Location: Horticultural Crops Production and Genetic Improvement Research Unit
2018 Annual Report
Objectives
Objective 1: Develop new improved small fruit cultivars for the commercial fruit industry, including, thornless, machine harvestable blackberry cultivars with excellent flavor; high yielding, virus tolerant, high quality strawberry cultivars with outstanding processing characteristics; virus tolerant, high yielding, black raspberry selections with flavor and color characteristics similar to the current standard cultivars; and high quality primocane fruiting red raspberry cultivars with broad adaptation.
Objective 2: Evaluate, and incorporate new sources of genetic variability from Rubus, Vaccinium, Fragaria and other minor crops. Specifically, selections of Rubus occidentalis populations from across the country will be evaluated for fruit quality, plant growth, and aphid resistance, and strawberry populations for the presence of repeat flowering characteristics.
• Subobjective 2A: Incorporate new/novel germplasm into breeding material to enhance adaptation.
• Subobjective 2B: Determine whether trait-associated markers can be developed and if developed, can they be used to identify germplasm that expresses a phenotype of interest.
Objective 3: Characterize viruses that infect berry crops, and develop management strategies to minimize the impact of virus diseases on these crops.
• Subobjective 3A: Sequence novel viruses of small fruit crops and develop assays for their rapid detection, emphasis will be on raspberry leaf curl disease and two novel virus-like diseases of grapevine.
• Subobjective 3B: Determine if endogenous Rubus yellow net virus (RYNV) in raspberry genomes pose a risk of long distance virus spread.
• Subobjective 3C: Eradicate Blueberry fruit drop associated virus from blueberry fields in the U.S.
Objective 4: Develop virus-tested planting stocks of berry cultivars for fruit production using thermal therapy and other virus elimination techniques, and test RNAi therapy as a new method for virus elimination in berry crops.
Approach
For each crop, a modified recurrent mass selection system will be used. Individuals that are selected in a given generation will be intercrossed to produce the next generation. For Rubus spp. and strawberry 4000-6000 seedlings, and 2500-4000 blueberry seedlings from 30-100 crosses will be evaluated annually. Approximately 0.5 to 1.0% of the seedlings are selected based on subjectively evaluated fruit quality, plant performance, ripening period, and yield. Frozen samples will be evaluated for processing characteristics. Selections identified as being superior will be propagated for commercial trial and release. For nursery production, the ARS virology program in Corvallis, OR will help produce virus-tested propagation material. To broaden the germplasm base, superior individuals or representatives of superior populations of small fruit species will be crossed among themselves or with advanced selections or cultivars. Selections from these crosses will be used in our breeding program and distributed to other breeders. Emphasis will be on aphid resistance, disease resistance, fruit quality, thornlessness and tolerance to abiotic stresses associated with growing these crops in regions with more diverse climates.
This program collaborates with molecular geneticists in efforts to bridge the gap between genomics and applied plant breeding in berry crops. Our program helps to determine the mapping populations to develop or genotypes to include and how the various phenotypic traits (phenological, reproductive, and vegetative) will be evaluated. The phenotyping for each project is being coordinated across multiple locations with different climatic conditions. For raspberry leaf curl disease, suspect raspberry samples will be collected and their virome analyzed using Next Generation Sequencing. This approach will also be used to examine two novel diseases of grapevines in Oregon. Diagnostic assays will be developed and used for epidemiology studies, certification and quarantine purposes. Virus vectors will be identified and strategies for vector control developed as a means to manage virus diseases. Total genomic sequencing of five Rubus cultivars will be used to determine if the inserted RYNV sequences represent full-length or partial RYNV and if all insertions are at the same site. If the RYNV insertions are at the same site in each of these cultivars it would indicate that the insertion may have happened once and been passed on in breeding programs. Several approaches will be tested for applying gene silencing as a tool to eliminate viruses from growing points of plants (meristematic dome and several leaf primordia): 1. Virus specific dsRNA will be produced and provided to plants in tissue culture as an additive to the media; 2. dsRNA will be attached to positively charged clay nanoparticles and sprayed on plants in tissue culture or growth chambers; and 3. RBDV infected plants will be grafted onto transgenic plants (already developed red raspberry) that are producing RNAi silencing of RBDV. Meristems will be collected at various times after treatments, plants regenerated and tested for RBDV.
Progress Report
This report documents progress for project 2072-21220-003-00D, which started in February 2018 and replaces project 2072-21220-002-00D, "Genetic Improvement and Virus Management of Small Fruit Crops."
In support of Objective, 1, plant patents were prepared for four blackberries and one blueberry. ‘Norman’ blueberry was released by the University of Arkansas with ARS in Corvallis, Oregon. Promising selections were moved to propagators to increase numbers for regional, national and international grower trials. These grower trials help determine the commercial suitability of these selections in varying environments. They are also the first chance commercial growers have to begin to optimize production.
Selections were made in black raspberry populations that had been screened for aphid resistance. Black raspberry germplasm had been collected and sources of aphid resistance identified and characterized (Sub-objective 2B). These selections are targeted to have greater durability in the field, as aphid resistance implies that they are resistant to the debilitating Black raspberry necrosis virus. ORUS 4670-1 is an amazing thornless blackberry selection based on its early evaluation. This is notable as it illustrates the long-term goal of incorporating new germplasm into advanced breeding material. Looking at the parents/grandparents in the pedigree - ‘Navaho’ and ‘Cherokee’ represent eastern erect germplasm, ‘Triple Crown’ an eastern semi-erect, ORUS 1122-1 a trailing blackberry germplasm, and most interesting of all, the Eurasian R. georgicus 824 (17-15). While the blending of eastern and western germplasm has been remarkable, the R. georgicus 824 (17-15) selection was made in 1994 from a Rubus georgicus population that the National Clonal Germplasm Repository in Corvallis, Oregon, had received in 1987 from the Vavilov Research Institute of Plant Industry in Russia. It was used as a parent in 1995 to capture its high yields and outstanding flavor, with no bitter hints that are often present in eastern germplasm. ORUS 4670-1, which will likely be released in 2020, is an example of what the program is striving for when useful new germplasm is incorporated into advanced breeding material (Sub-objective 2A).
Similar efforts are ongoing with R. parvifolius, R. coreanus and R. innominatus in red raspberry and R. caucasicus in blackberry (Sub-objective 2A). In other germplasm research, strawberry genotypes are being screened with cooperators for response to Macrophomina, Fusarium, and Verticillium (Sub-objective 2B).
As part of the blueberry virus survey, High Throughput Sequencing (HTS) was used to examine plants with unusual symptoms or inconsistent symptoms in the presence of a known virus. This led to the discovery of a new luteovirus as part of a virus complex associated with blueberry bronze leaf curl disease in Michigan. Plants with bronze leaf curl symptoms were examined using HTS as well as symptomless plants that tested positive for the Closterovirus identified earlier in bronze leaf curl diseased plants. Additionally, Tobacco streak virus in the plants with bronze leaf curl disease in Michigan was detected. This was the first finding of Tobacco streak virus in blueberries.
HTS was compared to other methods of detection with the goal of adopting HTS as an acceptable means to test for viruses for plant quarantine and certification. This was combined with doing ‘Ring Test’ in berries across five to nine labs to evaluate the robustness of the Polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) tests currently used in berry certification and quarantine programs. While the focus is on berries, efforts are being coordinated with other groups working on grapevines, citrus and tree fruit crops. HTS has some clear advantages if it can substitute for slower biological indexing. In the first year of comparisons, the HTS was as good as doing biological indexing, ELISA and PCR testing combined. However, there are some potential drawbacks. New viruses were identified using HTS, but there is no information on their biological importance. There are viruses that are not known to cause any disease, so trying to sort out the regulatory implications of the newly discovered viruses based strictly on sequence information is not possible. Information provided to the regulatory community based on biological significance to the regulatory community must be carefully vetted, so that regulatory actions are based on risk rather than the presence of an unknown sequence. This project is partially supported by a grant funded through the Farm Bill and via funding from the National Clean Plant Network (NCPN).
An informational database for the viruses of the crops included in the NCPN was developed with partners. The database provides current information on each of the viruses of these crops including: information on the virus itself, description of symptoms with photo documentation, synonyms, worldwide distribution, best methods for detection, virus vectors and their management, and a complete list of scientific publications related to all aspects of each virus. The project was initiated at the request of stakeholders of the National Clean Plant Network that are concerned about virus management. The work is partially supported by a grant from the NCPN.
A project has been developed to study the timing of transmission of Grapevine red blotch virus (GRBV). GRBV in the field and to identify vectors of the virus in Oregon vineyards. The one documented insect vector of GRBV (Three cornered alfalfa hopper) is very rare in Oregon, and in most cases has not been detected, suggesting there are other vectors that transmit this virus. Field trials have been established to expose healthy plants to natural transmission and the work is being done in vineyards with high incidences of GRBV (primarily in the Willamette Valley and southern parts of Oregon). Healthy grapevines have been exposed for 30 day intervals, from May through October. Plants were in the vineyard for one month, brought back to Corvallis, Oregon, and treated with insecticide and are being held for two years. The process is repeated each month of the growing season. In 2018, insects are being collected from infected vineyards every 14 days, sorted by genera and placed on infected plants for six days for virus acquisition. Then healthy plants are added to each cage and transmission allowed to occur for 6 days. The entire process is being repeated every two weeks throughout the growing season. This work is supported by grants from California Department of Agriculture, Erath Family Foundation, and Oregon wineries.
Raspberry leaf curl virus is the only virus of Rubus spp. that requires biological indexing for exporting nursery stock internationally. It has greatly limited the number of genotypes that can be shipped internationally and is limiting commerce. There are no known samples of this virus in collections, and thus, in collaboration with colleagues at the University of Arkansas, field samples that have symptoms similar to those described in the literature are being collected. Samples were collected from wild raspberry and/or blackberry in Maine, Wisconsin, Minnesota, Pennsylvania, Washington, Oregon, Montana, Idaho and Wyoming in the U.S. and in Ontario and Quebec, Canada. The virus status of each sample is being analyzed by HTS. Three novel viruses were identified. Detection assays were developed based on the sequence information for these viruses and the three novel viruses were detected in samples from the northeast U.S., eastern Canada, and in the Rocky Mountains. In further work, the aphid transmitted viruses are being inoculated singly and in mixed infections to raspberry cultivars grown in the 1950s and 1960s when the disease was common in the northeast U.S. The goal is to characterize the virus(es) that cause raspberry leaf curl disease. This project is partially funded with grants from NCPN and the Farm Bill.
Accomplishments
Review Publications
Finn, C.E., Strik, B.C., Yorgey, B.M., Mackey, T.A., Moore, P., Dossett, M., Jones, P., Lee, J., Martin, R.R., Ivors, K., Jamieson, A. 2018. ‘Marys Peak’ strawberry. HortScience. 53(3):395–400. https://doi.org/10.21273/HORTSCI12675-17.
Finn, C.E., Strik, B.C., Peterson, M.E., Yorgey, B.M., Moore, P., Jones, P.A., Lee, J., Martin, R.R. 2018. ‘Kokanee’ primocane-fruiting red raspberry. HortScience. 53(3):380–383. https://doi.org/10.21273/HORTSCI12691-17.
Gallardo, R.K., Zhang, Q., Klingthong, P., Dossett, M., Polashock, J.J., Rodriguez-Saona, C., Vorsa, N., Edger, P., Scherm, H., Ashrafi, H., Babiker, E.M., Finn, C.E., Iorizzo, M. 2018. Breeding trait priorities of the blueberry industry in the United States and Canada. HortScience. 53(7):1021-1028. https://doi.org/10.21273/HORTSCI12964-18.
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.
Finn, C.E., Sebasta, B.M., Clark, J.R. 2018. Register of new fruit and nut cultivars List 49 - Blackberry. HortScience. 53(6):752-754. https://doi.org/10.21273/HORTSCI536register-18.
Moore, P.P., Dossett, M., Finn, C.E. 2018. Register of new fruit and nut cultivars List 49 - Raspberry. HortScience. 53(6):770-771. https://doi.org/10.21273/HORTSCI536register-18.
Clark, J.R., Salgado, A., Draper, A., Finn, C.E., Sandefur, P., Boches, P. 2018. ‘Norman’ southern highbush blueberry. HortScience. 53(5):737–740. https://doi.org/10.21273/HORTSCI13003-18.
Hancock, J.F., Olmstead, J.W., Itle, R.A., Callow, P.W., Neils-Kraft, S.P., Wheeler, E.J., Mangandi, J., Sooriyapathirana, S.S., Rowland, L.J., Mackey, T.A., Bassil, N.V., Finn, C.E. 2018. Performance of an elite, hybrid family of a northern × southern highbush cross (‘Draper’ × ‘Jewel’). Euphytica. 214:95. https://doi.org/10.1007/s10681-018-2173-8.
Maes, P., Alkhovsky, S.V., Bào, Y., Beer, M., Birkhead, M., Briese, T., Buchmeier, M.J., Calisher, C.H., Charrel, R.N., Ryong Choi, I., Clegg, C.S., Carlos De La Torre, J., Delwart, E., Derisi, J.L., Di Bello, P.L., Di Serio, F., Digiaro, M., Dolja, V.V., Drosten, C., Druciarek, T.Z., Du, J., Ebihara, H., Elbeaino, T., Gergerich, R.C., Gillis, A.N., Gonzalez, J.J., Haenni, A., Hepojoki, J., Hetzel, U., Ho, T., Hong, N., Jain, R.K., Jansen Van Vuren, P., Jin, Q., Gilda Jonson, M., Junglen, S., Keller, K.E., Kemp, A., Kipar, A., Kondov, N.O., Koonin, E.V., Kormelink, R., Korzyukov, Y., Krupovic, M., Lambert, A.J., Laney, A.G., Lebreton, M., Lukashevich, I.S., Marklewitz, M., Markotter, W., Martelli, G.P., Martin, R.R., Mielke-Ehret, N., Mühlbach, H., Navarro, B., Fei Fan Ng, T., Teixeira Nunes, M., Palacios, G., Paweska, J.T., Peters, C.J., Plyusnin, A., Radoshitzky, S.R., Romanowski, V., Salmenperä, P., Salvato, M.S., Sanfaçon, H., Sasaya, T., Schmaljohn, C., Schneider, B.S., Shirako, Y., Siddell, S., Sironen, T.A., Stenglein, M.D., Storm, N., Sudini, H., Tesh, R.B., Tzanetakis, I.E., Uppala, M., Vapalahti, O., Vasilakis, N., Walker, P.J., Wáng, G., Wáng, L., Wáng, Y., Wèi, T., Wiley, M.R., Wolf, Y.I., Wolfe, N.D., Wú, Z., Xú, W., Yang, L., Yang, Z., Yeh, S., Zhang, Y., Zhèng, Y., Zhou, X., Zhu, C., Zirkel, F., Kuhn, J.H. 2018. Taxonomy of the family Arenaviridae and the order Bunyavirales: Update 2018. Archives of Virology. 163:2295. https://doi.org/10.1007/s00705-018-3843-5.
Martin, R.R., Tzanetakis, I.E. 2018. High risk blueberry viruses by region in the North America; implications for certification, nurseries, and fruit production. Viruses. 10(7):342-350. https://doi.org/10.3390/v10070342.
Thekke-Veetil, T., Ho, T., Postman, J.D., Martin, R.R., Tzanetakis, I.E. 2018. A virus in American blackcurrant (Ribes americanum) with distinct genome features reshapes classification in the Tymovirales. Viruses. 10(8):406. https://doi.org/10.3390/v10080406.
