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United States Department of Agriculture

Agricultural Research Service


Location: Plant Genetic Resources

2009 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
Phenotypically characterized tomato core collections (“landraces” and “geodiversity”) through field observations, collecting vine-ripened fruit, and optimizing and performing Vitamin C and lycopene assays in the lab. As part of an SCA with Ohio State University, phenotypic evaluations of a replicate set and SNP genotyping were carried out by his group. These data are being analyzed comparatively with an Ohio State University core set of fresh market, processing, and heirloom varieties. Hypotheses pertaining to centers of diversity and loss of diversity within modern breeding germplasm will be tested. A similar CGC grant is in progress for an heirloom core set in 2009. In collaboration with North Carolina State University, Ohio State University, and Cornell University, data will be collected from field trials in three locations.

Adopted and optimized a Real-Time PCR platform (Roche Light Cycler 480) for genotyping based on S. lycopersicum SNPs. We are applying a set of 12 markers to a set of putative duplicates and phenotypically evaluate the accessions in the field. The purpose is to evaluate genetic redundancy in duplicate accessions.

Analyzed DNA sequences for 50 genes in S. pimpinellifolium PI 370093 (source of Cf-2, Cf-3, Pto), S. habrochaites PI 125445 (B), and Peru Wild PI 303801(Ve), S. arcanum G 32951, S. peruvianum G 32592, S. peruvianum LA1537, and S. pennellii PI 414773. The purpose is to compare wild species’ alleles to S. lycopersicum to test hypotheses of linkage drag as a consequence of interspecific breeding for crop improvement.

PGRU L. peruvianum accessions will be reclassified into Solanum spp. based on the recently published Monograph by Peralta et al. (2008). Fifty accessions were grown in the greenhouse and keyed out. The entire collection is being grown in the field in 2009 and will be keyed out against known checks.

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. At Geneva, approximately 12,600 accessions of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, other cole crops, celery, tomatillo, asparagus and other vegetables were maintained for the long-term and 15 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 2009 approximately 269 accessions were regenerated at Geneva, NY and 84 accessions of short day onions were regenerated at New Mexico State University through a cooperative agreement; additionally, 170 biennial crop accessions were grown to produce plants for use in seed production in 2010. This allowed us to continue to distribute seed; 3574 seed lots of 2266 accessions were distributed in 362 orders (301 domestic and 61 foreign). This germplasm is available for use by qualified researchers and other bona vide users worldwide.

3. Identified mutations in tomato for improvement and protection: DNA diversity is known to be low in the tomato crop, this has severely limited the use of DNA-based tools for crop improvement within the 'cultivated tomato' gene pool. We studied 50 genes in diverse tomato lines conserved at PGRU. We discovered 188 total mutations in the genes. These mutations can serve as the basis for molecular tags for use in gene mapping and gene selection during crop improvement. The mutations also illustrate that conserved PGRU tomato populations can contribute to increased diversity of the tomato crop. New sources of diversity are important for continued crop improvement and protection against novel diseases, pests or environmental challenges.

4. Discovery of new sources of valuable tomato genes for variety improvement: Identifying sources of new genes within the tomato collection at PGRU will be valuable to breeders. We surveyed DNA sequences in a set of 30 accessions and one commercial type. Gene diversity was highest in populations that originated in Chile, Ecuador, and Peru. By comparing gene sequences to a wild tomato relative, we found evidence of cross breeding between the crop and wild tomato. Wild tomatoes are used extensively by breeders as sources of new genes. The PGRU populations are valuable in that many of the undesirable properties of wild tomatoes (for example small, green fruit) were previously eliminated either naturally or with the aid of humans. Observed patterns of gene diversity discovered in this study will be helpful to geneticists working on improving the crop in the future.

5.Significant Activities that Support Special Target Populations
There is need for increasing the proportion of US agriculture that is managed organically. A RCA (Northern Organic Vegetable Improvement Collaborative) with Oregon State University (funded by the Integrated Organic Program of the CSREES) provides support to PGRU for training of organic farmers and small seed producers in small-scale seed production of heirloom and new publicly improved vegetable varieties, whose production has been limited because of lack of seed. PGRU has the lead role in offering training and assistance in small-scale seed production of heirloom vegetable germplasm and new publicly bred, open-pollinated varieties to small-scale seed producers, organic farmers and the organic community. The introductory workshop for this project was held 25-27 September 2009 at the Common Ground Country Fair in Unity, Maine. The Common Ground Country Fair is attended by greater than 60,000 people, giving much exposure to the RCA and for PGRU. During the three day fair, PGRU staff conducted 3 hands-on demonstrations each day. Once the fair concluded, PGRU staff traveled to Highmoor Farm in Monmouth, ME September 28, 2009 for a selection and seed processing workshop targeting organic farmers. Highmoor Farm is part of the University of Maine’s Agricultural and Forest Experiment Station. This workshop provided vital training in small-scale seed production to growers and organic farmers interested in incorporating seed production into their existing farm systems. This has increased the availability of heirloom and new publicly bred germplasm for use by small and organic farmers. We expect to strengthen long-term partnerships between public and non-profit institutions, private industry and organic farmers. This network will be the foundation for a long-term support to both organic variety development and organic variety trialing. Through the workshops, participatory plant breeding and seed processing publications and eOrganic outreach activities, we expect a significant number or organic growers to become more educated on participatory breeding, seed production and trialing methods, allowing them increased autonomy to initiate projects or to participate effectively on projects with farmers. Working with eOrganic technical staff, we will be able to create a database of organic variety trial information and seed production techniques.

6.Technology Transfer

Number of Web Sites Managed1
Number of Other Technology Transfer3

Review Publications
Labate, J.A., Robertson, L.D., Wu, F., Tanksley, S.D., Baldo, A.M. 2009. EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato (Solanum lycopersicum). Journal of Theoretical and Applied Genetics. 118:1005-1014.

Labate, J.A., Robertson, L.D., Baldo, A.M. 2009. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.). Heredity 103:257-267.

Last Modified: 4/20/2014
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