Location: National Clonal Germplasm Repository
2022 Annual Report
Objectives
1: Efficiently & effectively acquire priority temperate-adapted fruit, nut, & other specialty crop genetic resources; maintain their safety, genetic integrity, health & viability; & distribute them & associated information worldwide. 1A Research heritage cultivars to broaden knowledge of the historical cultivar base. Analyze NCGR-Corvallis crop wild relative collections for gaps in taxa, localities, & diversity. 1B Acquire international & domestic germplasm samples of Corylus, Fragaria, Humulus, Pyrus, Mentha, Ribes, Rubus, Vaccinium, & their crop wild relatives via plant exploration & exchange. Fill gaps, & as opportunities arise through country agreements, acquire elite/enhanced breeding lines & heritage cultivars. 1C Efficiently & effectively establish & maintain crop genetic resources emphasizing temperate fruit, nut, & specialty crop germplasm. Identify duplication & eliminate unnecessary redundancy to maximize efficient germplasm management. 1D Distribute germplasm during the appropriate season for each crop to national & international researchers at public & private institutions & to educational groups.
2: Develop more effective genetic resource maintenance, backup, pathogen testing, & pathogen-elimination methods & apply them to priority temperate-adapted fruit, nut, & other specialty crop genetic resources. 2A Develop improved methods for conservation of temperate crop germplasm in field plantings & container production in protected environments; particularly examining pruning, media, irrigation & integrated pest management. 2B Collaborate with scientists at remote locations to improve backup conservation methods for our 8 primary genera, including growing plants in field plantings, tissue culture storage, & long term cryopreservation. 2C Apply bioassay, ELISA, & develop improved RT-PCR tests for important viruses, viroids, & phytoplasmas in primary plant collections. 2D Eliminate pathogens from select accessions with improved methods for heat therapy & meristem culture.
3: With other NPGS genebanks & Crop Germplasm Committees, develop, update, document, & implement best management practices & Crop Vulnerability Statements for priority temperate-adapted fruit, nut, & other specialty crop genetic resource & information management.
4: Develop more effective genetic resource characterization & evaluation methods, & apply them to priority temperate-adapted fruit, nut, & other specialty crop genetic resources. Record & disseminate characterization & evaluation data via GRIN-Global & other data sources. 4A Establish baseline genetic profiles for core collections with existing DNA fingerprinting sets & develop or optimize fingerprinting sets & enter information to databases. 4B Implement new high throughput genotyping systems in genetic diversity assessment (Fragaria, Pyrus), linkage & trait mapping (Rubus, Fragaria & Pyrus) and phylogenetic analysis (Rubus) & enter information to databases. 4C Develop & apply DNA tests that help identify phenotypes or useful horticultural traits for Fragaria, Rubus & Pyrus. 4D Evaluate phenotypes of flowering, ploidy, disease resistances, & upload data & image characterization to GRIN-Global.
Approach
Objective 1: Acquire, maintain, and distribute germplasm
The NCGR-Corvallis is responsible for temperate fruit, nut, and specialty crop genera: Corylus, Fragaria, Humulus, Mentha, Pyrus, Ribes, Rubus, and Vaccinium, as primary collections, and Actinidia and Juglans (J. cinerea) as security backup for other genebanks. Limited amounts of crop wild relative reference collections are also preserved. Primary collections are maintained in greenhouses, screenhouses, field, and as seed. Wild species are maintained as seed stored at -18 C, with some living plant representatives. Heritage cultivars and selections are maintained as clones. Gaps in the collections are determined by research using botanical and horticultural references and species analysis software, as well as referrals through scientific colleagues. New accessions are obtained through plant exploration and exchange. When new accessions are received, information is entered to GRIN-Global and the plant is propagated. Identity is checked by morphology. Orders are received through GRIN-Global and processed in the appropriate season for the crop and plant form, according to requestor needs. Phytosanitary certification is obtained and materials are distributed according to international, regional, and local plant importation regulations.
Objective 2: Improved maintenance, secure backup
Inventory locations are maintained in GRIN-Global. Clones are re-propagated according to crop to maintain vigor. Pathogen status is evaluated and recorded. Core collections are established and maintained in tissue culture (for backup and distribution); protocols for cryopreservation of dormant buds of the woody plants are being established. Backup greenhouse collections are maintained for the pear and pear relative field collections. Alternative backup procedures and remote backup locations are arranged and recorded. Coordination of in situ conservation of native US germplasm is continuing with other agencies.
Objective 3: Vulnerability statements and operations manual
Are prepared by the curator in collaboration with the Crop Germplasm Committees. Statements for the currants, gooseberries, mint, hops, and pears will be completed. Statements for strawberries, blackberries, raspberries, have been completed and will be annually updated. Statements are reviewed and revised by expert committees. Approved statements are uploaded to GRIN-Global. The operations manual for the unit will be updated.
Objective 4: Characterization and evaluation
Cultivar identification will be expanded with new markers and sequencing techniques. Identity of genotypes is being compared globally with clones in other genebanks. Phenotypes of accessions are being evaluated and linked with genotypes. Linkage maps and QTL association are being used for the development of marker-based tests for germplasm characterization traits of crops in the NCGR collection.
Progress Report
The USDA ARS National Clonal Germplasm Repository in Corvallis, Oregon, is a genebank that conserves temperate fruits, nuts, and specialty crops for research reference. The genebank continues to conserve more than 12,600 unique plant specimen of eight genera of horticultural and agronomic crops along with their wild relatives. This genebank is assigned to conserve hazelnuts, strawberries, hops, mint, pears, currants, gooseberries, blackberries, raspberries, blueberries, and cranberries. The primary collections are a library of living plants, maintained as orchards in the field, containerized plants in the screenhouse, or seeds representing species populations. Seeds are preserved in freezers on-site and off-site in Fort Collins, Colorado, and Spitsbergen, Norway. Valuable or vulnerable accessions are backed up as dormant buds, or shoot apices under cryogenic conditions at a collaborating site in Fort Collins, Colorado. A subset of the hazelnut collection is planted in collaboration at an ARS site in Parlier, California. In addition, duplicate collections of kiwifruit and butternuts are planted in Corvallis for the ARS Davis, California, genebank and of rhubarb for the ARS genebank Pullman, Washington.
In support of Objective 1, two plant exploration trips were taken and included a trip to western Colorado to collect wild North American hop resources and to Virginia to obtain blueberry and other fruit crop wild relatives. These combined trips resulted in an increase of 111 new accessions to our strawberry, blueberry, hop, blackberry, raspberry, currant and gooseberry collections and 43 plant vouchers from up to 22 taxa to the U.S. National Arboretum, Washington D.C. In addition to these expeditions, we worked with collaborators to obtain over 450 new accessions to add to our collections and ensure threatened plant species are properly conserved. After establishment, plant and seed accessions were preserved at the genebank in Corvallis, Oregon, and more than 31,000 unique plant specimen were distributed in 4,377 orders to stakeholders throughout the world for research purposes. Up to 4,492 images of fruit, plant, and their characteristics, and approximately3,500 genotypic and 18,513 phenotypic observations were made publicly available through the GRIN-Global database for use by researchers worldwide.
In support of Objective 2, ARS researchers identified blueberry cultivars that are potentially resistant to Blueberry shock virus; blueberry species that are resistant to the spotted wing drosophila fruit fly; pear and quince trees that are tolerant to leaf spot, rust, mildew and fireblight, and black currant accessions that are free of Black currant reversion virus. Forty-eight strawberry plants were found to be infected with Strawberry mild yellow edge virus. Virus-free strawberry plants were established using young apex culture. Virus-free plant representatives were also established from 18 virus-infected hop accessions. These virus-free plants replaced the infected plants in the respective collections. We also collaborated with ARS scientists at Fort Collins, Colorado, to establish a cost and time-effective protocol for back-up of important pear, currant and gooseberry trees/plants through cryopreservation of dormant buds.
In support of Objective 3, ARS researchers developed Crop Vulnerability Statements for currant, gooseberries and strawberries and made them publicly available through the Small Fruit Crop Germplasm Committee website. These reports encompass biological features, ecogeographic distribution of species, genetic basis of crop production, tribal use of primitive forms, economics of domestic and international production, crop vulnerabilities and threats, genetic uniformity, biotechnology of breeding, genetic erosion in situ, current and emerging biotic and abiotic threats, germplasm accessibility, genebank resources, holdings, gaps, designations of primary secondary and tertiary crop wild relatives, acquisition process, distribution and outreach, future goals, and facilities and equipment needed for ex situ conservation.
In support of Objective 4, the molecular genetics laboratory at the genebank developed DNA fingerprinting sets and used them to establish databases of genetic profiles for economically important blueberry, blackberry, hazelnut, hop, pear, and strawberry cultivars in the collection. In addition, we developed and implemented new genotyping techniques to identify and confirm chromosomal locations of fire blight resistance in pear, sweetness in blackberry, and continuous flowering and charcoal rot resistance in strawberry. DNA-based diagnostic tests were established for crown rot resistance in strawberry and existing DNA tests for strawberry were compiled and documented in a publicly available DNA Testing Handbook for strawberry. Plant and fruit quality characteristics were determined for over 280 cultivars of strawberry and data was entered into the Germplasm Resources Information Network (GRIN) database for public accessibility.
Accomplishments
1. Analyses of phenotypic data in strawberry identifies cultivars with superior characteristics. Strawberry is one of the most widely produced and consumed fruits worldwide and provides significant nutritional value. The gene pool of some breeding programs over the past decades has tended to include a reliable but limited set of well-known cultivars. The ARS National Clonal Germplasm Repository in Corvallis, Oregon, contains a collection of a diverse set of strawberry cultivars and some could have desirable traits that can be used by breeders to expand the genepools of their breeding material. The researchers generated phenotypic data over two years for 16 traits in a diversity set of 284 cultivated strawberry accessions. Traits included phenology, plant morphology, and fruit quality traits at full ripeness. Analyses of this data identified two selections and one cultivar with a combination of the highest fruit quality traits, a cultivar with a large number of daughter plants, and two cultivars with a relatively short ripening time. This data is valuable for researchers and breeders to select cultivars and selections with desired traits.
2. Bioinformatic tools and blueberry sequence variants detected for development of a dense genotyping tool for blueberry. Blueberry is an important fruit crop that lacks a dense genotyping tool to assist researchers in identifying chromosomal regions that control traits of economic importance. Development of such a tool is the first step towards facilitating DNA-based molecular breeding and eventual release of cultivars with novel and desirable traits. In collaboration with the scientific community in the United States and New Zealand, ARS researchers at the National Clonal Germplasm Repository in Corvallis, Oregon, obtained blueberry DNA sequences and new genome sequences and identified 50,000 chromosomal locations in blueberry to test for establishing a universal genotyping platform for this important fruit crop. This universal genotyping platform is a valuable tool for the blueberry scientific community and will lead to significant advances in blueberry breeding and cultivar release.
3. DNA-based fingerprinting sets identify true-to-type, mis-identified and unknown hop cultivars. Hop cultivars are difficult to identify using vegetative traits, as grown in a genebank setting. The United States National Hop Collection is maintained by ARS researchers in Corvallis, Oregon, and serves as a valuable source of novel and disease resistant genes for breeders, along with being an important resource to researchers across multiple disciplines. The ARS researchers developed and implemented two DNA tests in hop and used them to establish a database of fingerprints for 603 accessions from the ARS collections. This allowed them to classify 171 hop accessions as true-to-type (TTT) or clones, and determine that 42 accessions had been previously mis-identified. When compared to genotypes of 26 unknown plants from a collection used to breed local cultivars for brewing from Lincoln, Nebraska, 24 had genetic profiles that suggested they are likely to be unique. Two samples had the same genotype as ‘Cascade’, one had a genotype that matched ‘Chinook’, and two were duplicates. Comparison of genetic profiles of unknown hop plants to those in this database will allow researchers to confirm identity of these plants and properly deploy these genotypes in their breeding programs.
Review Publications
Edger, P.P., Iorizzo, M., Bassil, N.V., Benevenuto, J., Ferrao, L.F., Giongo, L., Hummer, K.E., Lawas, L.F., Leisner, C.P., Li, C., Munoz, P., Ashrafi, H., Atucha, A., Babiker, E.M., Canales, E., Chagne, D., DeVetter, L., Ehlenfeldt, M.K., Espley, R.V., Gallardo, K., Gunther, C.S., Hardigan, M.A., Hulse-Kemp, A.M., Jacobs, M.L., Lila, M., Luby, C.H., Main, D., Mengist, M.F., Owens, G.L., Perkins-Veazie, P., Polashock, J.J., Pottorff, M., Rowland, L.J., Sims, C.A., Song, G., Spencer, J., Vorsa, N., Yocca, A.E., Zalapa, J.E. 2022. There and back again; historical perspective and future directions for Vaccinium breeding and research studies. Horticulture Research. 9. Article uhac083. https://doi.org/10.1093/hr/uhac083.
Willman, M.R., Bushakra, J., Bassil, N.V., Finn, C.E., Dossett, M., Perkins-Veazie, P., Bradish, C.M., Fernandez, G.E., Weber, C.A., Scheerens, J.C., Dunlap, L., Fresnedo-Ramirez, J. 2022. Analysis of a multi-environment trial for black raspberry (Rubus occidentalis L.) quality traits. Genes. 13(3). Article 418. https://doi.org/10.3390/genes13030418.
Driskill, M.J., Pardee, K., Hummer, K.E., Zurn, J., Amundsen, K., Wiles, A., Wiedow, C., Patzak, J., Henning, J.A., Bassil, N.V. 2022. Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers. PLoS ONE. 17(4). Article e0257746. https://doi.org/10.1371/journal.pone.0257746.
Redpath, L., Aryal, R., Lynch, N., Spencer, J.A., Hulse-Kemp, A.M., Ballington, J.R., Green, J., Bassil, N.V., Hummer, K.E., Ranney, T., Ashrafi, H. 2022. Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids. Scientia Horticulturae. 297. Article 110955. https://doi.org/10.1016/j.scienta.2022.110955.
Zurn, J., Hummer, K.E., Bassil, N.V. 2022. Exploring the diversity and genetic structure of the U.S. national cultivated strawberry collection. Horticulture Research. 9. Article uhac125. https://doi.org/10.1093/hr/uhac125.
