Project : USDA ARS

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

Location: National Clonal Germplasm Repository

2020 Annual Report

Objectives
1: Efficiently & effectively acquire priority temperate-adapted fruit, nut, & other specialty crop genetic resources; maintain their safety, genetic integrity, health & viability; & distribute them & associated information worldwide. 1A Research heritage cultivars to broaden knowledge of the historical cultivar base. Analyze NCGR-Corvallis crop wild relative collections for gaps in taxa, localities, & diversity. 1B Acquire international & domestic germplasm samples of Corylus, Fragaria, Humulus, Pyrus, Mentha, Ribes, Rubus, Vaccinium, & their crop wild relatives via plant exploration & exchange. Fill gaps, & as opportunities arise through country agreements, acquire elite/enhanced breeding lines & heritage cultivars. 1C Efficiently & effectively establish & maintain crop genetic resources emphasizing temperate fruit, nut, & specialty crop germplasm. Identify duplication & eliminate unnecessary redundancy to maximize efficient germplasm management. 1D Distribute germplasm during the appropriate season for each crop to national & international researchers at public & private institutions & to educational groups. 2: Develop more effective genetic resource maintenance, backup, pathogen testing, & pathogen-elimination methods & apply them to priority temperate-adapted fruit, nut, & other specialty crop genetic resources. 2A Develop improved methods for conservation of temperate crop germplasm in field plantings & container production in protected environments; particularly examining pruning, media, irrigation & integrated pest management. 2B Collaborate with scientists at remote locations to improve backup conservation methods for our 8 primary genera, including growing plants in field plantings, tissue culture storage, & long term cryopreservation. 2C Apply bioassay, ELISA, & develop improved RT-PCR tests for important viruses, viroids, & phytoplasmas in primary plant collections. 2D Eliminate pathogens from select accessions with improved methods for heat therapy & meristem culture. 3: With other NPGS genebanks & Crop Germplasm Committees, develop, update, document, & implement best management practices & Crop Vulnerability Statements for priority temperate-adapted fruit, nut, & other specialty crop genetic resource & information management. 4: Develop more effective genetic resource characterization & evaluation methods, & apply them to priority temperate-adapted fruit, nut, & other specialty crop genetic resources. Record & disseminate characterization & evaluation data via GRIN-Global & other data sources. 4A Establish baseline genetic profiles for core collections with existing DNA fingerprinting sets & develop or optimize fingerprinting sets & enter information to databases. 4B Implement new high throughput genotyping systems in genetic diversity assessment (Fragaria, Pyrus), linkage & trait mapping (Rubus, Fragaria & Pyrus) and phylogenetic analysis (Rubus) & enter information to databases. 4C Develop & apply DNA tests that help identify phenotypes or useful horticultural traits for Fragaria, Rubus & Pyrus. 4D Evaluate phenotypes of flowering, ploidy, disease resistances, & upload data & image characterization to GRIN-Global.

Approach
Objective 1: Acquire, maintain, and distribute germplasm The NCGR-Corvallis is responsible for temperate fruit, nut, and specialty crop genera: Corylus, Fragaria, Humulus, Mentha, Pyrus, Ribes, Rubus, and Vaccinium, as primary collections, and Actinidia and Juglans (J. cinerea) as security backup for other genebanks. Limited amounts of crop wild relative reference collections are also preserved. Primary collections are maintained in greenhouses, screenhouses, field, and as seed. Wild species are maintained as seed stored at -18 C, with some living plant representatives. Heritage cultivars and selections are maintained as clones. Gaps in the collections are determined by research using botanical and horticultural references and species analysis software, as well as referrals through scientific colleagues. New accessions are obtained through plant exploration and exchange. When new accessions are received, information is entered to GRIN-Global and the plant is propagated. Identity is checked by morphology. Orders are received through GRIN-Global and processed in the appropriate season for the crop and plant form, according to requestor needs. Phytosanitary certification is obtained and materials are distributed according to international, regional, and local plant importation regulations. Objective 2: Improved maintenance, secure backup Inventory locations are maintained in GRIN-Global. Clones are re-propagated according to crop to maintain vigor. Pathogen status is evaluated and recorded. Core collections are established and maintained in tissue culture (for backup and distribution); protocols for cryopreservation of dormant buds of the woody plants are being established. Backup greenhouse collections are maintained for the pear and pear relative field collections. Alternative backup procedures and remote backup locations are arranged and recorded. Coordination of in situ conservation of native US germplasm is continuing with other agencies. Objective 3: Vulnerability statements and operations manual Are prepared by the curator in collaboration with the Crop Germplasm Committees. Statements for the currants, gooseberries, mint, hops, and pears will be completed. Statements for strawberries, blackberries, raspberries, have been completed and will be annually updated. Statements are reviewed and revised by expert committees. Approved statements are uploaded to GRIN-Global. The operations manual for the unit will be updated. Objective 4: Characterization and evaluation Cultivar identification will be expanded with new markers and sequencing techniques. Identity of genotypes is being compared globally with clones in other genebanks. Phenotypes of accessions are being evaluated and linked with genotypes. 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 in 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 25 genera of horticultural and agronomic crops. This genebank is assigned to conserve hazelnuts, strawberries, hops, mint, pears, currants, gooseberries, blackberries, raspberries, blueberries, cranberries and their crop wild relatives. The primary collections are a library of living plants, maintained as orchards in the field, 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 seed lots, dormant buds and other cryogenic techniques at a collaborating site in Ft. Collins, Colorado. A subset of the hazelnut collection is planted in collaboration at an ARS site in Parlier, California. In addition, back-up collections of kiwifruit and butternuts are planted in Corvallis for the ARS Davis, California, repository and it also serves as a back-up for rhubarb for the ARS Pullman, Washington, repository. Plant explorations are planned to expand the genebank to obtain: strawberries that have genes for disease resistance and continuous blooming; raspberries and blueberries that are repeat blooming or low chilling; and pears and their relatives that are dwarfing, disease resistant, or cold hardy. The site staff works with the requestors and quarantine inspectors to ensure that the plant materials meet importation permit requirements and have USDA phytosanitary certification when required. The genebank distributed more than 6,605 samples during the past year to international and domestic requestors. The molecular genetics laboratory at the genebank developed DNA fingerprinting sets for many economically important cultivars in the collection. In addition, scientists are performing studies to link genotype and phenotype for specific plants. Gender, ploidy, and phenotypes are being determined for the major fruit cultivars of the collection. This data is being entered into the Germplasm Resources Information Network (GRIN) database for public accessibility. More than 440 visitors toured the repository during 2019. The unit scientists collaborated with about 75 international scientists during this past year and obtained extramural funding for evaluation of assigned genera. Collaboration occurred through 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 Crop Germplasm Committee Plant Evaluation Grants, Northwest Center for Small Fruit Research, and USDA Animal and Plant Health Inspection Service.

Accomplishments
1. Using genes to identify loci controlling fruit sweetness in blackberry. ARS scientists in Corvallis, Oregon, searched for blackberry genes that are similar to those known for sugar production in other closely related crops. Potential genes were identified from apple, peach, and strawberry and were used to conduct targeted sequencing in 40 blackberry varieties with high and low sugar content from university and USDA breeding programs. Population modeling identified 173 genome locations that were linked with sugar production in these 40 blackberries. Molecular markers were developed and validated from the USDA and university breeding programs. The regions identified represent the first sweetness related genomic regions in blackberry. New, sweeter varieties developed using this information will become possible in the $31.1 million U.S. blackberry industry.

2. Development of the U.S. pear fingerprinting set. ARS scientists in Corvallis, Oregon, developed microsatellite or simple sequence repeat (SSR) genetic markers for variety fingerprinting, paternity testing, and identity certification in pears. The U.S. 10-SSR pear fingerprinting set was compared to the European set and had similar performance while being easier to use. The U.S. set was also compared to the new 70,000 high throughput pear marker platform and was able to come to the same conclusions when looking at pear diversity or parentage. The U.S. fingerprinting set was quick and inexpensive for determining variety identity and parentage. The U.S. set is being used to manage the U.S. pear genebank collection which breeders use to develop new varieties for the $457 million pear industry.

3. Mapping fire blight resistance in pear. ARS scientists in Corvallis, Oregon, used DNA markers from a new pear genotyping platform that contains 70,000 DNA markers, to construct genetic maps for three pear families. Use of phenotypic data for fire blight resistance for these three families and genetic maps, allowed them to detect a region on chromosome 2 determining resistance to the devastating disease fire blight. Fire blight resistance was reported in this region for the varieties ‘Harrow Sweet’ and ‘Moonglow’. A genomic analysis of the region using the new pear genome assembly identified 30 genes potentially associated with disease resistance. New tools will be developed to incorporate this resistance region into new pear varieties. Fire blight is the most devastating disease of pear in the United States and the world, causing $100 million in damage to pears and apples in the United States annually.

4. Black spot resistance in the shrub rose ‘George Vancouver’ and diagnostic markers for breeding. Four resistance genes to black spot have been identified in roses. The resistance gene from ‘George Vancouver’ had never been mapped and is thought to be unique and different from two previously identified resistance genes. ARS scientists in Corvallis, Oregon, mapped this gene in roses using data derived from a high throughput genotyping platform that contains 68,000 DNA markers, confirming it is different from the other genes. The mapping information was used in conjunction with the Chinese rose genome assembly to develop new tightly-linked tests for DNA-informed breeding. Three DNA markers in the test predicted the presence of this gene in 63 varieties. The improved diagnostic DNA test will be a great asset to the rose breeding community toward developing new disease-resistant cultivars for the $1 billion North American rose industry.

5. Identified true-to-type cultivars of blueberry in the national collection. ARS scientists in Corvallis, Oregon, used a DNA test to identify 54 blueberry varieties that match reported pedigree descriptions in the national USDA collection using parentage analysis. The identity-confirmed blueberry varieties will be the reference collection for future identification of named blueberry varieties. These results are critical to efficiently manage the U.S. national blueberry collection and special resources will be applied to manage and protect the identity of these correct varieties. The researchers will continue to add to the publicly available database, and seek parents or offspring to confirm identity through parentage analysis of the remaining varieties in the National collections. This DNA test was shared with researchers and service providers to use and provide input about its reproducibility and usefulness in confirming blueberry cultivar identity under their conditions. In 2016, the United States was the largest producer of blueberries in the world and fresh and processes cultivated blueberries were valued at $720.2 million.

6. Resistance to spotted wing drosophila in blueberry species and cultivars. ARS scientists from Corvallis, Oregon, and Poplarville, Mississippi, searched for blueberry resistance to the fruit fly, spotted wing drosophila. Samples from 29 blueberry species were sent from Oregon to Mississippi to test for resistance using a detached fruit bioassay using the fruit fly eggs, larvae, and adults. Ten blueberry species were resistant to the fruit fly and three of these were from East Asia, in the fruit fly’s native range. Blueberry species from Central and South America were also resistant. Most highbush blueberry cultivars were susceptible, though rabbiteye and other smaller, firmer types, were resistant. This fruit fly, which appeared in the United States in 2009, has now spread across the country and causes damage of more than $511 million annually to fruit production in the Western states. This research will inform breeders of parental lines than can be crossed to produce new cultivars resistant to the fly.

7. Significant plant introductions of seven temperate fruit, nut, and specialty crops. ARS scientists in Corvallis, Oregon, preserve more than 12,000 temperate fruit, nut, and specialty crop plants in a genebank. Recently seven plant introductions were featured that have contributed to the high economic value of hazelnuts, strawberries, hops, mint, pears, blackberries and blueberries. These seven plant introductions have been the basis of resistance to eastern filbert blight in hazelnuts, repeat blooming in California strawberries, Verticillium resistance in hop and mint, low chilling production of blueberries, and primocane fruiting of blackberries. The combined economic value of these germplasm contributions total more than $5 billion to annual agricultural production in the United States.

U.S. DEPARTMENT OF AGRICULTURE

National Clonal Germplasm Repository: Corvallis, OR