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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

2017 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
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 Celsius (about 0 degrees Fahrenheit) in chest freezers to extend their viability. Alternative secondary storage is maintained on-site through tissue cultures preserved at 4 degrees Celsius (40 degrees Fahrenheit). 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 was repropagated for planting at an ARS site in Parlier, California. Plant explorations are 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; and pears and their relatives that are dwarfing, disease resistant, or cold hardy. The genebank distributes plant material to researchers throughout the world. Propagules for greater than 4,500 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 prepared a single nucleotide 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, recently collected wild strawberry species, and older cultivars. Gender and ploidy levels of strawberries were determined.


Accomplishments
1. Developed a cost-effective high throughput genotyping tool for strawberry. ARS scientists in Corvallis, Oregon collaborated with national and international strawberry researchers to refine a genotyping tool for identification of strawberry samples. The objective of this project was to obtain a technique that provided information to identify strawberry clones from specific populations and to make the technique more efficient. As a result of this new technology, the cost for high throughput genotyping was reduced by half. As of 2017, 5,000 samples were genotyped by international plant breeders using this new technique with a cost savings for them of $300,000.

2. Developed a DNA test for resistance to large raspberry aphid and aphid-vectored viruses in black raspberry. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only three to four growing seasons. ARS scientists in Corvallis, Oregon, identified a region in the black raspberry genome that is associated with resistance to aphids/viruses and is thus able to distinguish resistant from susceptible seedlings. This test is being used by plant breeders to speed up development of black raspberry cultivars for the black raspberry industry. The value of black raspberry production in California, Oregon, and Washington combined is about $7.2 million for the fresh market and $9.5 million for the processed product.

3. Developed a DNA test for re-blooming and multiple cropping in strawberry. ARS scientists in Corvallis, Oregon, compared three DNA tests for re-blooming. They identified a molecular test that predicts whether strawberries will re-bloom with 93% accuracy. This test is valuable to breeders who would like to develop strawberry cultivars that will produce fruit multiple times throughout the growing season. This test was adopted by four breeding programs in the U.S. to accelerate the development of new re-blooming strawberry cultivars. The value of strawberry production in the U.S. is $2.2 billion.

4. Determined the volatile organic compounds of the Cascade strawberry. ARS scientists from Corvallis, Oregon, discovered a new strawberry species with 10 sets of chromosomes from the Oregon Cascades. The fruit of this new species was examined for aroma compounds and contrasted to those of two other strawberry species that grow nearby, the Alpine and the Virginia strawberries. The Cascade strawberry had a compound called acetophenone that was not in the other two species and linalool was 6 to 10 times higher in the Cascade strawberry than the other two. The special aroma pattern of the Cascade strawberry may be valuable to some breeding programs that plan to enrich the fruit aroma complexity of the strawberry. The U.S. strawberry crop has a production value of $2.2 billion dollars, surpassing apples and second only to grapes among noncitrus fruits.

5. Developed a cost-effective DNA test for fingerprinting hazelnut cultivars. ARS Scientists from Corvallis, Oregon, tested 20 DNA regions and identified 14 fingerprints that can distinguish hazelnut variants. The DNA fingerprints evaluated 102 hazelnut trees from different countries. It identified each of the cultivars released from major breeding programs and confirmed their parentage. Tools for DNA fingerprinting of clonally propagated horticultural crops like hazelnut are in demand by growers, nurserymen, and researchers and this procedure will be widely used as a reliable, less-time consuming, and more cost-effective procedure to determine cultivar identity than previous methods. In 2016, Oregon, which grows 99% of the U.S. hazelnut crop, harvested 36 tons of hazelnuts valued at about $129 million dollars.

6. Determined the northern limits and distribution of the wild Oregon strawberry, Fragaria cascadensis K.E. Hummer. Fragaria cascadensis is a wild endemic strawberry species with 10 sets of chromosomes that is found only in the Oregon Cascade Mountains at higher elevation. Recently excursions were taken by ARS scientists from Corvallis, Oregon, in the vicinity of Mt. Hood to seek the northern boundary of this species. This species was not observed in the north to northeast sector of the mountain; however, it was observed slightly to the east. This information will shed light on the evolutionary development, speciation, and phylogenetics of the genus. Knowing the northern limit of this endemic species is important to consider potential threatened or endangered status of a species. At a production value of $2.2 billion dollars, the U.S. strawberry crop surpassed apples and was second only to grapes among noncitrus fruits.

7. Determined perpetual flowering traits in strawberry crop wild relatives. USDA-ARS scientists from Corvallis evaluated wild strawberry species from North and South America for re-bloom. While the beach strawberry is known as blooming only once per year, some clones of this species had successive, repeat, remontant, or re-blooming tendencies while the Virginia strawberry had many clones that re-bloomed in the fall. This information is useful for geneticists who want to broaden their parental crosses to develop strawberries with repeated fruiting within one year. Growers for the $2.2 million U.S. strawberry industry are greatly interested in the repeat blooming quality – that could increase their production with two crops in one year.

8. Sequence of the black raspberry genome. ARS scientists from Corvallis, Oregon, sequenced the genomic DNA of black raspberry. This is the first publicly available diploid reference genome for raspberries. Botanically, the raspberry is in the rose family, so the raspberry sequence can be compared with other crops in that family. This resource supports breeders and researchers who are identifying and finding genes in raspberries and comparing them with genes of roses, strawberries, pears, and blackberries. The amount of time needed to breed new cultivars will be shortened because the selection process can be done by screening leaves of young seedlings for desired traits. The value of black raspberry production in California, Oregon, and Washington is about $7.2 million for the fresh market and $9.5 million for the processed product.

9. Developed a cost effective DNA test that can identify blackberry cultivars. ARS Scientists from Corvallis, Oregon, determined DNA markers that can be used in one test to verify parentage or confirm identity of blackberry plants, seeds, juice, or fruit. This technique can be used by scientists, growers or nursery personnel who wish to use plants with confirmed identities. The caneberry industry in the Pacific Northwest is applying this technique for intellectual property determination. Oregon produces about $70.5 million worth of blackberries annually.


Review Publications
Bradish, C.M., Overbaugh, E., Ballington, J., Fernandez, G.E., Bassil, N.V. 2016. Comparative diversity analysis of southeastern Rubus germplasm through molecular and pedigree techniques. Acta Horticulturae. 1127:157-162. doi: 10.17660/ActaHortic.2016.1127.25.
Bradish, C.M., Fernandez, G.E., Dossett, M., Bushakra, J., Bassil, N.V., Finn, C.E. 2016. Genotyping and phenotyping heat tolerance in black raspberry (Rubus occidentalis L.). Acta Horticulturae. 1127:321-324. doi: 10.17660/ActaHortic.2016.1127.50.
Hummer, K.E., Bassil, N.V., Alice, L. 2017. Small genomes in tetraploid Rubus L. (Rosaceae) from New Zealand and southern South America. Journal of American Pomological Society. 7(1):2-7.
Akin, M., Nyberg, A.M., Postman, J.D., Mehlenbacher, S., Bassil, N.V. 2016. A multiplexed microsatellite fingerprinting set for hazelnut cultivar identification. European Journal of Horticultural Science. 81(6):327-338.
Ulrich, D., Olbricht, K., Weisse, K., Hummer, K.E. 2017. Fragaria cascadensis K.E. Hummer: first investigation of volatile organic compounds of fruit. Acta Horticulturae. 1156:679-682. doi: 10.17660/ActaHortic.2017.1156.99.
Hummer, K.E., Davis, T. 2017. Seeking the northern boundary of the Cascade strawberry. Acta Horticulturae. 1156:111-116. doi: 10.17660/ActaHortic.2017.1156.15.
Vanburen, R., Bryant, D., Bushakra, J., Vining, K.J., Edger, P.P., Rowley, E.R., Priest, H.D., Michael, T.P., Lyons, E., Filichkin, S., Dossett, M., Finn, C.E., Bassil, N.V., Mockler, T.C. 2016. The genome of black raspberry (Rubus occidentalis). Plant Journal. 87(6):535-547. doi: 10.1111/tpj.13215.
Denoyes, B., Amaya, I., Liston, A., Tennessen, J., Ashman, T., Whitaker, V., Hytönen, T., van de Weg, E., Osorio, S., Folta, K., Slovin, J.P., Harrison, R., Monfort, A., Bassil, N.V. 2017. Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. Acta Horticulturae. 1156:13-24. doi: 10.17660/ActaHortic.2017.1156.3.
Verma, S., Bassil, N.V., van de Weg, E., Harrison, R., Monfort, A., Amaya, I., Denoyes, B., Mahoney, L., Davis, T., Fan, Z., Knapp, S., Whitaker, V. 2017. Development and evaluation of the Axiom® IStraw35 384HT array for the allo-octoploid cultivated strawberry Fragaria ×ananassa. Acta Horticulturae. 1156:75-82. doi: 10.17660/ActaHortic.2017.1156.10.
Mathey, M.M., Mookerjee, S., Mahoney, L.L., Gündüz, K., Rosyara, U., Hancock, J.F., Stewart, P.J., Whitaker, V.M., Bassil, N.V., Davis, T.M., Finn, C.E. 2017. Genotype by environment interactions and combining ability for strawberry families grown in diverse environments. Euphytica. 213(5):112. doi: 10.1007/s10681-017-1892-6.
Bushakra, J., Bassil, N.V., Weiland, G.E., Finn, C.E., Vining, K., Filichkin, S., Dossett, M., Bryant, D., Mockler, T. 2016. Comparative RNA-seq for the investigation of tolerance to Verticillium wilt in black raspberry. Acta Horticulture Proceedings. 1133:103-114. doi: 10.17660/ActaHortic.2016.1133.16.
Bushakra, J., Bradish, C., Weber, C., Scheerens, J.C., Robbins, L., Dossett, M., Peterson, M.E., Fernandez, G., Bassil, N.V., Finn, C.E. 2017. Toward understanding genotype x environment interactions on flowering and fruiting in black raspberry (Rubus occidentalis L.). Acta Horticulturae. 1117:25-30.
Bassil, N.V., Hummer, K.E., Finn, C.E. 2017. Lessons learned from DNA-based tool development and use in a genebank. Acta Horticulturae. 1156:25-36. doi: 10.17660/ActaHortic.2017.1156.4.
Salinas, N.R., Zurn, J.D., Mathey, M., Mookerjee, S., Denoyes, B., Perrotte, J., Pottier, A., Finn, C.E., Hancock, J.F., Stewart, P., Bassil, N.V. 2017. Validation of molecular markers associated with perpetual flowering in octoploid Fragaria germplasm. Molecular Breeding. 37:70. doi: 10.1007/s11032-017-0672-2.
Bassil, N.V., Nyberg, A.M., Kim, Y., Postman, J.D. 2015. Improved microsatellite markers for quince (Cydonia oblonga) genetic analysis. Acta Horticulturae. 1094:57-65.
Vanburen, R., Bryant, D.W., Bushakra, J., Vining, K.J., Edger, P.P., Rowley, E.R., Priest, H.D., Michael, T.P., Lyons, E., Filichkin, S.A., Dossett, M., Finn, C.E., Bassil, N.V., Mockler, T.C. 2016. The genome of black raspberry (Rubus occidentalis). Plant Journal. 87(6):535-547. doi: 10.1111/tpj.13215.
Hummer, K.E., Oliphant, J.M., Bassil, N.V. 2016. Flowering tendencies in strawberry species in the USDA collection. International Journal of Fruit Science. doi: 10.1080/15538362.2016.1195309.
Perkins-Veazie, P., Ma, G., Fernandez, G., Bradish, C.M., Bushakra, J., Bassil, N.V., Weber, C.A., Scheerens, J.C. 2016. Black raspberry fruit composition over two years from seedling populations grown at four U.S. geographic locations. Acta Horticulturae. 1133:335-338.
Bradish, C.M., Fernandez, G., Bushakra, J., Bassil, N.V., Finn, C.E., Dossett, M. 2016. Evaluations of sustained vigor and winter hardiness of black raspberry (Rubus occidentalis) grown in the Southeastern U.S. Acta Horticulturae. 1133:129-134.
Bassil, N.V., Nyberg, A.M., Finn, C.E., Clark, J.R., Peace, C., Iezzoni, A. 2016. Development of a multiplexed fingerprinting set in blackberry. Acta Horticulturae. 1133:89-96. doi: 10.17660/ActaHortic.2016.1133.14.
Bushakra, J., Bradish, C., Weber, C.A., Dossett, M., Fernandez, G., Weiland, G.E., Peterson, M.E., Scheerens, J.C., Robbins, L., Serce, S., Finn, C.E., Bassil, N.V. 2016. Toward understanding genotype x environment interactions in black raspberry (Rubus occidentalis L.). Acta Horticulturae. 1117:25-30. doi: 10.17660/ActaHortic.2016.1117.5.
Poothong, S., Reed, B.M. 2015. Increased CaCl2, MgS04 and KH2P04 improve the growth of micropropagated red raspberries. In Vitro Cellular and Developmental Biology - Plants. 51:648–658. doi: 10.1007/s11627-015-9720-y.