Location: National Clonal Germplasm Repository
2018 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
This report documents progress for project 2072-21000-049-00D, which started February 2018 and continues research from project 2072-21000-044-00D, "Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information."
The USDA ARS National Clonal Germplasm Repository, Corvallis, Oregon, is a genebank that conserves temperate fruits, nuts, and specialty crops for research reference. The genebank continues to conserve more than 12,000 accessions of 30 genera of horticultural and agronomic crops. It is the repository for hazelnuts, strawberries, hops, mint, pears, currants, gooseberries, blackberries, raspberries, blueberries, cranberries and their crop wild relatives. The primary collections are like a library of living plants, maintained as orchards in the field, or containerized plants in the screenhouse, or seeds representing species populations. Seeds are preserved in freezers to extend their viability. Alternative secondary storage is maintained on-site through tissue cultures preserved under refrigeration at a collaborating site, Ft. Collins, Colorado. A subset of the hazelnut collection is planted at an ARS site in Parlier, California. In addition, back up collections of kiwifruit and butternuts are planted in Corvallis for the Davis, California genebank.
More than 5,700 accessions were shipped during the year to researchers throughout the world. The ARS researchers worked with the requestors and quarantine inspectors to ensure that the plant materials met importation permit requirements and had USDA phytosanitary certification, when required.
A plant exploration was taken to Virginia during the reporting period to obtain blueberry and other fruit crop wild relatives to expand the diversity of the collection.
The molecular genetics laboratory at the genebank developed DNA fingerprinting sets for many economically important cultivars in the collection. In addition, scientists are performing studies to link genotype and phenotype for specific plants. Gender, ploidy, and phenotypes are being determined for the major fruit cultivars of the collection. This data is being entered into the Germplasm Resources Information Network database for public accessibility.
More than 440 visitors toured the repository this past year. ARS researchers are collaborating with about 75 international scientists during this past year and obtained $300,000 in extramural funding for evaluation of assigned genera. Collaborations included competitive grant opportunities in Specialty Crop Research Initiatives, commodity commission funding such as from Washington and California Tree fruit commissions, North American Bramble Growers, ARS Plant Evaluation Grants, USDA Plant Exploration Grants, and USDA Animal and Plant Health Inspection Service (APHIS).
Accomplishments
1. Managed 12,000 plant accessions. ARS scientists at the Corvallis genebank managed hazelnut collection against Eastern filbert blight and tested strawberry, raspberry, and blueberry plants for viruses and other pathogens. This team set up backup collections for about 20% of the collection. They continued their collaborative effort of tissue culture and cryopreservation of accessions at ARS in Fort Collins, Colorado, and duplicated plants on-site in a separate form and remote accessions at other ARS units such as Parlier, California. Information for these accessions was uploaded to the GRIN-Global database for public accessibility. More than 5,000 accessions were distributed to scientists domestically and internationally. This germplasm supports fruit, nut, and specialty crops valued at $10 billion for US annual production.
2. Collections of Vietnamese fruit and nut plants. ARS scientists in Corvallis, Oregon, worked with staff from the Plant Resources Center in Hanoi, Vietnam, to collect 74 additional fruit and nut accessions for the U.S. National Plant Germplasm System (NPGS). Teams of scientists traveled to six national parks and reserves in Vietnam at four times during the year to observe plants in flower and fruit. Seeds and voucher specimens were sent to ARS scientists in Corvallis for identification and donation into the U.S. NPGS. Scientists from both countries are collaborating on evaluation of this germplasm and publication of manuscripts. The crop wild relatives that were collected serve economic crops such as strawberries, raspberries, blackberries, blueberries, and pecans that are worth about $5 billion annually for U.S. production.
3. ‘Boysen’ blackberry DNA fingerprints. Multiple variants of ‘Boysen' blackberry have been observed since the cultivar was introduced in 1938. ARS scientists used DNA fingerprinting on a number of plants labeled ‘Boysen’ from public collections, plant nurseries, and private farms and tested its putative parents. A ‘Boysen’ type likely to be the original clone was identified and the pedigree for ‘Boysen’ was confirmed as ‘Logan’ x ‘Austin Mayes’. Misidentified ‘Boysen’ plants were present in the nursery trade, so confirming authenticity of named plants are recommended prior to purchase. The utilized production of the U.S. blackberry crop was worth about $26.4 million in 2016.
Review Publications
Vanburen, R., Bryant, D., Bushakra, J., Vining, K.J., Filichkin, S., Edger, P.P., Rowley, E.R., Priest, H.D., Michael, T.P., Dossett, M., Finn, C.E., Bassil, N.V., Mockler, T.C. 2018. Sequence and analysis of the black raspberry (Rubus occidentalis) genome. In: Hytönen T., Graham J., Harrison R., editors. The Genomes of Rosaceous Berries and their Wild Relatives. Compendium of Plant Genomes. Basel, Switzerland: Springer International Publishing. p. 185-197. doi:10.1007/978-3-319-76020-9
Koloniuk, I., Thekke-Veetil, T., Reynard, J., Plesko, I., Pribylova, J., Brodard, J., Kellenberger, I., Sarkisova, T., Spak, J., Lamovsek, J., Massart, S., Ho, T., Postman, J.D., Tzanetakis, I. 2018. Molecular characterization of divergent Closterovirus isolates infecting Ribes species. Viruses. 10(7):369. https://doi.org/10.3390/v10070369.
Bushakra, J., Dossett, M., Carter, K., Vining, K., Lee, J.C., Bryant, D., Vanburen, R., Lee, J., Mockler, T., Finn, C.E., Bassil, N.V. 2018. Characterization of aphid resistance loci in black raspberry (Rubus occidentalis L.). Molecular Breeding. 38:83. https://doi.org/10.1007/s11032-018-0839-5.
Hummer, K.E. 2018. Register of new fruit and nut cultivars list 49: blue honeysuckle. HortScience. 53(6):748. https://doi:10.21273/HORTSCI536register-18.
Verma, S., Osorio, L., Lee, S., Bassil, N.V., Whitaker, V. 2018. Genome-assisted breeding in the octoploid strawberry. In: Hytönen T., Graham J., Harrison R., editors. The Genomes of Rosaceous Berries and their Wild Relatives. Berlin, Germany: Springer, Cham. p. 161-184. https://doi.org/10.1007/978-3-319-76020-9_12.
Noh, Y., Mangandi, J., Verma, S., Zurn, J.D., Lu, Y., Fan, Z., Bassil, N.V., Peres, N., Whitaker, V.M., Lee, S. 2018. Development and validation of marker assays for high-throughput detection of Phytophthora crown rot resistance, FaRPc2, in the cultivated octoploid strawberry. Molecular Breeding. 38:104.
