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United States Department of Agriculture

Agricultural Research Service

Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository (Corvallis, Oregon)

2013 Annual Report


1a.Objectives (from AD-416):
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.


1b.Approach (from AD-416):
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.


3.Progress Report:
This report documents progress for this new project which started February 26,2013 and continues research from Project 5358-21000-038-00D, "Management of Temperate Fruit Nut and Specialty Crop Genetic Resources. 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 at 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 just determined the pedigree of many pear samples. Surprisingly, they discovered that one series of pear rootstocks had ‘Bartlett’ as the father – although for about 40 years pear breeders had assumed that ‘Farmingdale’ was the father. In addition to genotyping, the genetics lab has determined pedigrees for many cultivated types of hazelnut, strawberry, raspberry and blueberry plants. 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. Cold hardiness and disease resistance of quince was determined.


4.Accomplishments
1. Determined paternity of pear rootstocks using molecular markers and pedigree analysis. A series of pear rootstocks were named about 40 years ago, assuming that their pedigree was’ Old Home x Farmingdale’. Our research unexpectedly showed that ‘Bartlett’ not ‘Farmingdale’ is the pollen parent of these selections. These rootstocks are valued at millions of dollars annually in international nursery plant production. This research finding implies that ‘Farmingdale’ has not been – but could yet be – used in pear rootstock breeding programs for disease resistance and dwarfing quality.

2. Response-surface statistical analysis to improve growth of hazelnut plantlets in vitro. This technique used a quadratic model to estimate the complex response of plantlets. Content of some of the elements such as calcium and magnisium significantly improved plantlet growth for 5 cultivars tested. This research will provide the hazelnut industry with new tissue culture methods to grow plants faster. The hazelnut industry which was worth $89.3 million in 2011, could be expanded by 10% for rapid production of new disease resistant cultivars.

3. Response-surface statistical analysis to improve growth of red raspberry plantlets in vitro. This technique used a quadratic model to estimate the complex response of these plantlets. Content of calcium and magnesium compounds significantly improved plantlet growth for 5 cultivars tested. The statistical technique models and predicts results to estimate the optimal media for growing raspberries. This research supports the red raspberry industry which had a total US production value of about $50 million annually.

4. New quince evaluation. The pear industry uses quince as a dwarfing rootstock. Unfortunately the quince that has been traditionally used is not as cold hardy as the pears, so this approach cannot be used for growing pears in northern latitudes up until now. ARS researchers have identified 22 very cold-hardy Cydonia genotypes as potential productive, dwarfing pear rootstocks and a subsequent propagation study determined that softwood cuttings were more successful than hardwood cuttings. Worldwide, there are about 106,000 acres of quince in production with a total crop of 335,000 metric tons worth US $265 million. United States production is mainly in California’s San Joaquin Valley. This research could increase quince production by 10 % in the Pacific Northwest.

5. Evaluated Asian strawberry species for cold hardiness and disease resistance. While some strawberry species were sensitive to powdery mildew, leaf scorch, and frost, others were disease resistant and survived winter well. Knowing these traits will be useful to breeders who are selecting broader gene pools for their crossing populations. These wild strawberries with good traits could be used for parents to increase the strawberry gene pool for breeders. The strawberry industry in the US is worth $2.45 billion annually but with new diverse strawberries it could be increased by 10% in northern production areas.

6. Implemented a new technique called: microsatellite allele dosage configuration establishment (MADCE). This technique is useful in fingerprinting plants which have many sets of chromosomes. Commercial strawberries have 8 sets of chromosomes. A strawberry could have, say, 4 sets of the same allele. This technique measures “the area under the curve” to determine the dosage (number of alleles) of that individual. This will help determine plant ancestors by mapping out “subgenomes” and more accurately determine fingerprinting of particular plants.

7. Rejuvenation of the USDA living pear germplasm collection. An 8 acre orchard representing world diversity of pears was established in 1983. This year the 2,000 tree orchard, of which a majority are about 30 years old, was significantly pruned to reduce the height and open up the center of the trees. The invigorated trees will provide more propagating wood in the coming years. The drip irrigation was replaced and the entire orchard was relabeled with durable long-lasting identity tags. About 2,000 accessions are distributed annually. These trees are worth more than US $40,000 at face value, but include priceless diversity.

8. Developed the first high throughput single nucleotide polymorphism (SNP) chip for strawberries with 8 sets of chromosomes. This is much more complex to interpret in comparison with strawberries or other organisms having the usual 2 sets of chromosomes. The SNP chip allows researchers to determine genotypes for 1,500 markers simultaneously, so it is very efficient. These genotypic markers will be linked to the phenotypic evaluation performed of the same strawberry plants. Phenotypic traits such as remontancy (repeat blooming), disease evaluation, and fruit quality characteristics will be measured in the octoploid strawberries and will be linked to the SNP genotypes. This technique will allow breeders to screen strawberry seedlings much faster for traits of interest. It has the potential to revolutionize strawberry plant breeding techniques.


Review Publications
Wada, S., Niedz, R.P., De Noma, J.S., Reed, B.M. 2013. Mesos components (CaC12, MgSO4, KH2P04) are critical for improving pear micropropagation. In Vitro Cellular and Developmental Biology - Plants. 49:356-365.

Reed, B.M., Wada, S., De Noma, J.S., Niedz, R.P. 2013. Improving in vitro mineral nutrition for diverse pear germplasm. In Vitro Cellular and Developmental Biology - Plants. 49(3):343-355. DOI:10.1007/s11627-013-9504-1.

Hummer, K.E. 2013. Manna in winter: indigenous Americans, huckleberries, and blueberries. HortScience. 48:413-417.

Barney, D.L., Hummer, K.E. 2012. Rhubarb botany, horticulture, and genetic resources. Horticulture Reviews. 40:147-182.

Last Modified: 10/20/2014
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