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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

2018 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 is the final report for project 2072-21000-044-00D, which expired February 2018 and has been replaced by new project 2072-21000-049-00D, "Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information." For additional information, see the new project report. 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 32,800 accessions were shipped to requestors for research collaboration. 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. 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 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, raspberries and blueberries were determined. More than 2,200 visitors toured the genebank during the past five years. ARS researchers collaborated with more than 75 international scientists and obtained $1.5 million 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.


Accomplishments
1. DNA test to identify crown rot resistance in strawberries. ARS scientists in Corvallis, Oregon, evaluated known crown rot resistant and susceptible strawberries from California, Florida, Europe, and Oregon housed at the National Clonal Germplasm Repository in Corvallis, Oregon. The DNA test was effective at predicting resistance in California and Florida strawberries, but not those of Europe or Oregon. This test will be useful for all breeding programs which use California and Florida strawberries as parents to develop new cultivars. Strawberries with this heritage accounted for over 95% of U.S. strawberry production in 2017, a value of about $3.325 billion.

2. Bioinformatics pipeline for analysis of strawberry sub-genomes. ARS scientists in Corvallis, Oregon, used sequencing and family relatedness to determine which sub-genomes were associated with potential ancestral strawberry species. The high quality genetic markers identified using this technique created genetic maps. Despite large amounts of missing data, the approach identified some of the sub-genomes likely associated with ancestral species. Insights gained from this work provide a better understanding of the evolution and breeding of strawberry varieties for the U.S. strawberry industry, worth an annual $3.5 billion.

3. Potential resistance to Blueberry shock virus. U.S. blueberry production is worth $775 million annually. Blueberry shock virus is a serious pollen-born virus in the Pacific Northwest region of North America and causes a transient severe yield reduction when blueberry plantings first become infected. ARS scientists in Corvallis, Oregon, monitored a field collection for 10 years and some blueberry plants did not have the virus during this time. This study has determined which blueberry cultivars are slow to become infected with shock virus.

4. Diversity and identification of species relationships were determined by chloroplast DNA sequences. ARS scientists in Corvallis, Oregon, and Fort Collins, Colorado, sequenced conserved chloroplast regions of a section of pome fruits called the “Maleae.” These include 77 economically important crops, including apples and pears. The genetic relationships among pear species were complex, likely resulting from multiple hybridization and expansion/contraction events during the speciation process. These results will help to improve targeting of future germplasm collection efforts to improve the efficiency of conserving world genetic diversity of important Rosaceae genetic resources in the National Plant Germplasm System.

5. Black currant reversion virus (BRV) detected in black currants in Corvallis, Oregon. ARS scientists at Corvallis, Oregon, detected black currant reversion virus (BRV) in several black currant cultivars in the ARS ribes collection in Corvallis, Oregon. Reversion disease, caused by BRV, is devastating in European countries and has been kept out of the U.S. by a national quarantine. New techniques of next generation sequencing detected BRV for the first time in 2016, on plants in the U.S. that went through quarantine, and were growing in the country for the past 20 years. The presence of the virus was confirmed by two ARS labs and by the Animal and Plant Health Inspection Service (APHIS), but the eriophyid mite vector of BRV is not present in the U.S., so risk of spread is low. About 655,030 tons of black currants are produced in the world annually.

6. Propagation of dwarf pear rootstocks improved. Pear trees are difficult to propagate as self-rooted trees for rootstock trials. ARS scientists in Corvallis, Oregon, produced a way to select dwarf pears via inter-stem grats. They were able to bypass the propagation challenge, and using this procedure, pear selections were identified that have dwarfing potential. If interstems exhibit the same dwarfing ability as self-rooted rootstocks, the ability to screen germplasm for prospective rootstock candidates will be dramatically improved and the determination time will be reduced. U.S. pear production is worth $273 million annually.

7. Agapetes: jewels of the Himalayas. Several species of beautiful, delicately flowering shrubs, called Agapetes, were collected on an expedition by ARS scientists from Corvallis, Oregon, in collaboration with the Plant Resource Center, Hanoi, Vietnam. Agapetes are related to blueberries, but they are unusual because they are a semi-climbing plant that grows on other plants. During the Vietnamese-U.S. cooperative expedition to national parks and reserves in Northern Vietnam, five species were collected by ARS and Vietnamese genebank scientists. These plants could contribute to broadening the gene pool for cultivated blueberries, or could lead to new ornamentals with novel colors, textures, or plant habits, providing potential revenue for ornamental nurseries.


Review Publications
Hummer, K.E., Oliphant, J.M., Hoai, T., Nguyen, K. 2017. Wild Vietnamese relatives of blueberries. Acta Horticulturae. 1180:415-422. https://doi.org/10.17660/ActaHortic.2017.1180.58.
Bidani, A., Hummer, K.E., Rowland, L.J., Bassil, N.V. 2017. Development of an efficient DNA test for genetic identity confirmation in blueberry. Acta Horticulturae. 1180:363-368. https://doi.org/10.17660/ActaHortic.2017.1180.49.
Bidani, A., Hummer, K.E., Olmstead, J., Lyrene, P., Rowland, L.J., Bassil, N.V. 2017. Microsatellite markers for genetic analyses in southeastern Vaccinium species. Acta Horticulturae International Symposium on Vaccinium Culture. 1180:373-378. https://doi.org/10.17660/ActaHortic.2017.1180.51.
Hummer, K.E., Oliphant, J.M., Hoai, T., Nguyen, K. 2017. Agapetes: Jewels of the Himalayas. Acta Horticulturae. 1185:29-34. https://doi.org/10.17660/ActaHortic.2017.1185.6.
Hummer, K.E. 2017. Blackberries: an introduction. In: Hall, H.K., Funk, R.C., editors. Blackberries and their Hybrids. Oxford, England, United Kingdom: CABI. p. 1-16.
Verma, S., Zurn, J.D., Salinas, N., Mathey, M., Denoyes, B., Hancock, J., Finn, C.E., Bassil, N.V., Whitaker, V.M. 2017. Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria ×ananassa) breeding populations using pedigree-based QTL analysis. Horticulture Research. 4:17062. https://doi.org/10.1038/hortres.2017.62.
Zurn, J.D., Rouse, M.N., Chao, S., Aoun, M., Macharia, G., Hiebert, C.W., Pretorius, Z.A., Bonman, J.M., Acevedo, M. 2018. Dissection of the multigenic wheat stem rust resistance present in the Montenegrin spring wheat accession PI 362698. BMC Genomics. 19:67. https://doi.org/10.1186/s12864-018-4438-y.
Bassil, N.V., Bidani, A., Hummer, K.E., Rowland, L.J., Olmstead, J., Richards, C.M., Lyrene, P. 2017. Assessing genetic diversity of wild southeastern North American Vaccinium species using microsatellite markers. Genetic Resources and Crop Evolution. 65(3):939-950. https://doi.org/10.1007/s10722-017-0585-2.
Cai, W., Zurn, J.D., Bassil, N.V., Hummer, K.E. 2017. Perpetual flowering in strawberry species. HortScience. 52(11):1496-1500. https://doi.org/10.21273/HORTSCI12025-17.
Hummer, K.E. 2017. International regulations regarding exchange of Rubus plant material. In: Martin, R.R., Ellis, M.A., Williamson, B., Williams, R.N, editors. Compendium of Blackberry and Raspberry Diseases and Insects. St. Paul, MN: American Phytopathological Society. p. 146-147.
Oh, Y., Kim, S., Shin, H., Oh, S., Won, J., Oh, S., Han, Y., Kim, D., Kim, Y., Bassil, N.V. 2017. Classification of Korean native pear based on a standard set of microsatellite loci. Acta Horticulturae. 1172:237-240.