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ARS Home » Pacific West Area » Davis, California » Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes » Research » Research Project #434303

Research Project: Managing Genetic Resources and Associated Information of Grape, Tree Fruit, Tree Nut, and Other Specialty Crops Adapted to Mediterranean Climates

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

2020 Annual Report

The long-term objective of this project is to preserve the genetic diversity in the collections of the 14 Mediterranean crops for current and future generations. Specifically, during the next five years we will focus on the following objectives. Objective 1: Efficiently and effectively acquire priority Mediterranean climate-adapted grape, tree fruit, tree nut, and other specialty crop genetic resources; maintain their safety, genetic integrity, health and viability; and distribute them and associated information worldwide. Objective 2: Develop more effective genetic resource maintenance, evaluation, and characterization methods and apply them to priority Mediterranean climate-adapted grape, tree fruit, tree nut, and other specialty crop genetic resources. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources. Objective 3: With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for Mediterranean climate-adapted grape, tree fruit, tree nut, and other specialty crop genetic resource and information management. Basis for the objectives: The first two objectives describe the four basic tenets of the mission of the National Clonal Germplasm Repository Davis (NCGR); acquisition, maintenance, characterization and distribution of high quality, healthy, viable, true-to-type genetic resources and the associated evaluation and characterization information in GRIN-Global to the domestic and international scientific and educational communities. The third objective focuses on developing, implementing, and documenting best management practices for the collections and keeping the Crop Vulnerability Statements up-to-date. Acquisition has focused on crop wild relatives (CWRs) to fill important gaps and much of this germplasm is under quarantine and therefore in the pipeline to the Repository. Maintenance is best accomplished with young, vigorous plants and therefore the Repository is in the middle of a repropagation cycle for the collections. Distribution of germplasm to national and international researchers, breeders, and nurseries is primarily, but not limited to dormant cuttings or scionwood. Phenotypic evaluation and genetic characterization of the collections focus on understanding genetic diversity and increasing the visibility and value of the germplasm. Stakeholders are interested in phenotypic data on traits with breeding value. We use Bioversity International descriptors for germplasm evaluation and upload these data to GRIN-Global. Genetic markers discovered at the Repository and by collaborators can help clarify accession identity and assess genetic diversity, structure, and differentiation, and when combined with phenotypes will enhance the value and promote utilization of the germplasm.

Objective 1 Research Goal 1: Implement best management strategies for the acquisition, maintenance, and distribution of the genetic resources of the NCGR. Approach: This objective describes three of the four basic tenets of the mission of the National Clonal Germplasm Repository for tree fruits, nut crops and grapes (NCGR) of acquisition, maintenance of the germplasm, and distribution of high quality, healthy, viable, trueto-type genetic resources to the domestic and international scientific and educational communities. The fourth tenet is evaluation and characterization covered in Objective 2. This and other objectives are accomplished by 10 full-time staff, as well as 2-5 part-time student workers. Objective 2 Research Goal 2: To have better maintained and more thoroughly evaluated and characterized collections and to make the resulting descriptor information more complete and up-to-date in GRIN-Global. Approach: This objective describes making collection maintenance more effective and is well aligned with the maintenance portion of Objective 1. Evaluation and characterization of the collections increase the visibility and usefulness of this valuable germplasm to the stakeholder community. Phenotypic descriptors have great utilization and help guide breeders and others who must decide which accessions will help advance their program. Therefore, phenotyping is a focus of the NCGR. Genotypic descriptors, such as SSR and SNP markers are also developed for the collections and are useful to the scientific community and for combining with rich phenotypic data to discover QTLs. Objective 3 Research Goal 3: Regularly document best management practices and update Crop Vulnerability Statements every 3-4 years. Approach: This objective describes developing updated and documented best management practices for collection management and evaluation. It also is important to have up-to-date crop vulnerability statements to facilitate communication with stakeholders, identify gaps in the collection, and identify management improvements potentially increasing yield and quality of regenerated propagules. In addition, Crop Vulnerability Statements are used by Office of National Programs when communicating with leadership and lawmakers.

Progress Report
Progress was made on all 3 objectives, all of which fall under National Program 301, Component 2: Plant and Microbial Genetic Resource and Information Management; Problem Statement 2A: Plant and Microbial Genetic Resource and Information Management. Best management strategies for acquisition, maintenance, and distribution of the genetic resources of the Repository have been implemented within the current resources available. Field space is limited and the University of California, Davis, has been unable to allot more land to the National Clonal Germplasm Repository (NCGR). Therefore, all collections have stopped; however, the repository continues to receive Prunus, mainly almond seedlings each year as they clear APHIS quarantine in Beltsville, MD. To conserve valuable land, these seedlings are planted on 1 meter centers within rows. Although the Repository is not actively collecting new germplasm to fill gaps because of tight field space, there is Prunus germplasm (mainly wild almonds and apricots) that is slowly clearing APHIS quarantine in Beltsville, MD. Therefore, there is a backlog of new acquisitions arriving yearly, expanding the collections and fulfilling Objective 1. In January 2020, the Repository received 211 Prunus seedlings, representing 17 accession families. The Repository also received 8 accessions as grafted trees and 5 accessions as budwood. The budwood was grafted and the trees planted in the field. Tree and vine maintenance from Objectives 1 and 2, both in the field and nursery, are a major emphasis year-round. This year, the contractor who prunes the grapes lost his crew to another contactor who pays more. Once the Repository was notified, it was too late to get another contactor. Therefore, along with staff, a volunteer force was utilized to prune the National grape collection. The almond and persimmon collections continue to be repropagated and their locations switched because of an outbreak of oak root fungus (Armillaria) in the almond and the fact that there is resistance in the persimmons. To continue to make room, the old almond trees were pushed out in spring 2020 by a bulldozer. The apricots have largely been repropagated and reestablished. Therefore, the old apricot trees were bulldozed in Spring 2020 to make room for repropagating the cherry collection. As part of collection maintenance from Objectives 1 and 2, during the week of June 15, 2020 the pistachios, walnuts, wild and domestic peaches, apricots, plums, olives, and the field nursery plants that are mainly wild relative walnuts and almonds were mechanically hedged. Additional hand pruning was done on the peaches, kiwifruit, pomegranates, and figs. As well, crops were sprayed for powdery mildew, leaf-footed bug, and foliar phylloxera. Mowing and weed control are ongoing. During March 2020, the dormant cuttings were distributed to requestors in the scientific community who were able to receive the material in the middle of the pandemic. International shipments became impossible because there was nobody to receive them so they have been stopped. During the summer leaves and cuttings were distributed domestically, mainly to local collaborators. Backing up the collections is necessary where maintenance fails, or plants do not thrive. Because of the shutdown related to the pandemic, only a few samples of pollen were collected and shipped to ARS, Fort Collins, Colorado, for cryopreservation. It is important to evaluate the collections and post the results in the Germplasm Resources Information Network (GRIN) Global so that stakeholders can better understand and use the collections in their research. Knowledge of amount and patterns of distribution of genetic diversity within and among species' gene pools is of considerable value for effective conservation, enrichment, management, and utilization of genetic resources. Because of maximum telework, GRIN-Global has received considerable attention and is much more up-to-date with 5817 inventory records modified and 1989 inventory records created. More data, including three pictures each of 100 fig accessions have been added to GRIN-Global. Microsatellite markers and single nucleotide polymorphisms are used to: 1) quantify and describe the patterns of distribution and genetic diversity; 2) establish the genetic identity of accessions; 3) classify them based on genetic similarities and distances; and 4) analyze genetic structure differentiation. The table and wine grape collections were genetically characterized using 21 microsatellite loci and single nucleotide polymorphisms (SNPs). This portion of Objective 2 is currently in progress. The DNA of entire wine and table grape collections numbering about 1,400 clonal accessions has been re-extracted. The microsatellite genotyping for 21 loci has been completed and data are being scrutinized. Gaps and other anomalies in the data are being examined to correct the deficiencies in data to assemble a final data set. Upon completion, the data will be analyzed for assessing genetic structure and differentiation, in conjunction with approximately 1,800 loci SNP data. The goal of this project is to compare the effectiveness of microsatellite polymorphisms and SNPs in assessing the genetic diversity and classification of grape germplasm. The results will be published. In a related study with 1378 cultivated (Vitis vinifera) and the wild (V. v. ssp. sylvestris) grape representing the world-wide distributions indicated that there is a significant differentiation between the western European and the Caucasus wild grapes. As might be predicted, Caucasus wild grapes are closely allied with the Caucasus cultivated grapes and the western European wild grape showed close association with the European wine grapes.

1. Crop germplasm distribution. The germplasm collections were assembled and managed to be made available to scientists, especially geneticists and breeders who develop new cultivars to address the needs of growers and consumers. Most items were shipped in March 2020 as three to five cuttings per item or accession. Leaves, pollen, and fruit are also sent if requested. ARS scientists and staff in Davis, California, shipped 6,577 items to 256 stakeholders (9 international and 247 domestic) to research and education entities when genetic diversity or genetic standards are a requirement. Not all requests can be accommodated. The majority of the shipments, more than 93 percent, were to domestic customers.

2. Evaluation of rooting ability of Prunus germplasm. Not all accessions graft well and the ability to root cuttings is an alternate propagation technique that can be utilized. Stem cuttings were collected from cultivated and wild relatives of almond, peach, and plum. These cuttings were treated with various concentrations of the rooting compound, indolebutyric acid (IBA). The almond cuttings, regardless of accession and auxin concentration basically did not root; whereas there was moderate rooting of the peaches, with best rooting of the plums. There were differences among accessions, showing that there is a genetic component to the ability of a cutting to form adventitious roots.

3. Domestication history of cultivated grape unraveled. We investigated the level and pattern of distribution of genetic diversity in a set of 1378 cultivated (Vitis vinifere) and wild (V. v. ssp. sylvestris) grapes representing a world-wide distribution. Genetic polymorphisms at 20 microsatellite loci were assayed to examine the genetic structure and differentiation within and between cultivated and wild grapes. The results indicated that there is a significant differentiation between the Western European and the Caucasus wild grapes. As might be predicted, the Caucasus wild grapes are closely allied with the Caucasus cultivated grapes and the Western European wild grapes showed close affinity to the European wine grapes. The results of this study revealed the evolutionary dynamics of domestication and contributed significantly to the understanding of domestication history of cultivated grape.

Review Publications
Chater, J.M., Merhaut, D.J., Preece, J.E. 2019. Diagnosis and management of nutrient constraints in pomegranate. In: Anoop Kumar Srivastava, Chengxiao Hu, editors. Fruit Crops, Diagnosis and Management of Nutrient Constraints. 1st edition. Elsevier. p.681-691.
Aradhya, M.K., Velasco, D., Wang, J., Ramasamy, R., You, F.M., Leslie, C., Dandekar, A., Luo, M., Dvorak, J. 2019. A fine-scale genetic linkage map reveals genomic regions associated with economic traits in walnut (Juglans regia). Plant Breeding Reviews. 138(5):635-646.
Zhu, T., Wang, L., You, F.M., Rodriguez, J.C., Deal, K.R., Chen, L., Li, J., Chakraborty, S., Balan, B., Jiang, C., Brown, P.J., Leslie, C.A., Aradhya, M.K., Dandekar, A.M., Mcguire, P.E., Kluepfel, D.A., Dvorak, J., Lou, M. 2019. Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species. Horticulture Research. 6:.
Khoury, C.K., Kates, H.R., Carver Jr, D.P., Achicanoy, H.A., van Zonneweld, M., Thomas, E., Heinitz, C.C., Jarret, R.L., Labate, J.A., Reitsma, K., Nabhan, G.P., Greene, S.L. 2019. Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.). Plants, People, Planet. 2(3):269-283.
Johnson, E.P., Preece, J.E., Aradhya, M.K., Gradziel, T. 2019. Rooting response of Prunus wild relative semi-hardwood cuttings to indole-3-butryic acid potassium salt (KIBA). Scientia Horticulturae. 263.