Location: Plant Genetic Resources Unit (PGRU)
2024 Annual Report
Objectives
Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, then apply them to priority vegetable genetic resources to avoid backlogs in genetic resource and information management, and to support genetic enhancement of selected vegetable crops.
Sub-objective 1.A. Develop and apply methods to optimize vegetable seed production, seed storage, and regeneration protocols. Apply genotyping strategies to generate data to guide and enhance vegetable acquisition, distribution, and maintenance efforts.
Sub-objective 1.B. Apply existing and emerging technologies to characterize and evaluate vegetable germplasm resources for priority traits to ascertain their genetic control and support genetic enhancement and breeding projects. Evaluate priority vegetable genetic resources in accordance with appropriate Cucurbit, Crucifer, Leafy Vegetable, Root and Bulb, or Tomato Crop Germplasm Committee descriptors.
Sub-objective 1.C. Resolve backlogs in vegetable genetic resources by completing rescues of jeopardized accessions, increasing viability and pathogen testing throughput, and optimizing inventory management strategies. Resolve genetic resource information management backlogs by making associated data available on GRIN-Global and cross-validating inventory metadata.
Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority vegetable genetic resources and associated descriptive information.
Sub-objective 2.A. Identify and fill gaps in tomato, onion, brassica, winter squash, celery, and radish collections to expand genetic diversity through the collection, germplasm exchange, cooperator donations, and integration of expired Plant Variety Protection material. Distribute pure vegetable genetic resources and associated information to NPGS stakeholders.
Sub-objective 2.B. Maintain the safety of genetic resources by local and cooperative regenerations. Ensure the long-term safety of vegetable genetic resource collections by systematically completing backups at National Laboratory for Genetic Resource Preservation and other appropriate seedbanks. Collaborate with GRIN-Global and appropriate databases to ensure information associated with vegetable genetic resources are available and accessible via hyperlinking or searches.
Sub-objective 2.C. Work closely with other NPGS genebanks, Crop Germplasm Committees, GRIN-Global, and other stakeholders to develop and update Crop Vulnerability Statements for priority vegetable genetic resources.
Approach
Vegetable seed production and regeneration will be via replicated regeneration pollination experiments to determine optimal cage and pollinator parameters. Seed storage will be optimized via the development and application of a suite of Best Management Practices. Genotyping strategies will be applied to critical crops to better understand and characterize biotic and abiotic resistance in tomatoes and their crop wild relatives. Genotype by sequencing of the asparagus collection will be used to set conservation priorities and understand underlying population structure. CGCs will be actively engaged in routine and special characterization and phenotyping projects run against crop collections held at PGRU. All phenotype and molecular marker data will be captured within GRIN-Global to better serve the plant science and breeding community. Jeopardized accessions will be rescued in greenhouse and growth chambers with the expectation of further multiplying seed in field regenerations and subsequent distribution to NPGS Stakeholders. Special emphasis will be placed on historically underutilized crop groups. Special emphasis during the Project Plan will be placed on development and application of up-to-date Best Management Practices, testing, and inventory management practices. This work will apply gap analysis of current PGRU vegetable crop collections via hybrid approaches to aid in identification, restoration, and enhancement of genetic resources. To increase regeneration throughput, existing collaborative seed increase efforts will be supported, and new collaborations will be developed. Critical accessions will be targeted for regeneration and backed up. In collaboration with CGCs, and critical stakeholders, crop vulnerability statements will be drafted.
Progress Report
This project addressed NP301 Action Plan Component 2 “Plant and microbial genetic resource and information management”. Objective 1 is to conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall National Germplasm Resources Laboratory (NPGS) Plan, then apply them to priority vegetable genetic resources to avoid backlogs in genetic resource and information management, and to support genetic enhancement of selected vegetable crops. Objective 2 is to acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority vegetable genetic resources and associated descriptive information.
Delivery of seed to customers is the primary way in which ARS researchers in Geneva, New York, serve vegetable industry and research stakeholders. In total, approximately 200 vegetable species, and crop wild relatives are managed by the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, New York. PGRU maintains 12,684 active vegetable seed stocks (accessions) in cold storage (Objective 2). This seed provides the genetic diversity needed to develop new varieties with disease resistance, tolerance to weather events and other stresses, and varieties with improved eating quality and nutritional content. During the FY, six expired PVP cultivars were received from the Plant Variety Protection Office (Objective 2). During the 2024 growing season, 225 accessions of vegetables or medicinal plants (asparagus, radish, tomato, onion, brassica, winter squash, physalis, and Datura) were grown for the purpose of producing seed by PGRU. Additionally, seed samples of 35 varieties (short-day onion and vegetable brassicas) were sent to collaborators in Parlier, California, and Las Cruces, New Mexico, for seed production (Objective 2). PGRU distributed (or is in the process of distributing) 14,287 aliquots of vegetable seed to requestors across 219 orders since Sept 1, 2023 and 9,958 samples across 169 orders January – July 2024(Objective 2).
In collaboration with the University of Arkansas, ARS researchers in Geneva, New York, initiated a genome-wide association study for biotic and abiotic stress-resistance in tomato. This work will identify germplasm and the genetic architecture underpinning resistance to bacterial wilt, salt tolerance, and other factors. Phenotypic data generated from with work will strengthen the value of the PGRU tomato collection for breeding resistant cultivars (Objective 1).
ARS researchers in Geneva, New York, have partnered with many groups to provide training and outreach, including leading presentations at the Foodlink, New York, Community Gardening Workshop. ARS researchers in Geneva, New York, have led a seed saving workshop at the Maine Organic Farmers and Gardeners Association Common Ground Country Fair reaching an audience of approximately 60,000 attendees.
ARS researchers in Geneva, New York, participated in a collaborative Crop Germplasm Committee Germplasm Evaluation Grant effort with Cornell University to grow, genotype, and phenotype the entire NPGS bottle gourd collection (approximately 174 accessions). This work is generating approximately 75,000 data points for priority data on traits of interest to breeders, seed, flower, and fruit characters, and SNP molecular markers and these data will be made publicly available Germplasm Resources Information Network GRIN-Global.
Accomplishments
1. Maintenance of critical vegetable crop genetic resources. Critical vegetable crop seed has been maintained. Worldwide, vegetable breeders and other researchers require high levels of genetic diversity to develop new, improved vegetable crops. ARS researchers in Geneva, New York, maintained 12,684 varieties of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, celery, tomatillo, asparagus, and other vegetables including related crop wild relatives in support of crop improvement efforts. Specifically, this work provides the allelic diversity needed to develop vegetable varieties with disease and pest resistance, tolerance to heat, cold, and drought stress, and varieties with improved flavor, quality, and nutrition.
2. Distribution of critical vegetable crop genetic resources. USDA-ARS researchers in Geneva, New York, ensured that genetic seed resources for vegetable crops were continuously grown, harvested, and stored to support crop improvement efforts. This PGRU ensured that enough seed of diverse vegetable crops were available for distribution. During the reporting year, regeneration or rescue of approximately 250 vegetable or medicinal (radish, tomato, onion, Brassica, winter squash, tomatillo, Datura) accessions were in progress or were completed. Seed samples of 35 onion, brassica, and winter squash accessions were sent to collaborators in Parlier, California, and Las Cruces, New Mexico, for seed regeneration. A total of 14,287 aliquots of vegetable seed were distributed to requestors across 219 orders. Distribution of critical vegetable crop genetic resources is important because this forms the basis for development of new vegetable crop varieties with desirable traits, such as enhanced abiotic stress tolerance, enhanced disease resistance, and/or improved yield and other market performance qualities like flavor, aroma, texture, appearance, nutrition, and shelf-life.