Page Banner

United States Department of Agriculture

Agricultural Research Service

Related Topics


Location: Plant Genetic Resources Research

2010 Annual Report

1a. Objectives (from AD-416)
1. Strategically expand the genetic diversity in genebank collections and improve associated information for priority buckwheat, tomato, cole crops, bulb and bunching onions, and other specialty vegetable crops (celery, radish, asparagus, winter squash, and tomatillo) and their wild relatives. 2. Conserve and regenerate priority buckwheat, tomato, cole crop, bulb and bunching onion, and other specialty vegetable crop (celery, radish, asparagus, winter squash, and tomatillo) genetic resources efficiently and effectively, and distribute pathogen-tested samples (whenever feasible) and associated information worldwide. 3. Strategically characterize (“genotype”) and evaluate (“phenotype”) priority buckwheat, tomato, cole crop, bulb and bunching onion, and other specialty vegetable crop (celery, radish, asparagus, winter squash, tomatillo) genetic resources for molecular markers and highly heritable horticultural and morphological traits.

1b. Approach (from AD-416)
The objectives of this project will be met by a) expanding the genetic diversity in genebank collections and improving associated information for priority buckwheat, tomato, cole crops, bulb and bunching onions, and other specialty vegetable crops (celery, radish, asparagus, winter squash, and tomatillo) and their wild relatives, b) conserving and regenerating genetic resources of these taxa efficiently and effectively, and distributing pathogen-tested samples (whenever feasible) and associated information worldwide, and c) characterizing (“genotype”) and evaluating (“phenotype”) genetic resources of these taxa for molecular markers and highly heritable horticultural and morphological traits. In the next five years the major activities of the project will emphasize upgrading standards for viability and number of seed stored in the active and base collections. Characterization for minimal descriptor lists will be completed for tomatoes, Crucifers, and onions. The primary link with users will be through Crop Germplasm Committees that define crop priorities for collection and evaluation.

3. Progress Report
Wild tomato Lycopersicon peruvianum has been reclassified into four new Solanum spp. taxa. We grew 120 PGRU accessions in the field in 2009 and reclassified them using the new taxonomic keys. Leaves, flowers and fruits of all accessions were scanned. The reclassification of wild tomato accessions based on their revised taxonomy will ensure that stakeholders can obtain field-verified material. In addition to standard characterization activity during routine regenerations, 51 tomato lines were grown in Geneva, NY in 2010 as part of a ‘fruit shape diversity’ National Science Foundation grant awarded to (The Ohio State Univ). We evaluated these lines plus 52 obsolete varieties for fruit nutritional traits and morphology. In addition, we collaborated with Research Chemist (USDA-ARS) for performing precision assays on tomato fruit samples in a subset of these lines. High performance liquid chromatography will be used for identification and measurement of nitrogen-containing metabolites. These compounds regulate chemical processes and influence fruit ripening and fruit quality in various crops and are an important class of natural products that contribute to quality and utilization and include essential nutrients that can influence mood and mental well-being. Based on passport data, we estimate that 15% or more of the 5,800 accessions of domesticated tomato at the PGRU may be unwanted duplicates. Molecular markers are one line of evidence to support de-accessioning of materials, but the process of refining holdings does not rely solely on molecular genotyping of accessions. We use a two-pronged approach to identify duplicates. First, passport data, especially plant IDs, have been used to identify putative duplicates for de-accessioning. Second, molecular genetic methodologies for identification of duplicates are being designed and applied. We have completed genotyping of 46 representative samples of duplicate San Marzano, Baltimore and Globe varieties using 17 single nucleotide polymorphism (SNP) markers and are in the process of data analysis for reporting. Markers and methodologies that were developed and tested during this project plan will be used to genotype putative duplicate accessions in future project plans. Tomato breeders and researchers have observed that genetic variation within tomato is oftentimes associated with genes that were introduced by breeding with wild tomato species, so-called “introgressions”. In some instances, introgressions of valuable genes such as disease resistance have been correlated with undesirable effects on the crop such as reductions in yield. We have completed analysis of 50 genes in wild tomato species in order to compare them to cultivated tomato genes to study the consequences of introgressions. All data have been scored and are currently being analyzed by a second software program to ensure quality control and high confidence in the results. This study will provide estimates of the extent of introduction of unwanted genes into tomato as a result of crosses with wild relatives, and will help improve methods for eliminating unwanted wild genes using molecular markers.

4. Accomplishments
1. Maintained genetic resources of vegetables for crop improvement and research: Genetic resources are the diverse plant varieties and lines maintained in a collection that provide the genes needed for crop improvement and research. Worldwide, vegetable breeders and other researchers need a ready source of genes to use to provide new vegetable varieties that have disease and pest resistance, tolerance to abiotic stresses, increased quality, and improved nutrition. ARS scientists at Geneva, NY maintained approximately 12,475 accessions of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, other cole crops, celery, tomatillo, asparagus and other vegetables for the long-term and 18 new accessions were acquired. This provided the genetic diversity needed to develop vegetable varieties with disease and pest resistance, tolerance to abiotic stresses, and varieties with improved quality and nutrition; and ensured its future availability in the long-term.

2. Ensuring sufficient quantities of seed of vegetable genetic resources are available for distribution: There is a continuing need for regeneration of vegetable varieties, wild plants, and researcher’s lines to have seed available for crop researchers that provide necessary genes for crop improvement and research. This is due to loss of viability over time and the usage of seed as it is distributed for crop improvement and research. During FY 2010 approximately 371 accessions were regenerated by ARS researchers at Geneva, NY and 56 accessions of short day onions were regenerated at New Mexico State University through a cooperative agreement; additionally, 142 biennial crop accessions were grown to produce plants for use in seed production in 2011. This allowed us to continue to distribute seed; 3673 seed lots of 2497 accessions were distributed in 299 orders (225 domestic and 74 foreign). This germplasm is available for use by qualified researchers and other bona vide users worldwide.

3. Evaluated gene diversity and fruit quality in a global sample of tomato: Tomato, due to its high consumption, is an important source of vitamins and minerals in the human diet. As such, improvement of fruit quality and nutritional value are important goals. The nutrient lycopene, which gives the red fruit color, is believed to reduce risk of certain cancers and chronic diseases. ARS researchers at Geneva, New York completed a study to help predict where to find new genes in the tomato seed collection that influence traits such as lycopene. We compared tomato lines that originated in different parts of the world (Europe, USA/Canada, Mexico/Central America, Asia or South America). We found that South America showed slightly more gene diversity than the other regions. Traits such as lycopene, vitamin C, sugar, color, size and shape were highly diverse in our sample. South American germplasm seems promising as a source of new genes but, based on overall results, no geographical region should be viewed as a poor source of new genes to help improve the crop.

4. Nutritional characterization of heirloom tomato germplasm: Heirloom tomato varieties are appealing through their diverse range of color, size, shape, texture and flavor. Heirlooms are mostly unimproved for traits such as yield or disease resistance; as such they are attracting efforts of breeders for creation of specialty varieties. Characterization of the heirloom tomato varieties maintained by ARS researchers in the Plant Genetic Resources Unit in Geneva, New York tomato collection will increase its value to breeders and help them make choices of which varieties to work on. Replicate plots of 44 heirloom varieties were grown in three locations (Ohio, North Carolina and New York) in 2009. Data were collected for horticultural traits and fruit quality traits ascorbic acid (vitamin C), lycopene, titratable acids and brix. We have found significant differences among varieties and among locations in the traits. The results will lead to new, improved tomato varieties that retain many of the desirable heirloom traits.

5. Significant Activities that Support Special Target Populations
The Northern Organic Vegetable Improvement Collaborative (NOVIC) is the result of a new Reimbursable Cooperative Agreement (RCA) with Oregon State University, USDA, ARS – Plant Genetic Resources Unit in Geneva, NY, Cornell University’s Department of Plant Breeding and Genetics, the University of Wisconsin, Washington State University and the Organic Seed Alliance. This RCA 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 the NOVIC RCA is centered on outreach activities and training in small-scale seed production and processing. In addition to providing training in seed production, PGRU is also responsible for the dissemination of information concerning winter squash pollination techniques, methods of preventing undesired outcrossing and how to best harvest and store winter squash seed to the traditionally underserved organic farming community. This information will be available through the Organic Seed Partnership website (, eOrganic (, eXention ( and during workshops and presentations. The OSP website has been updated to reflect the NOVIC goals and events and has had over 1,800 hits since March 2010. The site has been viewed by stakeholders in 38 countries and in 20 different languages. For FY10, three events were held at the Common Ground Country Fair, Unity, ME to help organic farmers and small-scale seed producers in farmer-led participatory plant breeding and seed production. In August 2010, a one-day plant breeding and seed production workshop was held at Cornell University’s organic farm in Freeville, NY. In September 2010, PGRU staff returned to the Common Ground Country Fair in Unity, ME for three days of seed production training and during the same weekend in September, additional PGRU staff will be presented NOVIC at the Mother Earth News Fair in Seven Springs, PA for the first of what PGRU hopes to be an additional annual trip to enhance the education of organic farmers in seed production and work accomplished through the NOVIC RCA.

Review Publications
Kopsell, D.A., Carl, S., Deyton, D., Abney, K., Kopsell, D., Robertson, L.D. 2010. Characterization of Nutritionally Important Carotenoids in Welsh Onion Accessions. HortScience. 45(3):463-465.

Last Modified: 05/26/2017
Footer Content Back to Top of Page