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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

2014 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 now conserves slightly less 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 about 7,000 accessions are shipped annually 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 recently determined the pedigree of many fruit samples. In addition to genotyping, the genetics lab has prepared a SNP chip for the octoploid strawberry. The tissue culture laboratory is using a response-surface statistical analysis to determine optimum media for growing cultures of pears, hazelnuts and raspberries. This new analysis allows examination of many factors through a modeling system. This has improved the culture of these crops in the laboratory. Cold hardiness and disease resistance of recently collected wild strawberry species were determined. Folic acid content of blueberry species was determined.


Accomplishments
1. High throughput 90K genotyping platform in strawberry. ARS researchers at the genetics laboratory at the Natioanl Clonal Germplasm Repositiory, Corvallis, Oregon, working with national and international colleagues developed the first high throughput 90K genotyping platform in strawberry, an octoploid (8x) crop. This accomplishment will allow scientists to associate phenotypic information with genes in the strawberry genome. This will assist strawberry breeders for more efficient selection of desirable offspring. The total value of U.S. strawberry production is more than $2.4 billion.

2. Improved microsatellite markers for quince. ARS researchers at the National Clonal Germplasm Repository, Corvallis, Oregon, developed improved microsatellite markers for quince and analyzed genetic fingerprints of more than 100 quince and related germplasm accessions. This accomplishment addresses the development of protocols for the identification of genebank accessions. This will be useful to international genebank managers, nursery production people, and fruit growers. About 575,924 metric tons of quince fruit were produced on the world market.

3. New hazelnut medium developed. ARS researchers at the National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, developed “Hazelnut 2013 Medium”, a new tissue culture medium, through analysis of major and minor nutrients using a system involving a response-surface statistical analysis. Higher concentrations of meso nutrients were successful in improving plantlet growth and survival. This new medium will be useful for tissue culture nurseries who wish to produce improved plantlets for commercial production. The hazelnut industry, which is worth about $89.3 million, could be expanded by 10% for rapid production of new disease resistant cultivars.

4. Folate in blueberries. An ARS researcher in Corvallis, Oregon, worked with the staff of the blueberry breeder at the University of Florida and researchers at Laval University in Quebec to provide fruit samples for analysis of diverse species and cultivars for nutritional components such as folate (an essential nutrient)and abscisic acid (an anti-diabetic compound). This accomplishment addresses the evaluation of plant genetic resources in the National Clonal Germplasm Repository (NCGR), Corvallis, Oregon, blueberry collection. This information will assist breeders in determining parents for crosses to improve the quality of blueberry fruit production. U.S. blueberry production is worth more than $781.8 million.

5. Microsatellite markers in black raspberry. ARS researchers at the National Clonal Germplasm Repository (NCGR), Corvallis, Oregon, used 15 polymorphic microsatellite markers to examine population structure and genetic diversity of black raspberry cultivars. This accomplishment addressed the evaluation of plant genetic resources of the NCGR raspberry collection. This information will assist breeders in determining parents for crosses to improve the quality of black raspberry fruit production. Black raspberries are a high value crop with a gross revenue potential of $12,000 per acre.

6. Ploidy levels in blueberry. ARS researchers at the National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, working with staff at the University of Florida, determined ploidy levels for blueberry species and related genera using flow cytometry. This accomplishment addressed the evaluation of plant genetic resources of the genebank blueberry collection. This information will allow breeders to choose genotypes within the same chromosome number that can be used for successful crossing to develop improved blueberries. U.S. blueberry production is worth more than $781.8 million.

7. Two new media for pear tissue culture. ARS researchers at the National Clonal Germplasm Repository in Corvallis, Oregon, finalized two new pear media, one for scion cultivars (Pear 1 Medium) and one for pear rootstocks (PRS). This accomplishment addresses the challenge of improving tissue culture medium for pears. These new media will be useful for tissue culture nurseries who wish to produce improved plantlets for commercial production. The pear industry which is worth about $100 million, could be expanded by 10% for rapid production of new rootstocks for fruit tree production.

8. Microsatellite marker association with red stele resistance in strawberry. The red stele disease has been spread internationally and causes death of susceptible cultivars throughout the world. ARS researchers at the National Clonal Germplasm Repository at Corvallis, Oregon, working with scientists at Agriculture and Agri-food Canada, validated the association of an SSR marker with the gene for red stele resistance in strawberry. This accomplishment addresses the need to associate phenotypes and genotypes in collections at genebanks. This result will aid strawberry breeders in screening seedlings for the desired trait.

9. Microsatellite markers determine diversity in medlar. Medlar is a historical European fruit mentioned by Shakespeare but with limited cultivation in the U.S. ARS researchers at the National Clonal Germplasm Repository in Corvallis, Oregon, used microsatellite markers to determine the genetic diversity and phylogenetic relationships of clonal medlar (Mespilus L.) accessions in the germplasm collection. This accomplishment addresses the need to evaluate genetic resources for assigned germplasm. These results will aid pome fruit breeders in improving fruit tree crops with more detailed knowledge of phylogeny of pome fruit.


Review Publications
Uchendu, E.E., Shukla, M.R., Reed, B.M., Saxena, P.K. 2013. Melatonin enhances the recovery of cryopreserved shoot tips of American elm (Ulmus Americana L.). Journal of Pineal Research. 55:435-442. DOI:10.1111/jpi.12094.
Zhumagulova, Z.B., Kovalchuk, I., Reed, B.M., Turdiev, T. 2014. Effect of pretreatment methods of dormant pear buds on viability after cryopreservation. World Applied Sciences Journal. 30(3):330-334. DOI: 10.5829/idosi.wasj.2014.30.03.14028.
Irish, B.M., Goenaga, R.J., Reed, B.M. 2014. Amending storage vessel and media improves transfer interval of Musa spp. tissue culture plantlets. Journal of Agriculture of the University of Puerto Rico. 97(1-2):1-3.
Jenderek, M.M., Holman, G.E., De Noma, J.S., Reed, B.M. 2013. Medium- and long-term storage of the Pycnanthemum (Mountain mint) germplasm collection. CryoLetters. 34:490-496.
Sitther, V., Zhang, D., Harris, D., Zee, F.T., Yadav, A., Meinhardt, L.W., Dhekney, S. 2014. Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-014-0078-5.
Hummer, K.E., Durst, R., Zee, F.T. 2013. Phytochemicals in fruits of Hawaiian wild cranberry relatives. Journal of the Science of Food and Agriculture. doi: 10.1002/jsfa.6453.
Postman, J.D., Bassil, N.V., Kim, D. 2013. OHxF paternity problem perplexes pear producers. Journal of American Pomological Society. 67(3):157-167.
Ren, L., Zhang, D., Shen, X., Reed, B.M. 2014. Antioxidants and anti-stress compounds improve the survival of cryopreserved Arabidopsis seedlings. Acta Horticulturae. 1039:57-62.
Hummer, K.E., Ballington, J.R., Davis, T.M. 2013. Asian germplasm influences on American berry crops. Journal of the American Society for Horticultural Science. 48(9):1090-1094.
Gilmore, B.S., Bassil, N.V., Barney, D.L., Knaus, B.J., Hummer, K.E. 2014. Short-read DNA sequencing yields microsatellite markers for Rheum. Journal of the American Society for Horticultural Science. 139:22-29.
Hummer, K.E. 2014. List 47: currants. HortScience. 49(4):400-401.
Hummer, K.E., Bors, R. 2014. List 47: blue honeysuckle. HortScience. 49(4):407-408.
Ren, L., Jiang, X., Gai, Y., Wang, W., Reed, B.M., Shen, X. 2013. Peroxidation due to cryoprotectant treatment is a vital factor for cell survival in Arabidopsis cryopreservation. Plant Science. 212:37-47.
Kovalchuk, I., Turdiev, T., Mukhitdinova, Z., Frovlow, S., Reed, B.M. 2014. Cryopreservation of native Kazakhstan apricot (Prunus armeniaca L) seeds and embryonic axes. CryoLetters. 35:85-89.
Reed, B.M., Wada, S., De Noma, J.S., Niedz, R.P. 2013. Mineral nutrition influences physiological responses of pear in vitro. In Vitro Cellular and Developmental Biology - Plants. 49:699-709.
Kovalchuk, I., Zhumagulova, Z., Turdiev, T., Reed, B.M. 2014. Growth medium alterations improve in vitro cold storage of pear germplasm. CryoLetters. 35:197-203.
Bian, Y., Ballington, J., Raja, A., Brouwer, C., Reid, R., Burke, M., Wang, X., Rowland, L.J., Bassil, N.V., Brown, A. 2014. Patterns of simple sequence repeats in cultivated blueberries (Vaccinium section Cyanococcus spp.) and their use in revealing genetic diversity and population structure. Molecular Breeding. 34(2):675-689.
Uchendu, E.E., Shukla, K.R., Reed, B.M., Saxena, P.K. 2014. Cryopreservation of medicinal plants: role of melatonin. Acta Horticulturae. 1039:233-242.
Poothong, S., Reed, B.M. 2013. Modeling the effects of mineral nutrition for improving growth and development of micropropagated red raspberries. Scientia Horticulturae. 165:132-141.
Kovalchuk, I., Turdiev, T., Mukhitdinova, Z., Frolov, S., Kairova, G., Reed, B.M. 2014. New technique for more rapid cryopreservation of dormant vegetative tree buds. Acta Horticulturae. 1039:137-146.
Reed, B.M. 2014. Antioxidants and cryopreservation, the new normal?. Acta Horticulturae. 1039:41-48.