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United States Department of Agriculture

Agricultural Research Service


Location: National Clonal Germplasm Repository

2013 Annual Report

1a. Objectives (from AD-416):
Strategically expand and improve genetic resource collections and associated information for priority fruit, nut, and other specialty temperate climate crops (and their wild relatives), especially, hazelnut, strawberries, hop, mint, pear, currants, gooseberries, brambles, blueberries, cranberries, hardy kiwifruit, and other small fruits. Strategically characterize, genotype and phenotype, priority fruit, nut, and other specialty crop genetic resources adapted to temperate climates for key traits such as genetic variability, adaptation, product quality, and other horticultural traits. Efficiently and effectively conserve and regenerate priority fruit, nut, and other specialty crop genetic resources adapted to temperate climates, and distribute disease-free samples and associated information worldwide.

1b. Approach (from AD-416):
Plant exploration expeditions will be taken in North Africa, Central Asia, Northern Europe for pome fruit and in China, Japan, Russia, Korea, Central and South America for berry crops. Plants from these areas will fill current gaps. Collecting trips will occur in collaboration with foreign scientist and quarantine officials. Horticultural and botanical experts in taxonomy will be consulted to verify the identity of accessions. Primary collections of woody plants will be maintained in field collections. Primary collections of herbacious perennial genera will be maintained in a screenhouse and repropagated. Duplicate plants will be maintained on site. Available plant materials will be distributed for research purposes. Backup hazelnut collection will be maintained in Parlier, California. Backup of small fruit, mint, and hop will occur on site. Tropical or sub tropical accessions will be protected from temperature extremes. Core collections will be propagated in vitro and in cryogenic storage at NCGRP, Fort Collins. Primary collections will be tested for pathogens and infected accessions will be subjected to therapy procedures to develop pathogen free replacments. Microsatellite fingerprinting sets will evaluate genetic diversity and determine clonal identity of blueberries, strawberries, hazelnuts, and pears. Clonal collections will be evaluated for high priority phenotypic characters including phenology, plant habit, fruit characters, and incidence of naturally occurring disease. Molecular and phenotypic information will be loaded to the public GRIN database.

3. Progress Report:
This is the final report for the project 5358-21000-038-00D terminated on February 25,2013. Details on the accomplishments of this project up to the termination date are presented in this final report. Project 5358-21000-044-00D, "Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information", continues the germplasm conservation and research efforts for temperate fruit, nut, and specialty crops. During the past 5 years, the National Clonal Germplasm Repository- Corvallis, Oregon, has strategically improved the genebank collection. Each year, this facility conserved about 10,000 seed and plant accessions for about 30 genera of horticultural and specialty crops. These included the main crops of hazelnuts, strawberries, hops, mint, pears, currants, gooseberries, blackberries, raspberries, blueberries, cranberries, and other crop wild relatives. To strategically expand the gene bank holdings, plant collecting expeditions were taken to Albania, Japan, and Nova Scotia to obtain temperate fruit and nut crops and obtained more than 1,000 new accessions. For the distribution objective, the NCGR shipped more than 31,932 accessions to requestors throughout the world. Among other projects, plant materials were distributed for studies on cryogenic preservation, genetic fingerprinting, and bioactive chemicals constituents. The staff of the repository has strategically characterized (genotyping and phenotyping) many of the genera in the collection. A new strawberry was discovered native to Oregon. Highbush and half-high blueberries were evaluated in a collaborative project with private growers on the Kenai Peninsula. Ohelo fruits, Hawaiian blueberry relatives, were analyzed for chemical constituents. Genebank collections were assayed for viruses and viroids. DNA-based molecular characterization was performed on blueberry, raspberry, and strawberry genetic resources. For genotyping, fingerprints were developed for strawberry, raspberry (red and black), pear, blueberry, quince cultivars using simple sequence repeat markers. Seed storage and germination protocols were developed for assigned crops. New tissue culture media were developed to improve the growth of pear cultures. Internal bacterial contaminants were identified in hazelnut trees. The maternal family tree for strawberries was evaluated. The diversity of black raspberry cultivars and species was determined through molecular marker evaluation.

4. Accomplishments
1. Genetic resource conservation of fruit and nut crops. Genetic resources of temperate fruit, nut and specialty crop germplasm need to be acquired, maintained and preserved for food security with access for researchers and breeders who are developing new crops. During 2008-2012 ARS scientists at the Corvallis Repository Genebank in Corvallis, Oregon, preserved more than 10,000 living plant and seed accessions of 30 genera of fruit and nut crops. New germplasm was acquired from Azerbaijan, Germany, South Korea, Japan, Albania, the Republic of Georgia and the United States. More than 31,000 accessions were distributed to international researchers over 5 years. These plant distributions provide material for crop improvement and genetic study, for nurserymen for new fruit crop sales and distribution, for hobbyists, and the general public for the preservation of heritage cultivars and unusual species types.

2. Karyotypic analysis of the strawberry genome. ARS scientists collaborated with Japanese scientists to examine chromosomes of the strawberry species of the Corvallis Genebank. A wild strawberry species with 10 sets of chromosomes was observed for the first time. This finding is significant to the botanical taxonomic scientific community and may provide insight into the origin of the cultivated strawberry and its wild relatives. The value of the strawberry industry in the US is greater than $1.5 million.

3. Cryopreservation of blueberry genetic resources. Backup storage of active collections is essential for clonal germplasm; however, cryogenic protocols are unavailable for blueberry plants. The Corvallis Repository Staff tested three ways of cryopreserving the growing tips of blueberry cultivars. They obtained between 65 and 95% survivability after being subjected to liquid nitrogen temperatures. This protocol was transferred to the National Center for Genetic Resource Preservation in Fort Collins, Colorado, for long term (decades) preservation of blueberry genetic resources. Other global genebanks can also use these techniques to store blueberry relatives. The preservation of this Vaccinium germplasm supports a global industry that is worth $500 million and now increasing in acreage and value.

4. Backup of plant genetic resources of fruit and nut crops. If only one copy of a plant genotype is preserved in a genebank, it is vulnerable to disease, climate change or disasters, and could be lost for future scientific access. The scientists at the Corvallis Repository Genebank at Corvallis, Oregon, are working with those at National Center for Genetic Resources Preservation in Ft. Collins, Colorado, and in Parlier, California, to backup active collections using whole plants, tissue cultures and cryogenic preservation (long term freezing). A backup clean hazelnut orchard in Parlier, California, maintains a back-up of 125 trees. Seeds and tissue cultures of hazelnuts, strawberries, hop, mint, pears, currants, gooseberries, raspberries, blackberries, blueberries, and lingonberries have been sent for long-term storage at Ft. Collins, Colorado. Improved tissue culture and cryogenic protocols have been developed in Corvallis. Backup collections of these invaluable plant genetic resources provide insurance against loss of primary collections due to insects, weather or disease, keeping the plants available for improving American agriculture now and in the future.

5. Pathogen detection and elimination in germplasm collection. Diseases for fruit and nuts are spreading within the United States, and new diseases are being discovered and there is a need to identify emergence of any new diseases. Eastern filbert blight, a significant disease of hazelnuts has not been detected by ARS scientists at the Corvallis Repository Genebank in Corvallis, Oregon, although the disease is in fields less than 2 miles away. ARS scientists are taking preventative measures to counter this disease. The Corvallis Repository continues to be certified free of sudden oak death by the Oregon Department of Agriculture. Testing and disease free certification allows the plant materials of the repository to be freely exchanged without spreading diseases.

6. Genotype and phenotype evaluation and identification of genetic resources of fruits. Researchers, nurserymen, and growers are in need of descriptive evaluation and identity confirmation of genetic resources. Genetic profiles, morphological characters, cold hardiness evaluation and disease resistance were evaluated by ARS scientists in Corvallis, Oregon, for crops at the repository. These data were added to the publicly accessible US national germplasm database (GRIN). These data provide information to breeders, growers and nurserymen so that they can better utilize the available plant germplasm in our collection.

7. Evaluation and identification of genetic resources of fruits. Descriptive evaluations and identity confirmation of temperate fruit, nut, and specialty crops are important to plant breeders, researchers, plant nurseries, and growers. ARS scientists in Corvallis, Oregon, evaluated genetic profiles, plant physical characters, cold hardiness, and disease resistance for crops at the repository. These data were added to the publicly accessible US National Germplasm database information (GRIN). Breeders, growers, and plant nurseries use this information to better develop, grow and produce improved crops.

8. Fingerprinting of fruit and nut crops. Industry sometimes has difficulty in determining the identity of different types of berries, fruit trees and nut trees. Researchers at ARS in Corvallis, Oregon, developed and archived molecular fingerprints for cultivated blueberries, cranberries, red and black raspberries strawberries, pears, quince, and hazelnuts. These baseline identification patterns are worth more than $15 million. This is considering the amount of matching funds provided by the small fruit, pome fruit, nut, and hop crop communities, including industry and private sources.

9. Identity and disease evaluation of quince. Quince is used for a dwarfing rootstock for pear and sometimes it can be injured by low winter temperatures. Researchers at ARS in Corvallis, Oregon, evaluated diverse quince cultivars for 4 types of fungal disease resistance, cold hardiness, and identity (using molecular markers). They identified 13 types of quince that were very cold hardy, resistant to fireblight and other diseases. Quince is grown on about 300 acres in California, and is a prized specialty fruit. Current pear rootstock selections do not impart sufficient dwarfing to the scion to accommodate yield efficient, high-density planting designs, but quince could be useful for these applications. These newly identified cold-hardy, disease resistant quince selections may lead to a better rootstock for pear and even a modest 10% increase in pear production is worth tens of millions of dollars to the industry.

10. Evaluation of ohelo for fruit production and as an ornamental potted plant. Native stands of ohelo, a blueberry relative, are being decimated on the Hawaiian Islands. Also production of alternative crops is being sought for Hawaiian farmers. Researchers in ARS in Corvallis, Oregon, collaborated with those in Hawaii to evaluate ohelo plants for commercial tissue culture potential, molecular fingerprinting, and fruit nutrient composition. They determined that ohelo seed dormancy could be broken by cryogenics; developed successful commercial tissue culture working with private collaborators; determined cryogenic preservation protocols and transferred the technology to base genebank collections; determined unique fingerprints for ohelo cultivars that were recently released; determined that the low growing ohelo berry has similar fruit nutrient composition to that of cranberries. Cultivation of this fruit could protect wild endangered populations and could replace part of lost farming that was estimated at $150 million in 2006 when the sugar producers left.

11. Molecular identity of black raspberry cultivars. For the past century, many berry researchers have wondered about the identities of black raspberries. Researchers at ARS in Corvallis, Oregon, used molecular markers to examine the identity of black raspberry cultivars in the National Rubus collection. Surprisingly, 6 black raspberry cultivars with different names were identical. Furthermore, 'Munger,' the most commonly grown cultivar, had 12 variants. This newly discovered genetic variation of ‘Munger’ could have resulted in variation in field performance and thus affected grower and processing industry profitability. Further study is needed to evaluate the extent of this potential loss of genetic diversity and the economic effect of genetic variability in the most commonly grown black raspberry cultivars.

12. New strawberry species named in Oregon. While the North American continent is known to have native strawberries, some areas where strawberries grow wild have not yet been fully examined. ARS staff in Corvallis, Oregon, discovered a new species of strawberry (with 10 sets of chromosomes) native to the Oregon High Cascade Mountains. The species was named: Fragaria cascadensis Hummer. This species represents additional diversity of the native species of strawberry previously unrecognized in Native American flora. This and other species with this large amount of chromosomes could form a new class of cultivated strawberries. The value of hybrid strawberry production in the US in 2009 was $2.1 billion.

13. Red raspberry fingerprinting. Confirming the identity of red raspberry cultivars can be difficult by looking at the plant, especially if it is not fruiting season. ARS scientists at Corvallis, Oregon, developed a set of molecular marker fingerprints that confirmed identity of many cultivars but it pointed out some misidentified ones as well. These markers can also identify relatives like blackberry and black raspberry cultivars. The availability of these markers allows growers and nurserymen to confirm cultivar identity and avoid millions of dollars in litigation from selling incorrect cultivars.

14. Identification of bacteria inside hazelnut trees. Internal bacterial contaminants inhibit growth of in-vitro grown hazelnut shoots and cause problems during commercial production. ARS scientists in Corvallis, Oregon, identified several types of the bacteria. Clean in vitro grown hazelnut shoots is the first step for use by commercial micropropagation laboratories. The hazelnut industry in Oregon was worth $89.3 million in 2011 and there is a big demand for rapid production of new cultivars.

15. Improved tissue culture medium for pears. The nursery industry would like efficient techniques to produce thousands of pear plants in a short time so they are considering micropropagation. Pear culture medium is not optimized for the growth of a wide range of pears. ARS scientists in Corvallis, Oregon, determined that modifications of the mineral nutrients of a standard medium were needed. This new medium improved the growth and propagation of many pears. This new medium could result in high density plantings of pears which would increase growers profit by $10,378 per hectare over standard plantings.

16. Maternal family tree of American strawberry species. Researchers have wondered about the origin of North American strawberry species. ARS researchers in Corvallis, Oregon, examined DNA sequences from the chloroplast. This part of the plant has DNA that is inherited only from the mother’s side of the family. A strawberry named “bracteata” was found to be the most likely “mother” for the development of many North American strawberry species. Knowing these genes will help breeders determine selections of parental lines for hybrid strawberry development. The value of hybrid strawberry production in the US in 2009 was $2.1 billion.

17. Diversity of black raspberries. Many black raspberries look very much alike. Researchers at ARS in Corvallis, Oregon, examined genetic diversity in 148 wild and cultivated black raspberries using 21 molecular markers. The markers indicated that wild black raspberry germplasm has diverse genes that have never before been used and are an untapped resource available for future breeding. These wild accessions can be crossed with named cultivars and to improve black raspberry cultivars. New cultivars will providea high value crop with a gross revenue potential of $12,000 per acre or more (retail) in peak production seasons

18. Blueberry relatives obtained from a Canadian Collection. Recently a major blueberry collection in Nova Scotia, Canada, became vulnerable to loss due to funding difficulties. ARS staff from Corvallis, Oregon, participated in an international plant exchange (Canada-US) to obtain about 80 blueberry species representatives from North America from this collection. Berry breeders and researchers are looking to expand production of berry fruits into cooler northerly latitudes. These northern distributed species have genes that could allow breeders and researchers to develop new cultivars adapted to the north. This wild germplasm will expand genes available to the > 50 public and private berry breeders throughout the US and the world. The general public will benefit from having greater access to locally grown blueberries.

Review Publications
Janick, J., Hummer, K.E. 2012. The 1500th anniversary (512-2012) of the Juliana Anicia codex: an illustrated discoridean. Chronica Horticulturae. 52(3):9-15.

Ward, J.A., Bhangoo, J., Fernandez-Fernandez, F., Moore, P., Swanson, J.D., Viola, R., Velasco, R., Bassil, N.V., Weber, C.A., Sargent, D.J. 2013. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. Biomed Central (BMC) Genomics. 14:2 DOI:10.1186/1471-2164-14-2.

Reed, B.M., De Noma, J.S., Wada, S., Postman, J.D. 2012. Micropropagation of pear (Pyrus sp). In: M. Lambardi, E.A. Ozudogru, and S.M. Jain (eds.) Protocols for Micropropagation of Selected Economically-Important Horticultural Plant. Springer, NY:Humana Press. p.554.

Postman, J.D. 2012. Quince (Cydonia oblonga Mill.) center of origin provides sources of disease resistance. Acta Horticulturae. 948:229-234.

Bassil, N.V., Boccacci, P., Botta, R., Postman, J.D., Mehlenbacher, S. 2012. Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars. Genetic Resources and Crop Evolution. 60:543-568. DOI:10.1007/s10722-012-9857-z.

Chambers, A., Carle, S., Njuguna, W., Chamala, S., Bassil, N.V., Whitaker, V.M., Barbazuk, W., Folta, K.M. 2013. A genome-enabled, high-throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.). Molecular Breeding. DOI:10.1007/s11032-012-9819-3.

Postman, J.D., Aradhya, M.K., Williams, K.A., Stover, E.W., Meyer, P. 2012. Recent NPGS coordinated expeditions in the Trans-Caucasus Region to collect wild relatives of temperate fruit and nut crops. Acta Horticulturae. 948:191-198.

Reed, B.M., Gupta, S., Uchendu, E.E. 2012. In vitro genebanks for preserving tropical biodiversity. In: M.N. Normah, H.F. Chin, and B.M. Reed. Berlin, Germany:Springer Verlag. p. 77-106.

Njuguna, W., Liston, A., Cronn, R., Ashman, T., Bassil, N.V. 2012. Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Molecular Phylogenetics and Evolution.

Normah, M.N., Chin, H.F., Reed, B.M. 2012. Conservation of tropical plant species. Springer Verlag. p.538.

Georgi, L., Johnson-Cicalese, J., Honig, J., Das, S.P., Rajah, V.D., Bhattacharya, D., Bassil, N.V., Rowland, L.J., Polashock, J.J., Vorsa, N. 2013. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. Theoretical and Applied Genetics. 126:673-692.

Fajardo, D., Morales, J., Zhu, H., Steffan, S.A., Harbut, R., Bassil, N.V., Hummer, K.E., Polashock, J.J., Vorsa, N., Zalapa, J.E. 2012. Discrimination of American cranberry cultivars and assessment of clonal heterogeneity using microsatellite markers. Plant Molecular Biology Reporter. 31(2):264-271.

Gilmore, B.S., Bassil, N.V., Nyberg, A.M., Knaus, B., Smith, D., Barney, D.L., Hummer, K.E. 2013. Microsatellite marker development in peony using next generation sequencing. Journal of the American Society for Horticultural Science. 138(1):64-74.

Last Modified: 05/28/2017
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