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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

2016 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 greater than 8,000 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, recently collected wild strawberry species, and older cultivar. Gender and Ploidy levels of strawberries were determined.


Accomplishments
1. Identified the genomic region responsible for aphid resistance in black raspberry. In the Pacific Northwest, where production of most of the U.S. black raspberry 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 researchers in Corvallis, Oregon have identified a region of the black raspberry genome that is associated with resistance to aphids. This is the first example of aphid resistance identified in this crop. Black raspberry production is valued at $16.8 million annually within the Pacific Northwest Region.

2. Developed the first linkage map for an ancestor of the cultivated strawberry. This Japanese strawberry species, Fragaria iinumae, is one of two known diploid ancestors of the cultivated strawberry. ARS scientists in Corvallis, Oregon worked with researchers at the University of New Hampshire to develop the first genetic linkage map for this species. This map provides a basis for future studies to understand the genomic structure and family history of the crop wild relatives of the cultivated strawberry. This research supports the U.S. strawberry industry which is valued about $464 million.

3. Constructed the first linkage map in highbush blueberry. Breeding new blueberry varieties is a slow process but could be accelerated and made more efficient if breeders could quickly identify seedlings from crosses that carry the most desirable traits. ARS scientists in Corvallis, Oregon worked with an international team of researchers to develop a genetic map of blueberry. The plants have four copies of each chromosome, which makes the genetics more complicated. Despite this, the map is currently the best available for blueberry, comprised of about 2,000 markers. Blueberry breeders and geneticists worldwide can use this map and population in future studies to identify markers associated with important blueberry traits.

4. Identified genomic regions responsible for Angular leaf spot in strawberry. Angular leaf spot is the only major bacterial disease of cultivated strawberry and may cause reductions of up to 8% of marketable yield in Florida winter annual production. No resistant cultivars have been commercialized but resistance is found in two wild accessions. Using a selective genotyping approach and pedigree-based analysis, ARS scientists in Corvallis, Oregon worked with University of Florida researchers to identify a single major-effect DNA region in two families, each descended from one of the resistant accession. Characterization of this region will facilitate marker-assisted selection toward the development of new resistant cultivars.

5. Obtained 95 samples of Rubus and Vaccinium from Vietnam. ARS researchers in Corvallis, Oregon, working with Plant Resources Center in Hanoi, Vietnam collected seeds, plants, and herbarium voucher specimens in October and November from four National Parks in Northern Vietnam. This accomplishment addressed the significant new acquisition of plant genetic resources for the U.S. Rubus and blueberry crop wild relatives. These unique species of crop wild relatives of blueberries and raspberries could contribute genes for low chilling, heat tolerance, or pest and disease. This new germplasm will broaden the genepool for U.S. breeders to develop and improve raspberries and blueberries for production in warmer climates. U.S. blueberry production is worth more than $781.8 million.

6. Developed microsatellite markers to assess genetic diversity and phylogenetic relationships of quince. ARS researchers in Corvallis, Oregon, and a visiting scientist from South Korea, screened simple sequence repeat markers in the quince collection. These markers distinguished duplicates and identity of this diverse international collection. This accomplishment addressed the evaluation of plant genetic resources of the genebank pome fruit collection. This information will allow plant scientists to coordinate the identity of international quince clones and will be useful in future studies of disease resistance and cold tolerance. The world production of quince is about 596,532 metric tons and the plant is used in the U.S. as a rootstock for pear production.

7. Improved shoot culture media for raspberries with nitrogen salts. ARS researchers in Corvallis, Oregon, optimized the raspberry tissue culture growing medium through analysis of the source of nitrogen. Combinations of intermediate or high nitrate and intermediate to high ammonium produced the best growth in most cultivars. 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.


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Review Publications
Hummer, K.E., Dempewolf, H., Bramel, P., Markham, R., Stover, E.W. 2015. Status of global strategies for horticultural fruit crops. Acta Horticulturae. 1101:147-152. doi: 10.17660/ActaHortic.2015.1101.22.
Fernandez, G.E., Hummer, K.E., editors. 2016. Proceedings of the XI international Rubus and Ribes symposium. Acta Horticulturae. 526 p.
Hummer, K.E., Bassil, N.V., Rodriguez, A., Olmstead, J.W. 2016. Vaccinium species ploidy assessment. Acta Horticulturae. 1101:199-204. doi: 10.17660/ActaHortic.2015.1101.30.
Zheng, X., Cai, D., Potter, D., Postman, J.D., Liu, J., Teng, Y. 2014. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences. Molecular Phylogenetics and Evolution. 80:54-65.
Postman, J.D., Bassil, N.V., Bell, R.L. 2015. Ploidy of USDA (United States Department of Agriculture) world pear germplasm collection determined by flow cytometry. Acta Horticulturae. 1094:75-81.
Schaefer, K., Nyberg, A.M., Postman, J.D., Bassil, N.V. 2015. Genetic diversity of medlar (Mespilus germanica) germplasm using microsatellite markers. Acta Horticulturae. 1094:47-56.
Reed, B.M., De Noma, J.S., Wada, S., Niedz, R.P. 2016. Determining optimum in vitro mineral nutrition for diverse pear germplasm using response surface methodology. Acta Horticulturae. 1113:79-84.
Poothong, S., Reed, B.M. 2016. Optimizing shoot culture media for Rubus germplasm: the effects of NH4+, NO3-, and total nitrogen. In Vitro Cellular and Developmental Biology - Plants. 52(3):265-275. doi: 10.1007/s11627-016-9750-0.
Hummer, K.E., Bassil, N.V., Alice, L. 2016. Rubus ploidy assessment. Acta Horticulturae. 1133:81-88. doi: 10.17660/ActaHortic.2016.1133.13.
Mahoney, L., Sargent, D., Wood, D., Ward, J., Bassil, N.V., Handcock, J., Folta, K., Davis, T. 2016. A high density linkage map of the ancestral diploid strawberry F. iinumae using SNP markers from the ISTRAW90 array and GBS. The Plant Genome. 9(2). doi: 10.3835/plantgenome2015.08.0071.
Evans, K., Fernandez-Fernandez, F., Bassil, N.V., Nyberg, A.M., Postman, J.D. 2015. Comparison of accessions from the UK and US national pear germplasm collections with a standardized set of microsatellite markers. Acta Horticulturae. 1094:41-46.
Roach, J., Verma, S., Peres, N., Jamieson, A., Van De Weg, E., Bink, M.C., Bassil, N.V., Lee, S., Whitaker, V. 2016. FaRXf1: a locus conferring resistance to angular leaf spot caused by Xanthomonas fragariae in octoploid strawberry. Theoretical and Applied Genetics. 129(6):1191-1201. doi: 10.1007/s00122-016-2695-1.