2013 Annual Report
1a.Objectives (from AD-416):
Objective 1: Efficiently and effectively conserve, back-up, regenerate, characterize, and evaluate genetic resources of grape, tree fruit, tree nut, and other specialty crops adapted to Mediterranean climates, and distribute germplasm and associated information worldwide.
Objective 2: Strategically fill gaps in the current coverage of genetic resource collections for grape, tree fruit, tree nut, and other specialty crops adapted to Mediterranean climates through international and domestic germplasm exchanges and plant explorations.
Sub-objective 2A- Acquire Vitis, Prunus, Juglans, Ficus, Olea, Pistacia, Diospyros, Actinidia, and Morus and related wild relatives from their centers of origin and diversity in Eurasia (Mediterranean, Caucasus, and Central Asian nations) through plant exchanges and explorations.
Sub-ojective 2B - Acquire germplasm of Vitis, Prunus, Juglans, Diospyros, and Morus native to the U.S. though domestic explorations and exchange.
Objective3: In collaboration with other NPGS genebanks and research projects, devise and apply superior tissue culture and cryopreservation methods to safeguard germplasm collections of grape, tree fruit, tree nut, and other specialty crops adapted to Mediterranean climates.
Objective 4: In collaboration with other NPGS genebanks and research projects, develop novel genetic marker systems for characterizing genetic resources of grape, tree fruit, tree nut, and other specialty crops adapted to Mediterranean climates. Apply those markers to more efficiently and effectively manage the site's germplasm collections and to facilitate their use in germplasm acquisition, breeding and research projects.
Sub-objective 4A- In cooperation with ARS and university collaborators, develop and apply new genetic markers such as simple sequence repeat (SSR) and single nucleotide markers (SNPs) to quantify and describe genetic diversity in the collections.
Subobjective 4B- Generate multilocus fingerprint data to fill in existing gaps and to expand on the existing molecular data for priority crops such as Vitis, Prunus, Juglans, Ficus, Olea, and Pistacia to determine the identity, diversity, and systematic relationships within and among species for effective conservation, management, and utilization of genetic resources. Upload characterization data on to the Germplasm Resources Information Network (GRIN-Global) database.
Sub-objective 4C- Continue on-going phenotypic evaluation of germplasm collections of priority species such as Vitis, Prunus, Juglans, Ficus, Olea, and Pistacia, and upload the data to GRIN-Global.
1b.Approach (from AD-416):
Strategically acquire germplasm and conserve a broad spectrum of genetic diversity in the genetic resources assigned to the repository, and characterize them for effective management and utilization collections. In collaboration with university and ARS researchers, develop, and apply novel genetic markers and genomic techniques for effective characterization of collections and apply in-vitro and cryopreservation techniques to backup collections. In partnership with the private nurseries, acquire appropriate rootstocks to propagate and establish new germplasm blocks as a part of periodic rejuvenation program. Develop and execute collaborative disease testing and disease elimination programs to improve phytosanitary status of collections. Consult Crop Genetic Resources Committees and crop breeders for phenotyping germplasm collections to facilitate genotype-phenotype correlations to enhance utilization. Upload all updated inventories of field, backup, and in-vitro collections, molecular, genomic, and phenotypic data and results on to the Genetic Resources Information Network (GRIN) for public access.
Carefully plan and execute plant explorations in the crop centers and secondary centers of origin, diversity, and domestication as per the guidelines of the USDA-ARS/NGRL Plant Exchange Office (PAO) and in accordance with the Convention of Biological Diversity to enrich and fill-in gaps in collections. Plan and execute domestic explorations and exchanges within the U.S. for strategic enrichment of germplasm collections of native taxa. Plant explorations and exchange programs will focus on enriching both cultivated and wild taxa in different gene pools. Collect extensive passport data including the GPS coordinates of collection locations and upload on to the GRIN. Follow all federal and state quarantine regulations and route all germplasm shipments through the USDA-ARS National Plant Germplasm Quarantine Center for inspection, testing, and pathogen elimination and release. Follow post-entry quarantine process and procedures for newly acquired germplasm and upon inspection and release by the state and county inspectors, propagate and establish plants in field and backup collections. Standardize and apply plant tissue culture techniques for in-vitro backup and cryopreservation of germplasm collections and also virus elimination as appropriate.
Genotype germplasm collections using microsatellite and Single Nucleotide Polymorphism Markers to assess genetic diversity, structure, and differentiation and to quantify and describe genetic diversity within and among population and taxa. Utilize cpDNA sequence variation to study taxonomic diversity and phylogenetic relationships within and among crop genera. Perform appropriate univariate and multivariate statistical techniques, and quantitative, and population genetic, and taxonomic analyses to analyze genetic diversity within and among taxa in different gene pools.
Distribute appropriate germplasm in the form of seed, bud and graftwood, pollen, and DNA, and associated information, nationally and internationally to private and public sector breeders, nurserymen, researchers, and others.
This report documents progress for 5306-21000-020-00D which started March 8, 2013 and continues research from 5306-21000-018-00D, "Management of Genetic Resources for Vitis, Prunus, Juglans, Ficus, Olea, Pistacia, Punica, Diospyros, Actinidia, and Morus". Because this is a continuation, the accomplishments build on those in the 5306-21000-018-00D progress report.
This report continues the progress reported for the first half of FY2013. In addition to continuing these activities, the following progress has been made:
Studies on the genetic diversity in the collections has continued throughout the fiscal year continuing previous studies, with focus on walnuts, grapes, olives, pomegranate, and Prunus.
The National Clonal Germplasm Repository (NCGR) continues to collaborate with ARS scientists at Fort Collins, Colorado, on cryopreservation studies. During this cycle, the focus has been on grapes.
Although no new germplasm has been acquired since March 2013, an exploration proposal was submitted to the USDA, ARS, National Germplasm Repository Laboratory (NGRL) Plant Exchange Officer, Beltsville, Maryland. The proposal is to fund an plant exploration trip to collect Prunus spp. germplasm in the Central Asian Republics of Kazakhstan and Kyrgyzstan during July-August, 2014. This region is near the center of origin of many of the crops in the collection making the genetics especially valuable. Continuing to enrich the collection greatly enhances its value.
The genetic diversity in walnuts and grapes continues to be analyzed. The focus on the grapes is the diversity in the wild progenitor, V. vinefera sylvestris. Understanding this diversity leads to greater insight into cultivated grapes and the center of origin of these grapes. This is not only useful to breeders, but to curators looking to fill genetic gaps in collections.
Selecting seedling wild relatives. During 2010, ARS scientists at Davis, California, established a field nursery to allow for evaluation of seedling populations of wild relatives of the crops in the collection. Using both genetic markers and phenotypic traits, the seedlings continue to be evaluated. From each population, the 5 most diverse seedlings will be selected for inclusion into the permanent collection. Use of the nursery makes land use much more efficient than adding every seedling to the permanent collection.
Repropagation. The propagation of the entire peach collection has been completed and the grafted trees are growing in the National Clonal Germplasm Repository (NCGR) container nursery. The field at University of California, Davis, Wolfskill Experimental Orchard in Winters, California, is being prepared for planting in mid to late September. Additionally, the fig collection continues to be repropagated. The Kiwifruit collection has been consolidated in Davis after being split between the NCGR-Davis, California, and NCGR-Corvallis, Oregon and progation efforts continue. The orchard is being prepared for light fertilization this fall and again next spring. This repropagation not only consolidates the collections, but results in younger, healthier, and more robust plants.
Genetic diversity in pomegranate. Very little has been published on genetic diversity in pomegranates. ARS scientists at Davis, California, have conducted studies to discover genetic (microsatellite) markers that show polymorphism in pomegranate. Some markers have been discovered with polymorphism in pomegranate. This will further elucidate the genetic variation and therefore usefulness of the pomegranate collection.
Germplasm distribution. ARS scientists at Davis, California, routinely distribute germplasm. Distribution of cuttings was completed. In addition, pollen, leaves, and leafy cuttings were distributed. The collection exists so that it can be utilized. Distribution of the genetics to scientists worldwide helps solve many challenges related to production of these tree fruits, nut crops, and grapes.
Preece, J.E., Aradhya, M.K. 2013. The Prunus collection at the National Clonal Germplasm Repository in Davis, California. Acta Horticulturae. 985:47-54.