Location: Plant Genetic Resources Unit (PGRU)
2018 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
ARS researchers in Geneva, New York conserve 12,690 distinct varieties of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, other cole crops, celery, tomatillo, asparagus and other vegetables and their wild relatives. This provides the genetic diversity needed to develop vegetable varieties with resistance to diseases and pests, tolerance to abiotic stresses, varieties with improved quality and nutrition, and ensures its long-term availability. During field season 2018, 172 varieties were planted to produce seed or bulbs by ARS researchers in Geneva, New York and seed samples of 30 varieties were distributed to cooperators for seed production. In addition, 11 onion varieties not currently in the collection are being grown for seed by a cooperator. ARS researchers in Geneva, New York distributed an average of 1,300 samples per month of vegetable seed to requestors for breeding, research, and higher education.
Seed collections are a critically valuable source of genetic diversity for plant breeding and research. The ability to make optimal use of seed collections is facilitated by genetic characterization. ARS researchers in Geneva, New York are participating in a collaborative project to develop functional panels of squash and melons based on DNA sequencing. To this end, ARS researchers have provided squash seed and data for a large genotyping-by-sequencing (GBS) analysis of the USDA collections of watermelon, melon, cucumber, and squash (5,840 total samples). Results will be used to establish functional panels of 300-400 varieties per crop representing ~99% of the genetic diversity along with key disease resistance, fruit quality, horticultural and agronomic traits.
The species Brassica oleracea is unique in that it has been domesticated into numerous distinct crops including broccoli, brussel sprouts, cabbage, cauliflower, kale, kohlrabi, and several lesser known crops such as walking stick kale and marrow cabbage. These crops include important leaf and root vegetables, as well as animal feed. One unique characteristic of these vegetable crops is the presence of glucosinolates, bitter tasting compounds that evolved for herbivory defense, and exhibit anti-carcinogenic properties. Using GBS of USDA seed collections, ARS researchers in Geneva, New York are examining patterns of relationships among the various crops and their wild relatives. We plan to determine the most closely related wild species of B. oleracea to discover its origin of domestication. Lastly, using gene mapping techniques, we will identify genes underlying crop traits of economic importance.
The USA is the fourth largest producer of dry onion (Allium cepa) bulbs in the world. However, production of this specialty crop has been badly affected by fungal diseases. One of the most devastating fungal diseases is Fusarium basal rot (FBR), which is prevalent in all onion-growing regions across the globe. Approximately 100 varieties from the ARS-PGRU (Plant Genetics Research Unit) Allium cepa collection are being infected and screened for disease resistance to FBR. Disease incidence will be calculated as the percentage of inoculated bulbs exhibiting FBR symptoms. A subset of samples will also be analyzed using a digital imaging technique. Steroidal saponins will be measured as a potential biochemical marker of antifungal activity. Results from screenings, digital image analysis and saponin assays will identify breeding material for improving onion cultivars for FBR resistance.
ARS researchers in Geneva, New York participated in a proficiency test to examine uniformity of seed viability test results among 15 USDA National Plant Germplasm System (NPGS) sites. Five seed lots, with 100 seed x 4 replications per seed lot, were tested for percent viable. Results were analyzed against refereed samples and a statistical test was applied to evaluate accuracy. Among sites, Association of Official Seed Analysts (AOSA) certified testers were more accurate than non-certified testers. Although USDA, ARS Plant Genetic Resources Unit (PGRU) in Geneva, New York does not have an AOSA certified tester, all test results were very accurate. This result showed that PGRU can continue to perform in-house viability tests with confidence. Additional training on pure seed definition, identification of abnormal seedlings and dormancy testing would be beneficial.
The Northern Organic Vegetable Improvement Collaborative (NOVIC) is a collaboration among scientists at Oregon State University, USDA, ARS Plant Genetic Resources Unit in Geneva, New York, Cornell University, University of Wisconsin-Madison, Washington State University, and the Organic Seed Alliance. This research project serves small-scale seed producers and farmer plant breeders in the organic farming community throughout the country but with an emphasis in the Northern United States. PGRU’s main focus in NOVIC is centered on outreach activities and training in small-scale seed production and processing. PGRU continues to provide outreach for NOVIC at several venues including the Common Ground Country Fair (Unity, Maine), Ohio Ecological Food and Farm Association (Dayton, Ohio), and Northeast Organic Farming Association of New York (Saratoga Springs, New York).
Accomplishments
