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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Research Project #423186

Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

2015 Annual Report


Objectives
Objective 1. Conservation: Efficiently and effectively conserve, back-up, regenerate, characterize, and evaluate temperate-adapted fruit, nut and specialty crop genetic resources and distribute germplasm and associated information worldwide. Sub-objective 1a. Efficiently and effectively manage crop genetic resources emphasizing temperate fruit, nut, and specialty crop germplasm including Corylus, Fragaria, Humulus, Mentha, Pyrus, Ribes, Rubus, and Vaccinium and their crop wild relatives; test for and eliminate pests and pathogens; Backup/regenerate primary collections via on-site replicated plantings, in vitro culture, or conservation at remote sites. Sub-objective 1b. Characterize and evaluate (genotype and phenotype) to confirm taxonomic and horticultural identity, and evaluate character traits of assigned germplasm. Sub-objective 1c. Distribute assigned germplasm and document plant information in the Germplasm Resources Information Network (GRIN) and GRIN-Global. Objective 2. Acquisition: Strategically fill gaps in the current coverage of temperate-adapted fruit, nut and specialty crop collections through international and domestic germplasm exchanges and plant explorations. Sub-objective 2a. Acquire germplasm samples of Corylus, Fragaria, Humulus, Pyrus, Mentha, Ribes, Rubus, Vaccinium, and their relatives via plant exploration and exchange. Target germplasm from the Americas, Asia, Europe, and North Africa to fill current gaps identified in crop germplasm committee vulnerability statements and as opportunities arise through country agreements. Sub-objective 2b. Survey existing U.S. domestic collections of priority crops; acquire material to fill gaps in NPGS collections. Emphasize Corylus, Fragaria, Humulus, Mentha, Pyrus, Ribes, Rubus, and Vaccinium, and their relatives. Objective 3. Tissue culture and Cryogenics: Safeguarding Collections: In collaboration with other NPGS genebanks and research projects, devise superior tissue culture and cryopreservation methods to safeguard temperate-adapted fruit, nut and specialty crop collections. Sub-objective 3a. Improve mineral nutrition of in vitro plants. Sub-objective 3b. Optimize mineral nutrition of in vitro storage medium on plantlet storage time. Sub-objective 3c. Determine the effect of addition of antioxidants on plant recovery from cryopreservation. Objective 4: Genetic Marker Systems: In collaboration with other NPGS genebanks and research projects, develop novel genetic marker systems for temperate-adapted fruit, nut and specialty crop genetic resources. Apply those markers to more efficiently and effectively manage the site’s germplasm collections and to facilitate their use in breeding and research projects. Sub-objective 4a. Develop reliable fingerprinting sets and enter information to the GRIN-Global or other databases. Sub-objective 4b. Develop new high throughput genetic marker systems (Fragaria and Rubus). Sub-objective 4c. Develop trait-associated markers for efficiently identifying strawberry germplasm with desired red stele resistance and remontancy phenotypes.


Approach
The Corvallis Repository genebank has responsibility for temperate fruit, nut, and specialty crop genera: Corylus, Fragaria, Pyrus, Rubus, and Vaccinium, Cydonia, Humulus, Mentha, Ribes, Actinidia and Juglans (J. cinerea). Clones of specific genotypes are maintained in greenhouses, screenhouses, field collections, and as tissue cultured plants. Wild species are maintained as seed. When new accessions are received, information is entered to GRIN. Identity is checked by morphological and molecular means, and recorded. Locations are entered. Pathogen status is evaluated and recorded. Alternative backup procedures and remote backup locations are arranged and recorded. Genotype and phenotype are evaluated and added to GRIN. Background, passport, and pedigree information will be entered. Information will be migrated to the new system GRIN-Global. In-vitro cultures will be used as alternative storage and as a secure backup. Cultures of core accessions, requested germplasm, and accessions at risk in the field and screenhouse will be initiated into culture, multiplied, and stored at 4' C. Collection of genera will be prioritized by season, material available, requests and research in progress. Assistance with in vitro culture and cold storage protocols will be provided to other laboratories. Healthy, pathogen negative plants will be maintained and propagules will be distributed for research purposes. Phytosanitary certification is be obtained and materials are distributed according to international, regional and local quarantine regulations. Representative seedlots of diverse wild species with long-lived seeds are kept in freezers. Many species are also represented as clones from a specific seedlots. Seedlots are tested for viability. Representative seed samples are be sent for backup preservation in base collections. The Corvallis Genebank participates in inter-agency in situ conservation programs. The repository acquires new germplasm from foreign and domestic sources. New and improved culture media are being researched for repository genera. Effect of antioxidants in cryopreservation protocols are being examined. Cultivar identification is being expanded through new marker technology. Identity of genotypes of world genebanks is being compared. Genomic infrastructure for discovering valuable markers linked to traits of economic importance is being developed. 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 this continuing project which started February 26, 2013, and is numbered Project 2072-21000-044-00D, "Management of Temperate 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. The genebank continues to conserve more than 12,000 accessions of 30 genera of horticultural and agronomic crops. These include the economically important crops of hazelnuts, strawberries, hops, mint, pears, currants, gooseberries, blackberries, raspberries, blueberries, cranberries and their crop wild relatives. The primary collections are maintained as orchards in the field, or containerized plants in the screenhouse, or seeds representing species populations. Seeds are preserved at -17 degrees C (about 0 degrees F) in chest freezers to extend their viability. Alternative secondary storage is maintained on-site through tissue cultures preserved at 4 degrees C (40 degrees F). Also meristems, tiny domes of cells cut from the tops of growing shoots, are stored in liquid nitrogen at an ARS facility in Ft. Collins, Colorado. A backup orchard of the core collection of hazelnuts is planted at an ARS site in Parlier, California. Plant explorations are being strategically planned to expand the genebank: to obtain strawberries that have genes for disease resistance and continuous blooming; raspberries and blueberries that are low chilling; pears and their relatives that are dwarfing, disease resistant, or cold hardy. The genebank distributes plant material to researchers throughout the world. Propagules for about 11,000 accessions were shipped during the past year to requestors. The site staff works with the requestors and quarantine inspectors to insure that the plant materials that are shipped meet importation permit requirements and have USDA phytosanitary certification when required. The molecular genetics laboratory at the genebank just prepared a single nucleotyde polymorphism chip for the strawberry octoploid genome. In addition to genotyping, the genetics lab has confirmed pedigrees for many cultivated types of hazelnut, strawberry, raspberry and blueberry plants. The tissue culture laboratory has used a response-surface statistical analysis to determine optimum media for growing cultures of pears, hazelnuts and raspberries. This analysis allows examination of many factors through a multi-dimensional modeling system. This has improved the culture medium of these crops in the laboratory. Disease resistance of recently collected wild strawberry species and older cultivars were determined. Ploidy levels for raspberry and blueberry relatives were determined.


Accomplishments
1. Raspberry tissue culture medium was optimized. ARS researchers at the National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, optimized the raspberry tissue culture growing medium through analysis of major and minor nutrients using a system involving a response-surface statistical analysis. Higher concentrations of meso nutrients were successful in improving plantlet growth and survival. This new medium will be useful for tissue culture nurseries who wish to produce improved plantlets for commercial production. The raspberry industry, which is worth about $461.83 million, could expand their tissue culture cultivar production using these media revisions.

2. Publication of the first high throughput 90K genotyping platform in strawberry. ARS researchers at the genetics laboratory at the Natioanl Clonal Germplasm Repositiory, Corvallis, Oregon, working with national and international colleagues, developed and published information on the first high throughput 90K genotyping platform in strawberry, an octoploid (8x) crop. This accomplishment is allowing scientists to associate phenotypic information (what the plant looks like) with strawberry genes. This is assisting strawberry breeders to make efficient selection of desirable offspring. The total value of U.S. strawberry production is more than $2.4 billion.

3. Wild Oregon blueberry species were found to have 4 and 6 sets of chromosomes. ARS researchers at the National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, working with staff at the University of Florida, determined that a particular species of blueberry, native to Oregon, did not have 2 sets of chromosomes, as its European counterpart species does. Instead this Oregon species can have 2, 4, or 6 sets of chromosomes. This accomplishment addressed the evaluation of plant genetic resources of the genebank blueberry collection. This information will allow breeders to choose genotypes within the same chromosome number that can be used for successful crossing to develop improved blueberries. U.S. blueberry production is worth more than $781.8 million.

4. Raspberry species from the Pan-South Pacific have small chromosomes. ARS researchers at the National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, working with staff at the Western Kentucky University, determined ploidy levels and genome size for unusual wild relatives of raspberry species using a laboratory technique called flow cytometry. These species have the same number of chromosomes as some raspberry species in the Northern Hemisphere, but had much smaller chromosome sizes. This accomplishment addressed the evaluation of plant genetic resources of the genebank raspberry collection. This information will allow plant scientists to determine more about the origin of and development of raspberry species around the world and will allow breeders to choose genotypes within the same chromosome number that can be used for successful crossing to develop improved blueberries. U.S. raspberry production is worth more than $461.36 million.

5. Improved the microsatellite markers to evaluate quince identity. The pear industry uses quince as a dwarfing rootstock. Unfortunately the quince that has been traditionally used is not as cold hardy as the pears, so this approach cannot be used for growing pears in northern latitudes up until now. ARS researchers have identified improved DNA markers for determining quince identity, including more than 100 types at the quince genebank in Corvallis, Oregon. Worldwide, there are about 106,000 acres of quince in production with a total crop of 335,000 metric tons worth U.S. $265 million. United States production is mainly in California’s San Joaquin Valley. This research could increase quince production by 10% in the Pacific Northwest.

6. Harmonized the pear microsatellite markers used in England and the U.S. DNA microsatellite techniques can be used but separate sets were developed in England and in the U.S. USDA ARS and English researchers worked together to harmonize these markers. Many of the main cultivars were identical in both countries but a few were suspected to be incorrectly labeled. Knowing the correct identity of pears is important for breeders and for growers. Mislabeled trees could cause economic difficulty with the total U.S. production of 858,250 tons, valued at $437.1 million.

7. Obtained samples of the threatened Oregon species, the Barton raspberry. ARS scientists in Corvallis, Oregon, worked with scientists from Western Kentucky University and the Forest Service to obtain seeds and plants of a threatened raspberry relative that lives only on the eastern edge of Oregon and the western edge of Idaho in the Snake River Canyon. Scientists have concern that the habitat of this species may be challenged by an invasive European blackberry species. Studies are continuing concerning the distribution, propagation, and evaluation of this species. This study will provide information for reclamation sites and conservation of this threatened species at the Corvallis Oregon genebank.

8. Tested foundation plant material at the genebank for viruses. ARS scientists at the National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, applied enzyme linked immunisorbant assays to test 907 raspberry/blackberry and 732 blueberry clones and 846 hazelnuts for viruses. Pathogen negative clones are now available for distribution this coming dormant winter season. The NCGR distributes about 1100 accessions annually to researchers throughout the world so more clonal plant material will be available to meet importation regulations. These distributions could be estimated at a value of $11,000 to stakeholders. Having twice the amount of plants that test clean will allow more cooperators to receive plant material, increasing the value conservatively by double ($22,000).


Review Publications
Hand, C., Reed, B.M. 2014. Minor nutrients are critical for the improved growth of Corylus avellana shoot cultures. Plant Cell Tissue And Organ Culture. 119:427-539. doi: 10.1007//s11240-014-0545-x.
Hummer, K.E., Dossett, M., Finn, C.E. 2015. Luther Burbank's best berries. HortScience. 50(2):205-210.
Hummer, K.E., Postman, J.D., Preece, J.E. 2015. Managing nut genetic resources under disease threat. Acta Horticulturae. 1070:193-200.
Bushakra, J., Bassil, N.V., Finn, C.E., Hummer, K.E. 2015. Sambucus genetic resources at the USDA. National Clonal Germplasm Repository, Corvallis, Oregon. Acta Horticulture Proceedings. 1061:135-14.
Hummer, K.E., Hancock, J. 2015. Vavilovian centers of diversity: implications and impacts. HortScience. 50(6):780-783.
Hummer, K.E. 2015. In the footsteps of Vavilov: plant diversity then and now. HortScience. 50(6):784-788.
Bushakra, J., Bryant, D.W., Dossett, M., Vining, K.J., Vanburen, R., Gilmore, B.S., Lee, J., Mockler, T.C., Finn, C.E., Bassil, N.V. 2015. A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag4 conferring resistance to the aphid Amphorophora agathonica. Theoretical and Applied Genetics. 128:1631-1646.
Dossett, M., Bushakra, J., Gilmore, B.S., Koch, C., Kemplar, C., Finn, C.E., Bassil, N.V. 2015. Development and transferability of black and red raspberry microsatellite markers from short-read sequences. Journal of the American Society for Horticultural Science. 140(3):243–252.
Bassil, N.V., Davis, T., Zhang, H., Ficklin, S., Mittman, M., Webster, T.A., Mahoney, L.L., Wood, D.J., Alperin, E.S., Rosyara, U., Koehorst-Van Putten, H., Monfort, A., Amaya, I., Denoyes, B., Sargent, D.J., Bianco, L., Van Dijk, T., Pirani, A., Iezzoni, A., Main, D., Peace, C., Yang, Y., Whitaker, V., Verma, S., Bellon, L., Brew, F., Herrera, R., Van De Weg, E.W. 2015. Development and preliminary evaluation of a 90K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria ×ananassa. Biomed Central (BMC) Genomics. 16:155.
Hand, C., Maki, S., Reed, B.M. 2014. Modeling optimal mineral nutrition for hazelnut micropropagation. Plant Cell Tissue and Organ Culture. 119:411-425. doi: 10.1007/s11240-014-0544-y.
Chen, G., Ren, L., Zhang, J., Reed, B.M., Zhang, D., Shen, X. 2014. Cryopreservation affects ROS-induced oxidative stress and antioxidant response in Arabidopsis seedlings. Cryobiology. 70(1):38-47.