Location: Plant Genetic Resources Unit (PGRU)
2020 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 GRIN-Global and other data sources, and Objective 3 - with other 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, 148 types of vegetable crops and their wild relatives are managed by ARS researchers in Geneva, New York, in the form of more than 12,700 seed samples 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 2019, three commercially developed, expired PVP vegetable stocks were newly acquired consisting of two radish and one cauliflower. A broccoli x Chinese kale mapping population represented by 175 inbred lines was also acquired to add to PGRU’s collection (Objective 1). During the 2020 growing season, approximately 159 varieties of vegetables (cabbage, radish, tomato, onion, buckwheat and celery) were planted for the purpose of producing seed by ARS researchers in Geneva, New York, and seed samples of 40 varieties (onion, winter squash) were sent to collaborators in Parlier, California, and Las Cruces, New Mexico, for seed production (Objective 1). We backed up 501 accessions in 2019 at the National Laboratory for Genetic Resource Preservation (NLGRP), including cole crops, mustard, onion, radish, tomato and winter squash (Objective 1). ARS researchers in Geneva, New York, distributed 10,340 samples of vegetable seed to requestors in 239 orders during 2019, and 2,859 samples in 89 orders from January – June 2020 (Objective 1).
ARS researchers in Geneva, New York, participated in a genetic diversity study of pumpkins, squashes and gourds. The interrelationships and geographical ranges of the crops’ wild relatives were studied. The potential ranges of all 16 currently known wild relatives were modelled and their conservation status was assessed. Ecology and geographic information were used to examine their potential adaptations to abiotic stresses. Substantial ecogeographic variation was observed both across types and between populations within types, with respect to low temperatures, high and low precipitation, and other adaptations of potential interest for crop breeding. These results help further the understanding of genetic relationships needed for continued improvement of this highly diverse and economically valuable set of vegetable crops (Objective 2).
ARS researchers in Geneva, New York, acquired a broccoli x Chinese kale mapping population consisting of 175 inbred lines. The lines are fully characterized using 1,881 DNA markers. Seed will be made available from the USDA National Plant Germplasm System so that this population can be used by the research and education communities. Allocations of five seeds per line will be available to requestors for free (Objective 1). The population is valuable as a research and teaching tool in numerous ways. The relatively short time from sowing seed to flowering plants means that a research project can be completed within several months. The same set of plants can be used by several teams, each analyzing a different set of traits. For example, evaluation of nutritional quality and flower structure could be conducted concurrently using the same plants. Studies of this population will contribute to knowledge needed for the continued successful breeding of superior vegetable varieties (Objective 2).
ARS researchers in Geneva, New York, participated in a genetic diversity study of onion. Onion is an ancient crop that is economically valuable throughout the world. The life cycle of onion requires two years to complete with bulb formation in year one and flowering in year two. Onion varieties are closely tailored to their growing environments because of day length, insect pollinators, and other requirements needed for successful bulb, flower and seed formation. These requirements present challenges for breeding and improving onion varieties. We performed partial genome sequencing on several onion breeding lines and 94 onion strains 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 onion breeding (Objective 2).
ARS researchers in Geneva, New York, participated in a multiregional project to support organic farming. The demand for organic food in the U.S. continues to increase at two to three times the rate of demand for non-organic food and a large portion of this is organic vegetables. Farmers lack access to a wide array of certified-organic seed and vegetable varieties adapted to organic conditions. The Northern Organic Vegetable Improvement Collaborative (NOVIC) was established to increase the diversity and choice 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 outreach events and workshops, education was provided to growers to enable them to produce their own seed and to breed their own crop varieties. Outreach activities have occurred in about a dozen states through plant breeding workshops, and videos and publications are freely available online (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 12,700 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 FY2020, approximately 159 varieties of vegetables (cabbage, radish, tomato, onion, buckwheat, and celery) were planted for the purpose of producing seed by ARS researchers in Geneva, New York, and seed samples of 40 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 10,340 samples of vegetable seed to requestors in 239 orders during the calendar year 2019, and 2,859 samples in 89 orders from January – June 2020.
