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United States Department of Agriculture

Agricultural Research Service


Location: Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes

2011 Annual Report

1a. Objectives (from AD-416)
The long-term objective of this project is conservation, characterization, and distribution of plant genetic resources of designated Mediterranean-adapted fruit and nut crops and their wild-species relatives. Over the next 5 years we will focus on the following objectives: Objective 1: Strategically expand the genetic diversity in genebank collections and improve associated information for priority vine, tree fruit, and nut crops (and their wild relatives) adapted to Mediterranean-like climates. Sub-objectives: a. Acquire samples of Vitis, Prunus, Juglans, Pistacia, and Punica from Turkey and the Caucasus nations to fill current gaps in NPGS collections of these priority genera. b. Survey existing U. S. domestic (California and other states) collections of priority crops, identify material that would fill gaps in NPGS collections, and begin acquiring and characterizing them, initially emphasizing Vitis, Prunus, and Ficus cultivated material and germplasm of related wild species. Objective 2: Conserve and regenerate priority vine, tree fruit, and nut crop genetic resources adapted to Mediterranean-like climates efficiently and effectively, and distribute disease-free samples (whenever feasible) and associated information worldwide. Sub-objectives: a. Conserve, regenerate, and distribute vine, tree fruit, and nut genetic resources and associated information, emphasizing Vitis, Prunus, Juglans, Ficus, Olea, and Punica. b. Backup primary collections of Vitis, Prunus, Juglans, Ficus, and Olea, via high-density nurseries, cryopreservation, and tissue culture. c. In collaboration with University of California, Davis Foundation Plant Services and the Canadian Plant Germplasm System, process 70 accessions of NPGS warm-season grapes through quarantine and make them available for distribution. Objective 3: Strategically characterize (“genotype”) and evaluate (“phenotype”) priority vine, tree fruit, and nut crop genetic resources adapted to Mediterranean-like climates for molecular markers and key horticultural traits such as adaptation and product quality. Sub-objectives: a. In cooperation with other ARS and university collaborators, develop and apply new genetic markers for phylogenetic and genetic diversity analyses of priority crops, emphasizing simple sequence repeat (SSR) in Vitis, Prunus, Juglans, Ficus, Olea, and Pistacia. b. Generate SSR “fingerprints” for ca. 1,000 accessions of priority crops, emphasizing Vitis, Prunus, Juglans, Ficus, Olea, and Pistacia, and use them to determine the identity, diversity, and systematic relationships of these genetic resources, and to enhance the effectiveness of genetic resource management. Incorporate characterization data into GRIN and/or other databases. c. Extend ongoing cooperative research to evaluate horticultural quality for ca. 1,000 accessions of Vitis, Prunus, Juglans, Ficus, Olea, and Pistacia, and incorporate phenotypic data into GRIN and/or other databases.

1b. Approach (from AD-416)
Obtain new acquisitions to fill collection gaps and broaden diversity. Make contacts with appropriate institutions to exchange diverse germplasm. Through interactions with CGC's, develop exploration proposals. Engage in cooperative research on cryopreservation of buds. Place evaluation, passport, and source data on GRIN and local database. Expand assessment of genetic diversity by SSR technique and other molecular techniques in Vitis and other genera. Obtain descriptor data for traits of most value to users. Distribute to researchers worldwide. Inform public.

3. Progress Report
The entire NCGR persimmon (155 accessions) collection was genotyped for 13 microsatellite loci. This also included 53 accessions from the UC Davis collection, and 70 from the UC South Coast Experimental Station (SCES, Irvine). The fragment analysis is currently being performed to size alleles for different loci. The multilocus genotype data will be analyzed to establish genetic identity and estimate similarity between different collections. The new genotypes, if there are any in the UC Davis and SCES collections, will be added into the NCGR collections. Peach and almond data updated recently are being analyzed to quantify and describe genetic diversity and differentiation within and between the collections. Five diverse almond genotypes along with five wild almond accessions will be sequenced and combined with peach sequences developed in a different UC collaborator’s project for SNP discovery. The SNPs will be in mapping genes conferring resistance to soil borne diseases in a Prunus rootstock development project. We have examined the possibility of using tetra-nucleotide repeat microsatellite loci to genotype olive collections. Out of a dozen loci tried, seven amplified but showed low polymorphism. In the walnut industry/UC Discovery funded project we have phenotyped the entire NCGR collection Juglans regia for two years and the data are being tabulated for use in association analysis. In collaboration with the Crops Pathology and Genetics Group, characterization of wild Juglans to identify novel sources of resistance to soil borne diseases is continuing. So far a number of J. microcarpa, J. major, J. hindsii, and one J. cathayensis accessions have shown promising levels of tolerance to crowngall, Phytophthora spp., and/or lesion nematodes. They are being crossed with J. regia to produce interspecific hybrids to test them for commercial exploitation as new rootstocks. To date, more than 300 hybrids have been put into ovule culture to clonally propagate them for further testing and establishment of field trials. The Actinida (kiwifruit) collection has been re-consolidated in Davis. Because of concern about how the cold hardy kiwifruit would survive in Davis, the cold-hardy kiwifurit collection was moved to the Corvallis genebank. The remaining backup plants in Davis have grown well with no problems. The Corvallis site will become the backup site for the hardy kiwifruit.

4. Accomplishments
1. Germplasm distributions. Germplasm distribution from the National Clonal Germplasm Repository at Davis, CA, occurs twice yearly during early Spring and Fall and includes clonal shoots, seed, pollen, and DNA samples. Customers include private and public sector breeders; geneticists; members of the academic community; and nursery, private, and backyard growers. The demand for fruit and nut crop germplasm has remained steady over years, with minor crops, such as pomegranate and figs in great demand. The distribution is essential to increase the genetic diversity in fruit and nut crops, facilitating adaptation to changing climate and both insect and disease pressures. This aids in the development of new crop cultivars to address grower and consumer needs.

2. Germplasm conservation and management. Genetic resources of vine, tree fruit and nut germplasm adapted to Mediterranean climates need to be maintained and preserved for food security with access for researchers and breeders who are developing new crop cultivars. Corrective dormant and Spring pruning of almond, walnut, persimmon, and Mulberry collections has been completed by ARS scientists in Davis, CA, to improve overall health of the collections and phenological and phenotypic evaluations. Repropagation of the entire fig and kiwi collections along with recently quarantine-released germplasm has been undertaken to rejuvenate and replant fig and kiwi collections. Twenty-five cold hardy kiwi species from the Corvallis repository has been propagated for field planting and olive trees which were destroyed during 2011 wind storm were replanted from the backup collection.

3. Characterization of genetic resources of vine, tree fruit, and nut crops. In an effort to enhance the value and utility of germplasm collections, ARS scientists at Davis, CA, have characterized the following germplasm collections using molecular markers: (1) The entire olive collection of 127 accessions was genotyped using 15 microsatellite loci; (2) Three hundred forty accessions representing 52 taxa of Vitis were analyzed using 18 microsatellite loci and 2471 AFLPs to unravel the genetic structure and phylobiogeography; (3) Genetic structure and differentiation was analyzed in cultivated walnut by genotyping the entire collection with 21 microsatellte loci; (4) The walnut industry/UC Discovery funded project has identified 6000 single nucleotide polymorphisms to be used in genotyping the walnut collection and the data will be merged with twenty-five economic phenotypes collected across two consecutive years to perform association analysis; and (5) The collaborative efforts with the plant pathology and genetic group to screen wild walnut germplasm for crown gall, nematode, and Phytophthora has identified a number of resistant accessions to be used in rootstock development. All molecular data have been uploaded onto GRIN for public access.

Review Publications
Preece, J.E. 2011. Micropropagation in stationay liquid media. Propagation of Ornamental Plants. 10(4):183-187.

Pitcher, A.M., Aradhya, M.K., Soleri, D., Smith, J.L., Polito, V.S. 2010. Molecular characterization of genetic diversity, structure, and differentiation in the olive (Olea europaea L.) germplasm collection of the united states department of agriculture. Genetic Resources and Crop Evolution. 58:519-539.

Gunn, B.F., Aradhya, M.K., Salick, J.M., Miller, A.J., Yongping, Y., Lin, L. 2010. Genetic variation in walnuts (Juglans regia and J. sigillata; Juglandaceae): Species distinctions, human impacts, and the conservation of agrobiodiversity in Yunnan, China1 . American Journal of Botany 97:660-671.

Ibrahimovi, Z., Mcgranahan, G.H., Leslie, C.A., Aradhya, M.K. 2010. Genetic diversity in walnut (Juglans regia) from the caucasus nation of Azerbaijan. Acta Horticulturae. 861:163-170.

Aradhya, M.K., Woeste, K., Velasco, D. 2010. Genetic Diversity, Structure and Differentiation in Cultivated Walnut (Juglans regia L.). Acta Horticulturae. 861:127-132.

Myles, S., Boyko, A., Owens, C.L., Brown, P., Fabrizio, G., Aradhya, M.K., Prins, B.H., Reynolds, A., Chia, J., Ware, D., Bustamante, C., Buckler IV, E.S. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences. 10.1073/pnas.1009363108.

Last Modified: 06/25/2017
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