2011 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.
In addition to standard characterization activity during routine regenerations, 52 tomato lines representing varieties from five different decades as determined by dates for PVPs were grown in Geneva, NY in 2011 for a second year of evaluation. These accessions were evaluated for fruit nutritional traits and morphology. In addition, we collaborated with Research Chemist (USDA-ARS) for performing high performance liquid chromatography of fruit samples which will be used for identification and measurement of nitrogen-containing metabolites.
A major undertaking to prepare samples of the entire cultivated tomato germplasm collection for preservation at the Global Seed Vault in Svalbard, Sweden was completed in FY2011. Approximately 6100 samples of tomato germplasm were prepared for preservation (500 seed per accession). This facility is a secure seedbank located on the Norwegian island of Spitsbergen and is located in an area of permafrost which will aid in preservation, even in the event of a power loss. This is a worldwide effort with more than 525,000 samples already stored.
A ‘core collection’ confers utility as a representative subset of a large collection of germplasm. A Plant Genetic Resources Unit (PGRU) core collection of tomato was assembled during 2011. Seed was obtained from IPK Gaterslaben, Tomato Genetics Resources Center (TGRC) and other sources for building a core collection of 185 accessions. The major components of the core were: heirloom, fruit shape diversity, landraces and ‘obsolete U.S.’ varieties. Phenotypic data including fruit quality components and agronomic traits were evaluated in the field. Molecular genetic variation was estimated using 18 single nucleotide polymorphisms (SNP). We and our collaborators are in the process of reporting these results at national conferences and in peer-reviewed publications. The manageable number of samples makes the core collection a useful tool for aiding in conservation and efficient use of the larger collection.
Heirloom tomatoes are old varieties that typically originated in home gardens or on family farms. These types are becoming increasingly popular with consumers due to their appealing shapes, textures and flavors. However, many varieties remain agronomically unimproved for traits such as disease resistance, stress tolerance and yield. With our collaborators, we are in the process of preparing a manuscript for peer-reviewed publication that characterizes 44 PGRU heirloom tomato accessions. The accessions were evaluated in the field in 2009 and 2010, genotyped using 18 SNP markers, and evaluated for fruit quality (vitamin C, lycopene, titratable acids, and brix). Using quantitative genetic analysis, all fruit quality traits were found to be heritable, with a genotype by environment interaction. Our results will assist breeders in choosing potential parents for continued improvement of heirloom varieties.
All these activities are in support of National Program 301 components 1 (Plant and Microbial Genetic Resource Management) and component 2 (Crop Informatics, Genomics, and Genetic Analyses) and are specified in the project’s three objectives.
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 2011 approximately 331 accessions were regenerated by ARS researchers at Geneva, NY, and 17 accessions of short day onions were regenerated at New Mexico State University through a cooperative agreement, 12 accessions of long day onions were regenerated at Nunhems, Inc., through a cooperative agreement; additionally, 147 biennial crop accessions were grown to produce plants for use in seed production in 2012. This allowed us to continue to distribute seed; 5559 seed lots of 3094 accessions were distributed in 502 orders (430 domestic and 72 foreign). This germplasm is available for use by qualified researchers and other bona fide users worldwide.
Published ‘AlleleCoder’, a software tool to help illustrate genetic diversity. With increasingly cheaper costs of DNA sequencing, new methods are required to analyze and interpret the enormous amounts of data that are being generated for applications in managing germplasm collections. We published a software tool and method that analyzes DNA sequences collected from plant samples and displays the results as points in a 3-dimensional, color-coded graph. Distances between the points, which represent individual plants, estimate the genetic relationships among the samples. Points near each other are closely related, while points distant from each other are more distantly related. ARS researchers at Geneva, NY, used this method to illustrate genetic relationships among 50 tomato populations conserved at Plant Genetic Resources Unit (PGRU). The results showed that populations originating from diverse geographical regions (North America, South America, Europe, Asia) were all rich sources of genetic diversity. This will aid in the conservation and exploitation of new alleles for tomato breeding and improvement.
Optimized work-flow for characterizing tomato fruit quality. PGRU conserves over 6,000 cultivated tomato (Solanum lycopersicum L.) lines that are made publically available for breeding and research through the National Plant Germplasm System (NPGS). An ongoing challenge is to characterize the collection for traits that are of interest to end-users. Recently ARS researchers at Geneva, NY, adopted and optimized laboratory methods to efficiently estimate fruit nutritional traits such as vitamin C (ascorbic acid), acidity, sugar content and lycopene content. Results were highly reproducible and we have found significant differences among genotypes for the various traits. These data will be made available through the Germplasm Resources Information Network http://www.ars-grin.gov/gen. We have made available the protocols and work scheme for efficiently assaying hundreds of samples during a field season. These protocols will be useful to other researchers interested in tomato fruit characterization, and our data will assist end-users in selecting PGRU material for breeding and crop improvement.
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 researchers at Geneva, NY, maintained approximately 12,513 accessions of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, other cole crops, celery, tomatillo, asparagus and other vegetables for the long-term and 3 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.
Labate, J.A., Robertson, L.D., Balch, T., Sheffer, S.M. 2011. Diversity and population structure in a geographical sample of tomato (Solanum lycopersicum L.) accessions. Crop Science. 51:1068-1079.
Baldo, A.M., Francis, D., Caramante, M., Robertson, L.D., Labate, J.A. 2011. AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis. Plant Genetic Resources: Characterization and Utilization. 10: 1-3.