2010 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.
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.
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.
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. Replacing 5306-21000-015-00D (3/08).
In FY 10, the repository acquired 148 new accessions representing 16 species of fruit and nut crop species through explorations in Azerbaijan and Kyrgyzstan. One hundred twenty-seven Prunus seedlings from nine accessions from Armenia have been established in the field nursery for further evaluation to select useful genetic material to be included on the collection. During 2009-10, 5348 germplasm samples were distributed to 487 stakeholders, nearly 90% of which went to U.S. public/private sector breeders, nursery industries, academic institutes, and private growers.
The molecular characterization of germplasm using microsatellite markers is ongoing and substantial progress was made filling gaps and analyzing data for peer reviewed publications and uploading of data onto GRIN. Since October 2009, 4963 genetic data, 80131 phenotypic, and 398 photographic images were uploaded on to GRIN. A rootstock block was established and grafting of peach accessions is ongoing to establish a new peach block. The entire olive collection of 127 accessions was genotyped and a manuscript submitted to the Journal “Genetic Resources and Crop Evolution.” Three hundred forty accessions representing 52 taxa of Vitis have been analyzed to unravel the genetic structure and phylobiogeography. Genetic diversity, structure and differentiation has been analyzed and a peer reviewed publication appeared in a 2010 issue of the international journal “Genetica.” Genetic structure and differentiation have been analyzed in cultivated walnut by genotyping the entire collection and results were published in the proceedings of the international walnut symposium. 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 25 economic phenotypes collected across two consecutive years to perform association analysis. The collaborative efforts with the plant pathology and genetic group to screen wild walnut germplasm for crown gall, nematode, and Phytophthora are ongoing and the results indicate a number sources of resistance to these soil-borne pathogens diseases. A morphometric analysis on a set of 500 cultivated grape accessions including wine, table and dual-use type using 25 nominal, ordinal, and metric traits has been performed and the results presented in the International Grape Breeding meeting in Geneva, New York during July-August, 2010.
Germplasm distributions. ARS scientists in Davis, CA, distribute germplasm twice yearly during early Spring and Fall and includes clonal shoots, seed, pollen, and DNA samples. Our 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 the years with minor crops, such as pomegranate and figs in great demand. The Davis repository shipped out 5348 germplasm items during 2009-10. 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.
Germplasm characterization. Genetic resources of vine, tree fruit, and nut crop germplasm adapted to Mediterranean climates need to be characterized for researchers and breeders who are developing new crops. ARS scientist in Davis, CA genotyped the entire olive collection of 127 accessions. Three hundred forty accessions representing 52 taxa of Vitis were analyzed to unravel the genetic structure and phylobiogeography. Genetic structure and differentiation were analyzed in cultivated walnut by genotyping the entire collection. 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 further genetic analysis. The collaborative efforts with the plant pathology and genetic group to screen wild walnut germplasm for crown gall, nematode, and Phytophthora is ongoing and the results so far indicate a number of sources of resistance to these soil-borne pathogens. A morphometric analysis on a set of 500 cultivated grape accessions including wine, table and dual-use type using 25 nominal, ordinal, and metric traits has been performed. Characterization of genetic resources increases its usefulness to breeders.
Acquisition of germplasm. Explorations were focused on collecting germplasm to fill in gaps in the collections, especially in the secondary and tertiary gene pools consisting of wild relatives, which are the main sources of genes for biotic and abiotic stresses and extended adaptation. The National Clonal Germplasm Repository (NCGR), Davis plant explorations during 2009 resulted in acquisition of 86 accessions representing 14 species of fruit and nut species from Azerbaijan and 62 accessions of walnut and almond from Kyrgyzstan. The exploration and exchange will provide genetic diversity previously unavailable to US scientists and other horticultural interests.
Preece, J.E. 2010. Acclimatization of plantlets from in vitro to the ambient environment. Wiley Encyclopedia of Industrial Biotechnology. DOI:10.1002/9780470054581.eib593 p. 1-9.
Aradhya, M.K., Stover, E.W., Velasco, D., Koehmstedt, A. 2010. Genetic structure and differentiation in cultivated fig (Ficus carica L.). Genetica. 138:681-694
Stover, E., Aradhya, M., Yang, J., Bautista, J., Dangle, G.S. 2010. Investigations into the origin of 'Norton' grape using SSR markers. In: Proceedings of Florida State Horticultural Society. 122:19-24.
Muganu, M., Dangl, G., Aradhya, M., Frediani, M., Scossa, A., Stover, E. 2009. Ampelographic and DNA characterization of local grapevine accessions of the Tuscia area (Latium, Italy). American Journal of Enology and Viticulture. 60:110-115.
Soleri, D., Koehmstedt, A.M., Aradhya, M.K., Polito, V., Pinney, K. 2010.Comparing the historic olive trees (Olea europaea L.) of Santa Cruz with contemporaneous trees in the Santa Barbara, CA area: a case study of diversity and structure in an introduced agricultural species conserved in situ. Genetic Resources and Crop Evolution. Genet. Resour. Crop Evol. 57:973-984.