Location: Plant Genetic Resources Research2011 Annual Report
1a. Objectives (from AD-416)
1. Strategically expand the genetic diversity in genebank collections and the quality and quantity of associated information for priority cold hardy grape, tart cherry, and apples and their wild relatives. 2. Conserve and regenerate priority cold hardy grape, tart cherry, and apple genetic resources efficiently and effectively, and distribute samples and associated information worldwide. 3. Strategically characterize ("genotype") and evaluate ("phenotype") priority cold hardy grape, tart cherry, and apple 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) Surveying existing domestic and international collections of Vitis, Malus, and Prunus (tetraploid cherry) to identify material that would refine and fill gaps in NPGS collections; b) acquiring new accessions of wild species and heirloom cultivars, and as appropriate, genetic stocks of apple, cold-hardy grape, and tart cherry that have been extensively characterized genetically; c) enlisting genetic marker and other information to refine the holdings of the preceding priority genera by de-accessioning materials that are misidentified or unnecessarily redundant; d) conserving, regenerating, and distributing cold hardy grape, tart cherry, and apple genetic resources and associated information; e) backing up primary collections of cold hardy grape, tart cherry, and apples via nursery plantings, cryopreservation, and seed samples; f) developing and applying genetic markers for phylogenetic and genetic diversity analyses, emphasizing SSRs and sequence-based markers in cold hardy grape, tart cherry, and apples; g) generating SSR fingerprints for all priority accessions (ca. 5,000) of cold hardy grape, tart cherry, and apples and use them to determine the identity, diversity, phylogeny, and systematics of these genetic resources, and to enhance the effectiveness of genetic resource management; and h) incorporate characterization data into GRIN and other databases, and evaluating in collaborative research program, highly heritable traits of cold hardy grape, tart cherry, and apples according to CGC-approved descriptors, and incorporate data into GRIN and other databases. The primary link with users will be through Crop Germplasm Committees that define crop priorities for collection and evaluation.
3. Progress Report
Maintenance and delivery of germplasm to clients and stakeholders is the primary objective in this project. Approximately 9,000 accessions of apple, grape and tart cherry were maintained in the field repositories and 2,879 accessions were further safeguarded in cryopreservation storage at Ft. Collins, CO. Characterization of the germplasm collections is another important objective in this project. We started quality characterization of the tart cherry collection in 2011 with samples taken for two trees per accession that were flash frozen in liquid nitrogen for further evaluation of polyphenolic compounds (anthocyanins, melatonin, and serotonin) by HPLC. Additional data was also taken on fruit weight and color. Titratable acidity is an important trait for apple improvement. In 2011 we started characterization of the apple germplasm collection for titratable acidity using the apple core collection (approximately 280 accessions). We also continued digital imaging of the apple and grape collections. In order to increase resolution and cross-talk between the USDA apple collection and the European collections three additional SSR markers (CH01h01, CH01f02, and CH02d08) vetted for low error rates were applied to 2,400 samples in the main U.S. collection representing Malus x domestica and Malus species accessions. We continued our effort in grape germplasm evaluation. We extracted DNA from approximately 400 vines to complete the SSR fingerprinting of all grapevines in the collection and to address collection management questions. In addition, we took approximately 3,000 each bud break and bloom date observations and started taking observations on veraison date (fruit ripening). In a collaborative project, we characterized 36 polyphenols for 340 V. vinifera accessions from the USDA-ARS Clonal Repository at Davis, California and 200 wild accessions of mainly native species from the Geneva repository. A paper has been accepted for publication by Food Chemistry. These secondary metabolites are important to human nutrition and health. We also supported a project for indexing of our grape germplasm collections for 17 economically important grape viruses and strains. The entire grape collections (approximately 3000 vines) were screened. 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.
1. Provision of unique genetic sources of apple, grape and tart cherries to fruit breeders and researchers for crop improvement. Genetic resources of apples, grapes and tart cherries need to be maintained in the collection to provide the genes needed for crop improvement and research. ARS researchers at Geneva, NY,distributed 194 orders for 1492 apple and tart cherry accessions and 78 orders for 367 grape accessions. These distributions will contribute to the new breakthroughs of fruit research in both US and the rest of the world.
2. Use of cryogenic storage for conservation of apple genetic resources. To provide additional safeguard for apple germplasm, ARS researchers at Geneva, NY, have 2,879 accessions of the collections backed up at NCGRP through cryogenic preservation of dormant buds. Presently 2,804 of 6,600 apple accessions in the main collection are backed up. Through this effort, the apple and tart cherry germplasm are well secured for future needs of varietal improvement.
3. A phylogenomic analysis of the grape genus. The genus Vitis contains upwards of 60 wild species relatives that harbor genes to resist biotic and abiotic stresses and also genes for novel fruit characteristics. ARS researchers at Geneva, NY, studied with a Chinese collaborator the genetic structure, relationships, and evolutionary history of the genus using DNA sequences of 27 gene fragments of 43 species. This information was used to correct the taxonomic identification of a number of accessions in the Vitis clonal repositories at Davis, CA, and Geneva, NY, which will lead to a more efficient use of the germplasm collection of grapes for developing improved varieties. This research also showed a tremendous genetic wealth in the genus which can be exploited to developed improved grape varieties.
4. Screen grape germplasm collection for polyphenols. Polyphenols (anthocyanins, flavonols, etc.) are important nutritional and quality traits for grape consumption. In collaboration with Cornell University scientists, ARS researchers at Geneva, NY, investigated variation in 36 polyphenolic compounds in 344 Vitis vinifera germplasm accessions held in Davis, CA, for two consecutive years. A wide range of values for the polyphenols was found. The identification of a number of accessions with much higher concentrations of various polyphenols will allow grape breeders to enhance and improve the composition and content of these compounds in wine and table grapes which will result in an improved nutritional value for consumers of wine and grapes.