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Research Project: Management of Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing Research

2017 Annual Report

Objective 1: Conserve, acquire, regenerate, back-up, and distribute genetic resources and associated information for cool season food and forage legumes, grasses, common beans, oilseeds, vegetables, beets, ornamentals, medicinal crops and related wild species. Objective 2: Conduct genetic characterizations and phenotypic evaluations of genetic resources of the preceding crops and related wild species for priority genetic and agronomic traits. Apply the preceding knowledge to genetic resource acquisition, management, and marker-trait association studies of selected taxa. Sub-objective 2A: Apply existing and newly developed DNA genetic marker technology to phylogenetic and genetic diversity analyses of priority crops, emphasizing core subsets of Phaseolus, Beta, Allium, Carthamus, Pisum, Vicia, Cicer, Lens, and temperate grass species. Incorporate characterization data into the Germplasm Resources Information Network (GRIN-Global) and/or other databases. Sub-objective 2B: Update and apply phenotypic descriptors for Allium, Beta, Lactuca, Pisum, Cicer, Phaseolus, Carthamus, and priority native and other cool season grasses. Incorporate phenotypic data into GRIN Global and/or other databases. Sub-objective 2C.1: Assess genetic (molecular) and phenotypic variation of reed canarygrass (Phalaris arundinacea, L.) and apply that information to curating the collection. Sub-objective 2C.2: Genecology of bottlebrush squirreltail, Thurber's needlegrass, and basin wildrye. Sub-objective 2D: Develop mapping populations and genomic resources of Pisum, Lens, Cicer and Vicia, for developing markers suitable for marker assisted selection of those crops. Objective 3: Identify pathogens causing emerging diseases associated with the preceding genetic resources, investigate interactions among these plant taxa and the pathogens, and devise and apply pathogen management strategies. Objective 4: Conduct initial pre-breeding programs for underutilized agronomic traits, and release genetically-enhanced populations for selected crops. Sub-objective 4A: Pre-breeding Safflower for improved oil concentration and high oleic fatty acids in winter safflower. Sub-objective 4B: Incorporate genes for improved nutritional content into faba bean pre-breeding populations.

Regenerate, conserve, and distribute more than 92,000 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 the established protocols and procedures. Ship high quality seed samples to National Center for Germplasm Resources Preservation at Ft. Collins, CO and the Svalbard Global Seed Vault in Norway for long-term security back-up. Conduct collaborative plant expedition and collection trips to acquire samples to fill gaps in NPGS collections, and to meet stakeholder needs. Apply existing and newly developed genomic tools and technologies to characterize phylogenetic relationship and genetic diversity of priority crop collections. Evaluate the phenotypic variation of economic traits of specialty crops independently or collaboratively. 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. Use both classical plant breeding methods and modern marker-assisted selection (MAS) to enhance the nutritional attributes and the resiliency to abiotic stress of safflower and faba bean. Publish research results and release improved germplasm to the user community.

Progress Report
Progress was made on all four objectives and their sub-objectives, all of which fall under National Program 301, Plant Genetic Resources, Genomics, and Genetics Improvement. This project focuses on Problem Statement 1A: Efficiently and Effectively Manage Plant and Microbial Genetic Resources. Introduced plant genetic resources are critical to supply of desirable genes for improving the current crops and developing new crops. Objective 1: Our curators and scientists successfully acquired 3,524 new accessions including 1,249 native plant accessions from the Seeds of Success (SOS) project, 1,353 common bean accessions from the International Center for Tropical Agriculture (CIAT) in Cali, Colombia, and 174 lupin from the Institute of Plant Genetics and Crop Research, Gatersleben, Saxony-Anhalt, Germany. Our common bean germplasm curator coordinated a domestic wild bean collection trip which resulted in the acquisition of 17 accessions of the North American wild kidney bean or thicket bean (a wild relative of common bean) from the states of Virginia and North and South Carolina. This trip was sponsored by the ARS National Plant Germplasm System (NPGS) Plant Exchange Office and conducted by one of our active collaborators, a research botanist from the Smithsonian Institution. As of June 28, 2017, the Western Regional Plant Introduction Station (WRPIS) collection included 97,869 accessions belonging to more than 5,000 plant species. Of these, 72,248 accessions were available for distribution to requesters in the global plant research community, which uses genetic resources for both applied crop improvement and basic biological research. During FY 2017, a total of 33,354 packets of high quality seed samples were distributed to 1,269 requesters in 46 foreign countries and 50 domestic states. We packed and stored 2,908 newly regenerated/harvested inventories of a broad range of plant species. For security backups, we sent 2,392 inventories to the National Laboratory for Genetic Resources Preservation (NLGRP) at Fort Collins, Colorado, and 4,706 inventories to the Svalbard Global Seed Vault, Longyearbyen, Norway, through the NLGRP during 2017. We determined seed quantities of 10,673 inventories in our collection. At the recommendation of the Forage and Turf Crop Germplasm Committee, we submitted a plant exploration proposal and obtained funding from the Plant Exchange Office to collect reed canarygrass from the Mediterranean basin, the likely center of origin of the species. After a lengthy negotiation on the conditions in compliance with French laws governing foreign access to germplasm, our collaborator, a retired research agronomist, traveled to France in June and July of 2017 to collect the needed germplasm to fill the gap in our grass collection. Objective 2: Our staff uploaded 45,092 observation data points on 9,876 accessions into the Germplasm Resources Information Network (GRIN)-Global database. These data points are on 168 established descriptors for 20 different crop species. Our collaborators contributed 6% and Western Regional Plant Introduction Station (WRPIS) staff provided 94% of the evaluation data. The database is accessible by researchers worldwide via the internet. We continued collaborative and independent research on cool season food legumes (pea chickpea, lentil and faba bean), safflower, garlic and ornamental bulb crop diseases, native plants and grasses. This work supports small to medium scale growers in the U.S., especially in the Pacific Northwest. The ARS Phaseolus curator, in collaboration with the researchers in the Department of Food Science and Human Nutrition, Washington State University, analyzed the content of extractable, non-extractable, and bonded phenolics in 120 heirloom bean accessions and investigated the relationship with seed coat colors and patterns. The resulting information will be useful to bean breeders for genetic improvement of health promoting qualities in beans. The collaborative effort on collecting and characterizing native plant materials for ecological restoration has been led by our Agronomy and Safflower germplasm curator and partially supported by grants from the Bureau of Land Management (BLM) and its Seeds of Success (SOS) project, the Great Basin Restoration Initiative, and the U.S. Forest Service. The activities include cleaning and increasing the seeds, entering the associated data into the GRIN-Global database, distributing samples to requesters and sending well-documented accessions to other National Plant Germplasm System (NPGS) repositories that have assigned responsibilities for these recently collected genera/species. An ARS geneticist in Pullman, Washington, obtained a germplasm evaluation grant from the Food Legume Crop Germplasm Committee to evaluate NPGS faba bean germplasm on an organic rice farm. One hundred faba bean accessions were planted in November, 2016, (after rice harvest) for collecting phenotypic data on the Lundberg Family Farms in California under a Non-Assistance Cooperative Agreement (NACA) #2090-21000-028-20S. Evaluation data, such as biomass, plant height, days to flower and seed yield, are being collected in 2017. We anticipate that these evaluations will identify genetic resources for breeding cover crops with potential under organic farming systems as well as generate data for NPGS GRIN-Global database. Objective 3: An ARS plant pathologist in Pullman, Washington, continued research, in collaboration with the Washington State University Plant Pathology Department and ARS scientists in Fort Pierce, Florida, to document host preference of seven Penicillium species across six bulb-forming hosts. We isolated fungi from camas (a Native American food plant) bulbs and seed and tested for pathogenic fungal taxa at two temperatures among the recovered isolates, including three Penicillium species (spp.), two Fusarium spp., one Trichoderma single species (sp.) and one Botrytis sp. It was found that one Botrytis strain, Cq23, exhibited significantly higher virulence among all isolates tested. Objective 4: An ARS geneticist continued the enhancement and development of winter hardy faba bean germplasm lines for pulse and cover crop development. Promising advanced breeding populations have been distributed under ARS Plant Evaluation Agreements (PEA) to researchers in several states, including Massachusetts, Pennsylvania, Wisconsin and Kentucky, that are located in various winter hardiness zones.

1. Community resource for utilizing genetic diversity in pea germplasm. Pea production in the U.S. brings $606 million farm gate value annually and farmers will benefit directly from increased yields. The USDA managed pea genetic diversity holds the key for unlocking the yield potential across the pea market classes. With collaborators, ARS researchers in Pullman, Washington, released 66,591 high quality single nucleotide polymorphisms (SNP) markers on 431 pea accessions. Plant scientists can download the data from the National Agriculture Library or from USDA Germplasm Resource Information Network (GRIN)-Global and access the germplasm directly for identifying new genes in pea for increasing yield and farmer returns and for expedited gene discovery through association mapping.

2. New species inducing blue mold of sugarbeet roots described. Storage losses regularly occur from molds and bacteria in stored sugarbeet piles and cost the sugar industry millions of dollars annually. Penicillium species are the most important storage molds in U.S. sugarbeet piles. ARS researchers in Pullman, Washington, and in Kimberly, Idaho, discovered and described a new species inducing blue mold of sugar beet roots. Aggressiveness of the new species has been documented across a range of storage temperatures. The published research results provided tools for diagnosis and to mitigate losses of sugar during sugarbeet storage via managing storage temperature.

Review Publications
Smykal, P., Varsheny, R., Singh, V., Coyne, C.J., Domoney, C., Kejnovsky, E., Warkentin, T. 2016. From Mendel’s discovery on pea to today´s plant genetics and breeding. Theoretical and Applied Genetics. doi: 10.1007/s00122-016-2803-2.
Dugan, F.M., Everhart, S. 2016. A leitmotif of contemporary mycology has challenges and benefits for plant pathologists. Plant Health Progress. doi: 10.1094/PHP-RV-16-0046.
Dugan, F.M., Lupien, S.L., Armstrong, C.M., Chastagner, G., Schroeder, B.K. 2017. Host ranges of Penicillium species causing blue mold of bulb crops in Washington State and Idaho. Crop Protection Journal. 96:265-272.
Landry, E.J., Coyne, C.J., Mcgee, R.J., Hu, J. 2017. A modified mass selection scheme for creating winter-hardy faba bean (Vicia faba L.) lines with a broad genetic base. Journal of Euphytica. 213:72.