed germination in 2020. In support of Objective 4, the development a pea gene mapping population progressed well. Several thousand seeds harvested from the F1 hybrid plants were segregated for seed coat color of yellow and green in the expected three to one ratio. Single Seed Descent (SSD) is being used to complete the inbred lines for distribution. F3 and F4 (3rd and 4th filial) generations were completed in 2020. Since the two parental varieties are being used for developing pea reference genome sequences, the lines we are developing will be especially useful for studying the genetic basis of important traits.

Accomplishments
1. New outreach video produced and released for the National Plant Germplasm System. The mission of the National Plant Germplasm System is to conserve crop plant genetic diversity for use in science and education but this mission is not well understood by the non-scientific community, which results in numerous requests to NPGS for home garden use. To aid in communicating the NPGS mission, a new video was created that featured several NPGS locations and the work involved and purpose of maintaining and distributing the plants and seed preserved in the System. A researcher in Pullman, Washington, in collaboration with the USDA Creative Media and Broadcast Center lead the project. The video can be found on the USDA YouTube channel, a link on the NPGS database, GRIN-Global, homepage, and at this URL https://youtu.be/0U7M1sPYpyo.

Review Publications
Coyne, C.J., Kumar, S., Von Wettberg, E., Marques, E., Berger, J., Redden, R., Ellis, N., Brus, J., Zablatzká, L., Smykal, P. 2020. Potential and limits of exploitation of crop wild relatives for pea, lentil and chickpea improvement. Legume Science. 2(2):1-25. https://doi.org/10.1002/leg3.36.
Zhang, H., Yang, T., Liu, R., Jin, F., Zhang, L., Yu, H., Hu, J., Yang, F., He, Y., Zong, X. 2020. Assessment of genetic diversity by using EST-SSR markers in Lupinus. Acta Anatomica. 46(3):330-340.
Wei, S., Yang, X., Huo, G., Ge, G., Liu, H., Luo, L., Hu, J., Huang, D., Long, P. 2020. Distinct metabolome changes during seed germination of lettuce (Lactuca sativa L.) in response to thermal stress as revealed by untargeted metabolomics analysis. International Journal of Molecular Sciences. 21(4):1481. https://doi.org/10.3390/ijms21041481.
Ma, Y., Coyne, C.J., Sankaran, S., Main, D., Porter, L.D., Mugabe, D., Smitchger, J., Zhang, C., Amin, M., Fasheed, N., Ficklin, S., McGee, R.J. 2020. Dissecting genetic architecture of Aphanomyces root rot resistance in lentil by QTL mapping and genome-wide association. International Journal of Molecular Sciences. 21(6):2129. https://doi.org/10.3390/ijms21062129.
Trneny, O., Brus, J., Hradilova, I., Rathore, A., Das, R., Kopecky, P., Coyne, C.J., Reeves, P.A., Richards, C.M., Smykal, P. 2018. Molecular evidence for two domestication events in the pea crop. Genes. 9(11). https://doi.org/10.3390/genes9110535.
Bauchet, G., Bett, K.E., Cameron, C.T., Campbell, J.D., Cannon, E., Cannon, S.B., Carlson, J., Chan, A., Cleary, A., Close, T., Cook, D., Cooksey, A., Coyne, C.J., Dash, S., Dickstein, R., Farmer, A., Fernandez-Baca, D., Hokin, S., Jones, E., Kang, Y., Monteros, M., Munoz-Amatriain, M., Mysore, K., Pislariu, C., Richards, C.M., Shi, A., Town, C., Udvardi, M., Wettberg, E., Young, N., Zhao, P. 2019. The future of legume genetic data resources: Challenges, opportunities, and priorities. Legume Science. 1(1):e16. https://doi.org/10.1002/leg3.16.
Du, Z.Z., Li, X.X., Song, J.P., Wu, Y.H., Zhao, Q., Xu, T., Zhang, X.H., Hellier, B.C., Hu, J., Wang, H.P. 2019. Phenotypic diversity and adaptability analysis of 228 accessions of introduced garlic genetic resources. Journal of Plant Genetic Resources. https://doi.org/10.13430/j.cnki.jpgr.20190119001.
Lin, S., Medina, C., Boge, B., Hu, J., Fransen, S., Norberg, S., Yu, L. 2020. Identification of genetic loci associated with forage quality in response to water deficit in autotetraploid alfalfa (Medicago sativa L.). Biomed Central (BMC) Plant Biology. 20. https://doi.org/10.1186/s12870-020-02520-2.
Hellwig, T., Flor, A., Saranga, Y., Coyne, C.J., Main, D., Sherman, A., Ophir, R., Abbo, S. 2020. Environmental and genetic determinants of amphicarpy in Pisum fulvum, a wild relative of domesticated pea. Plant Science. 298. https://doi.org/10.1016/j.plantsci.2020.110566.
Kreplak, J., Madoui, M., Capal, P., Novak, P., Labadie, K., Aubert, G., Bayer, P., Krishna-Kishore, G., Symes, R.A., Main, D., Klein, A., Berard, A., Fukova, I., Fournier, C., D'Agata, L., Belser, C., Berrabah, W., Simkova, H., Lee, H.T., Kougbead, A., Terezol, M., Huneau, C., Turo, C.J., Mohellibi, N., Neumann, P., Falque, M., Gallardo-Guerrero, K., McGee, R.J., Tar'An, B., Bendahmane, A., Aury, J., Batley, J., Le Paslier, M., Ellis, T., Warkentin, T., Coyne, C.J., Salse, J., Edwards, D., Lichtenzveig, J., Macas, J., Dolezel, J., Wincker, P., Burstin, J. 2019. A reference genome for pea provides insight into legume genome evolution. Nature Genetics. 51:1411-1422. https://doi.org/10.1038/s41588-019-0480-1.