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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

2018 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
This project began in March 2018 and continues the research from 2032-21000-020-00D, “Management of Genetic Resources and Associated Information for Grape, Tree Fruit, Tree Nut, and Other Specialty Crops to Mediterranean Climates”. See the report for the previous project for additional information. 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. No new germplasm was received since this project began in March 2018. Tree and vine maintenance, both in the field and nursery, are a major emphasis during the summer growing season. This summer the walnuts, peaches, and plums were mechanically hedged. Additional hand pruning was done on the walnuts, peaches, apricots, pomegranates, and olives. Crops were sprayed for powdery mildew, leaf-footed bug, and foliar phylloxera. Mowing and weed control are ongoing. During March 2018, the remaining dormant cuttings were distributed to requestors in the scientific community. During the summer peach fruit, leaves and cuttings were distributed both domestically and internationally. Backing up the collections is necessary where maintenance fails, or plants do not thrive. Flowering branches on some wild peach species were bagged to ensure self-fertilization and the seeds shipped to ARS, Ft. Collins, Colorado. Seeds are frozen in liquid nitrogen (N) intact, within the pit (endocarp). This year five accessions were bagged, but only two formed fruit. This is a viable way to back up wild relatives and a considerable improvement on not having any of the collection backed up. It is important to evaluate the collections and post the results in Germplasm Resources Information Network (GRIN) Global so that stakeholders can better understand and exploit the collections. 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. 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 project 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.

1. Crop germplasm distribution. The germplasm collections were created 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 2018 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, ship 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. Pruning of the collections. ARS scientists and staff in Davis, California, regularly prune the plant accessions in the repository as they are planted and spaced very closely. Mechanical hedging is much more efficient than hand pruning and was used on walnuts. The Prunus collection was also hedged to bring the canopy of the trees down so that they can be worked from the ground, making caring for them easier and more manageable. Hedging also reinvigorates the trees, allowing for new growth and increased sunlight and air-flow.

Review Publications
Preece, J.E., Chater, J.M., Merhaut, D.J., Jia, Z. 2018. Pomegranate. HortScience. 53(6):770.
Gasic, K., Preece, J.E., Karp, D. 2018. Register of new fruit and nut cultivars list 49. HortScience. 53(6):748-776.
Knap, T., Aradhya, M.K., Arbeiter, A., Hladnik, M., Bandelj, D. 2018. DNA profiling of figs (Ficus carica L.) from Slovenia and Californian USDA collection revealed the uniqueness of some North Adriatic varieties. Genetic Resources and Crop Evolution. 65:1503-1516.
Migicovsky, Z., Sawler, J., Gardner, K., Aradhya, M.K., Prins, B.H., Schwaninger, H.R., Bustamente, C., Buckler, E.S., Zhong, G., Brown, P., Myles, S. 2017. Patterns of genomic and phenomic diversity in wine and table grapes. Horticulture Research. 4:17035. doi: 10.1038/hortres.2017.35.
Al Rwahnih, M., Adib, R., Stevens, K., Diaz-Lara, A., Trouillas, F.P., Preece, J.E., Kallsen, C., Farrar, K., Golino, D. 2018. Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing. Plant Disease. 102(7):1419-1425.
Chater, J.M., Santiago, L.S., Merhaut, D.J., Jia, Z., Mauk, P.A., Preece, J.E. 2018. Orchard establishment, precocity, and eco-physiological traits of several pomegranate cultivars. Scientia Horticulturae. 235:221-227.
Chater, J.M., Merhaut, D.J., Jia, Z., Arpaia, M., Mauk, P.A., Preece, J.E. 2018. Effects of site and cultivar on consumer acceptance of pomegranate. Journal of Food Science. 83(5):1389-1395.
Chater, J.M., Merhaut, D.J., Jia, Z., Mauk, P.A., Preece, J.E. 2018. Fruit quality traits of ten California-grown pomegranate cultivars harvested over three months. Scientia Horticulturae. 237:11-19.
Gianaspro, A., Mazzeo, A., Giove, L.S., Zito, D., Marcotuli, I., Gallotta, A., Colasuonno, P., Nigro, D., Blanco, A., Aradhya, M.K., Gadaleta, A., Ferrara, G. 2017. Exploiting DNA-based molecular tools to assess genetic diversity in pomegranate (Punica granatum L.) selections and cultivars. Fruits. 72(5):292–305.
Potter, D., Bartosh, H., Dangl, G., Yang, J., Bittman, R., Preece, J.E. 2018. Clarifying the conservation status of northern California black walnut (Juglans hindsii) using microsatellite markers. Madrono. 65(3):131-140.
Chater, J.M., Santiago, L.S., Merhaut, D.J., Preece, J.E., Zhenyu, J. 2018. Diurnal patterns of photosynthesis and water relations for four orchard-grown pomegranate (Punica granatum L.) cultivars. Journal of American Pomological Society. 72(3):157-165.