Location: Plant Genetic Resources Unit (PGRU)
2023 Annual Report
Objectives
Objective 1: Efficiently and effectively acquire and maintain the safety, genetic integrity, health and viability of priority vegetable genetic resources, and distribute them and associated information worldwide. [NP301, C2, PS 2A]
Sub-objective 1.A. Fill gaps in collections of tomato, onion, cole crops, winter squash, celery and radish through germplasm exchange, cooperator donations, and expired Plant Variety Protection material. Perform routine regenerations of accessions locally and through cooperators. Rescue currently unavailable accessions with low inventory or low viability if possible.
Sub-objective 1.B. Ensure long term safety of collections by systematically completing backups of 2,000 seed per accession at Plant and Animal Genetic Resources Preservation (PAGRP), Ft. Collins, CO. Optimize workflow and seed storage operations to efficiently handle and distribute seed. Disseminate information associated with germplasm resources in publications and reports.
Objective 2: Develop more effective germplasm maintenance, evaluation, or characterization methods and apply them to priority vegetable genetic resources. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources. [NP301, C2, PS 2A]
Sub-objective 2.A. Improve methods for germplasm regenerations for onion, cole crops, and winter squash through applying and optimizing best management practices of plant and seed production. Optimize protocols for data collection from routine regenerations including CGC descriptors for tomato, onion, cole crops and winter squash, and for in-house germination and seed quality tests for crops conserved.
Sub-objective 2.B. Collaborate with ARS and other scientists to characterize quality traits in tomato, onion, and cole crops collections. Collaborate with Germplasm Resources Information Network (GRIN)-GLOBAL and appropriate public databases to ensure that data associated with germplasm resources are accessible via cross-links or searches.
Objective 3: With other National Plant Germplasm System (NPGS) genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for priority vegetable genetic resource and information management. [NP301, C2, PS 2A]
Sub-objective 3.A. Strengthen and implement best management practices for conservation of germplasm through cooperation and consultation with CGCs and with other NPGS genebanks for Cucurbita (NC7, S9), Brassica (NC7), Allium (W6), and tomato (TGRC). Update the Plant Genetic Resources Unit (PGRU) NE9 Manual of Procedures.
Sub-objective 3.B. Collaborate with Cucurbit, Crucifer, Leafy Vegetable, Root and Bulb, and Tomato CGCs to update crop vulnerability statements.
Approach
PGRU will fill gaps in collections through germplasm exchange, cooperator donations, and expired Plant Variety Protection materials. Genetic diversity of tomato, Brassica oleracea (cole crops), Brassica rapa, onion, winter squash, radish, celery, and buckwheat collections will be restored and enhanced by identifying gaps and sources of germplasm to fill the gaps. We will use best management practices (BMP) to preserve and safe guard the collections. Any seed accession that drops below minimum requirements for seed quantity (1,000) or viability (70%) is routinely regenerated. We will ensure the long term safety of collections by systematically completing backups of accessions at PAGRP, Fort Collins, CO. Data from GRIN-Global will be used to analyze backup status of all accessions. Backup samples will be produced either from currently stored seed, or if this is not available, from regeneration of an accession. Distribution of vegetable crops is directed towards research and crop improvement needs. Whenever seed is requested for an accession with low seed supply, it is given priority for regeneration. We will cooperate with scientists from ARS and other public and private sectors to characterize priority traits in collections. PGRU will carry out the characterization and evaluation of key morphological, horticultural, genetic, and biochemical attributes of accessions during regeneration activities. Data for CGC descriptors for tomato, onion, cole crops, and winter squash will be routinely collected from regeneration plots during the growing season. Descriptor data will be collected on scheduled days depending on the crop and trait, and entered into a portable electronic tablet or smartphone. Characterization and evaluation data are distributed via GRIN-Global and other databases. Many accessions are unimproved for disease, pest and abiotic stress resistances or tolerances. Heat treatment of seed can effectively control a broad range of seed-borne pathogens. Heat treatment will be optimized and adopted as part of an integrated pest control program. Germination tests of regeneration plots will be performed each year. The knowledge, expertise, and experience of CGC members, and staff at other NPGS and international germplasm repositories will be leveraged to strengthen and improve germplasm conservation through BMP. Curators and other scientists meet on a regular basis at scientific conferences, CGC meetings, Regional Technical Advisory Committee meetings, and Plant Germplasm Operations Committee meetings. This provides many opportunities for mutually beneficial consultation, exchange of information, formulation of new ideas, and soliciting recommendations. All components of PGRU operations will be reviewed and documented as BMP with sufficient detail to reduce risk of any lapse in operations. Thereafter, the finalized PGRU Operations Manual will be reviewed and updated annually. We will also collaborate with Cucurbit, Crucifer, Leafy Vegetables, Root and Bulb, Tomato, Apple, Grape, and Prunus CGCs to update the Crop Vulnerability Statements.
Progress Report
This project addressed NP301 Action Plan Component 2 “Plant and microbial genetic resource and information management”. Objective 1 is to efficiently and effectively acquire and maintain the safety, genetic integrity, health and viability of priority vegetable genetic resources, and distribute them and associated information worldwide. Objective 2 is to develop more effective germplasm maintenance, evaluation, or characterization methods and apply them to priority vegetable genetic resources, and to record and disseminate evaluation and characterization data via Germplasm Resource Information Network (GRIN)-Global and other data sources. Objective 3 is to work with other National Plant Germplasm System (NPGS) gene banks and Crop Germplasm Committees to develop, update, document, and implement best management practices and Crop Vulnerability Statements for priority vegetable genetic resource and information management.
Delivery of seed to customers is the primary way in which ARS researchers in Geneva, New York, serve vegetable industry and research. 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. Plant Genetics Resources Unit (PGRU) maintains 12,739 unique seed stocks in cold storage (Objective 1). 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, four expired PVP cultivars were received from the Plant Variety Protection Office (Objective 1). During the 2023 growing season, 224 accessions of vegetables (radish, tomato, onion, brassica, winter squash, and physalis) were grown for the purpose of producing seed by PGRU and seed samples of 38 varieties (short-day onion and winter squash) were sent to collaborators in Parlier, California, and Las Cruces, New Mexico, for seed production (Objective 1). PGRU distributed 10,537 aliquots of vegetable seed to requestors in 332 orders since Jan 1, 2022 and 5,823 samples in 137 orders from January – June 2023 (Objective 1).
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 2).
ARS researchers in Geneva, NY collaborated to support organic farming via the Northern Organic Vegetable Improvement Collaborative (NOVIC) to increase the diversity of vegetable varieties available to organic farmers. The long-term goal is to increase the proportion of U.S. agriculture that is managed organically. (Objective 2). ARS researchers in Geneva, NY have partnered with many groups to provide training and outreach, including leading presentations at the Foodlink, NY Community Gardening Workshop. ARS researchers in Geneva, NY 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. In addition, these ARS researchers and have coordinated with local community based agricultural initiatives to provide support for displaced communities from Nepal and Myanmar.
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 will generate 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 GRIN-Global.
Accomplishments
1. Critical vegetable crop seed 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 12,739 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. Seed produced for vegetable crops breeding, research, and education. Plant Genetics Resources Unit (PGRU) genetic resources must be continuously grown, harvested, and stored seed to ensure seed availability to support crop improvement efforts. PGRU ensured enough seed of diverse vegetable crops were available for distribution. During the reporting year, PGRU attempted regeneration or rescue of approximately 259 vegetable (cabbage, radish, tomato, onion, Brassica, winter squash, and celery) accessions. Seed samples of 38 onion, brassica, and winter squash accessions were sent to collaborators in Parlier, California, and Las Cruces, New Mexico, for seed regeneration. ARS researchers in Geneva, New York, distributed 10,569 aliquots of vegetable seed to requestors in 334 orders since Jan 1, 2022.
