Location: Plant Genetic Resources Unit (PGRU)
2021 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 - 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 - 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 Germplasm Resources Information Network (GRIN)-Global and other data sources, and Objective 3 - with other National Plant Germplasm System (NPGS) gene banks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for priority vegetable genetic resource and information management.
Delivery of vegetable seed to customers is the primary way in which ARS researchers in Geneva, New York, serve the vegetable industry. In total, 197 types of vegetable crops and their wild relatives are managed by ARS researchers in Geneva, New York, in the form of 12,716 seed stocks kept in cold storage (Objective 1). This seed provides the genetic diversity needed to develop new vegetable varieties with disease resistance, tolerance to weather events and other stresses, and varieties with improved eating quality and nutritional content. During 2021, two commercially developed, expired Plant Variety Protection broccoli cultivars were newly acquired (Objective 1). During the 2021 growing season, approximately 176 varieties of vegetables (cabbage, radish, tomato, onion, Brassica, winter squash, and celery) were planted for the purpose of producing seed by ARS researchers in Geneva, New York, and seed samples of 35 varieties (short-day onion, winter squash) were sent to collaborators in Parlier, California, and Las Cruces, New Mexico, for seed production (Objective 1). ARS researchers in Geneva, New York, distributed 5,395 samples of vegetable seed to requestors in 180 orders during the calendar year 2020, and 4,128 samples in 124 orders from January – June 2021 (Objective 1).
ARS researchers in Geneva, New York, are regenerating and genotypically characterizing the Plant Genetic Resources Unit (PGRU) asparagus (Asparagus officinalis) collection. In 2020, we began an increase of a new asparagus field regeneration using 51 unavailable or jeopardized seed stocks. In addition, we initiated a genotype-by-sequencing study evaluating 116 unique Asparagus stocks and cultivars from 29 countries. This work is evaluating overall genetic diversity and population structure within the broader pool of asparagus germplasm, as well as putative genetic bottlenecks that occurred during domestication processes. Initial work has identified several critical sub-clusters within asparagus germplasm using approximately 41K high quality DNA markers (Objective 1, Objective 2).
ARS researchers in Geneva, New York, developed high-throughput hemp seed increase protocols that control for dioecious and wind-pollination biology with private and public hemp breeding collaborators (Objective 1). During the first half of 2021, collection of hemp germplasm resources was delayed due to non-agency federal approval processes, although associated information on diverse hemp germplasm resources from 17 entities was gathered. This constitutes an estimated 1,000 hemp accessions to be added to the collection once enhanced security systems are approved (Objective 1).
ARS researchers in Geneva, New York, carried out a genetic diversity study of tomato. Tomato producers require new sources of genetic diversity to remain competitive and meet increasing consumer demands for the beneficial vitamins, minerals, dietary fiber, and other nutrients provided by this highly popular vegetable. We performed partial genome sequencing on 190 tomato stocks from our seeds collection. These stocks originated from 31 countries and included various market types such as fresh fruit, ornamental, paste or sauce, breeders’ lines, farmer varieties, and home gardening types. The results of this study provided gene discovery tools and other genetic information that can be used to increase the efficiency of choosing genetic stocks for tomato research and breeding (Objective 2).
ARS researchers in Geneva, New York, performed a genetic diversity study of radish. Radish is an ancient crop that is economically valuable throughout the world. Radish is largely consumed raw as a condiment or salad ingredient in Europe and the U.S., while it is a key ingredient in the cuisines of Japan, China, and Korea. This different emphasis in usage combined with environmental differences has produced distinct cultivars between the two regions. We performed partial genome sequencing on 152 radish stocks from around the world. The results of this study provided gene mapping tools and other genetic information that can be used to increase the efficiency of developing new, improved radish cultivars (Objective 2).
ARS researchers prepared a NPGS Hemp Germplasm Characterization and Descriptor Handbook based on a thorough review of 368 peer-reviewed publications, trade journals, plus a stakeholder survey. The goal of this handbook is to assist breeders and other researchers in identifying accessions with specific traits, to facilitate the selection of germplasm in crop improvement programs, to designate and maintain a core collection of diverse materials, to identify duplicate accessions and reduce costs of hemp genetic resource conservation, to identify gaps in the existing collections and help formulate strategies for future collection and conservation efforts, and to increase stakeholder utility and accessibility of hemp germplasm resources (Objective 2). This handbook will set a precedence for evaluation and inclusion of associated fiber, oil, secondary metabolite, and other priority trait information within GRIN-Global.
In FY21, PGRU received one new short-day onion variety that is resistant to thrips; the seed is now available to order (Objective 1).
ARS researchers in Geneva, New York, participated in a collaborative project to support organic farming. The goal of the Northern Organic Vegetable Improvement Collaborative (NOVIC) is 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. Through virtual outreach over the internet in 2020, vegetable seed samples of cucumber, squash, tomato, and curly kale were available to order by any requestor, free of charge. Educational materials on seed-saving and where to find related online resources were also distributed over the internet. Vegetable seed for gardening has been in high demand during the global pandemic; this outreach helped to address the demands of gardeners and farmers to produce their own food, save the seed, and develop their own varieties (Objective 2).
Accomplishments
1. Critical vegetable crop seed maintained. Worldwide, vegetable breeders and other researchers need a ready source of genes to use to develop new, improved vegetable crops. ARS researchers in Geneva, New York, maintained 12,716 varieties of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, celery, tomatillo, asparagus, and other vegetables including related wild plants for the long-term needs of crop improvement. This provided the genetic 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, and ensured its availability in the long-term.
2. Seed produced for vegetable crops breeding, research, and education. There is a continuing need to grow, harvest, and store seed of vegetable crops and related wild plants to have seed available to provide necessary genes for crop improvement. This is due to the loss of seed stocks over time due to aging and the depletion of seed as it is sent out around the world for breeding, research, and education. ARS researchers in Geneva, New York, ensured sufficient quantities of seed of diverse vegetable crops were available for distribution. During FY2021, approximately 176 varieties of vegetables (cabbage, radish, tomato, onion, Brassica, winter squash, and celery) were planted for the purpose of producing seed by ARS researchers in Geneva, New York, and seed samples of 35 varieties (onion, winter squash) were sent to collaborators in Parlier, California, and Las Cruces, New Mexico, for seed production. This ensures that seed is freely available upon request for qualified users worldwide. ARS researchers in Geneva, New York, distributed 5,395 samples of vegetable seed to requestors in 180 orders during the calendar year 2020, and 4,128 samples in 124 orders from January – June 2021.
