Location: Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes
2023 Annual Report
Objectives
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.
Approach
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 report documents progress made in FY23 for bridging project 2032-21000-026-000D, titled "Managing Genetic Resources and Associated Information of Grape, Tree Fruit, Tree Nut, and Other Specialty Crops Adapted to Mediterranean Climates". This bridging project replaces project number 2032-21000-024-000D with the same name and objectives, which expired in February 2023. For more information, please review the final FY23, 2032-21000-024-000D project report. The current bridging project will be replaced in FY24 with a new project after completion of an ad-hoc OSQR review.
In support of Objective 1, research continued on the implementation of best management strategies for the acquisition, maintenance, and distribution of genetic resources tree fruits, nut crops, and grapes in Davis, California (the Repository). Field space continues to be limited and the University of California, Davis (UCD), which leases land for the research, has not been able to allot more land to the permanent field collections. Although this project is not seeking to greatly expand the collections due to limited field space, previously collected germplasm of Prunus (mainly apricots and plums) and other crops continue to slowly clear USDA Animal and Plant Health Inspection Service (APHIS) quarantine in Beltsville, Maryland. Therefore, there is a backlog of new acquisitions arriving yearly, expanding the collections and addressing part of Objective 1.
The irrigation well supplying water to the southern half of the research orchard began to fail in summer 2021, and since then field staff have worked closely with UCD staff, neighboring farms, and the local irrigation district to ensure the trees are irrigated. In addition, the well supplying the north side of the farm in addition to UCD research fields has been intermittently out of service and irrigation there requires careful coordination with multiple research groups. This situation has caused significant disruption to regular field operations. Procurement efforts are underway by both UCD and USDA-ARS to construct new irrigation wells. For the USDA-ARS effort, the initial design is complete and bids are currently open for the first phase of construction.
Due to this uncertainty in the water supply, new field plantings of trees have been limited. Grapes are relatively tolerant to inconsistent watering as young plants however, and about 250 replacement vines were planted in late spring. In addition, another 430 accessions were grafted to produce replacement plants for next year. Additionally, approximately 50 fig and kiwi accessions have been repropagated and are being held at the nursery for future planting. These vines replace older plants that have suffered from age-related decline. A detailed grape inventory of over 4,500 accessions was conducted to incorporate changes from replantings in recent years into the GRIN-Global database.
Tree and vine maintenance in the field and nursery continue to be the major emphasis and are year-round activities. The grapes were pruned and trained by hand, and leftover pruning debris removed from the walnut and pistachio blocks. Sprays were employed for insect pests and diseases caused by microbes and nutrient deficiencies. Weed control (i.e., herbicides) and removal activities continued to require significant effort from the staff. In-house spring hedging was performed on some of the Prunus collections.
Backing up the clonal tree collections via cryopreservation of dormant budwood remains a challenge, and scientists at Fort Collins, Colorado, are still in the process of developing effective protocols for the taxa maintained in the Davis collection. In order to provide a backup for critical genetic diversity in the meantime, staff at Davis have begun collecting and shipping pollen of pistachio and walnut accessions to be cryopreserved at the National Laboratory for Genetic Resource Preservation in Fort Collins, Colorado. In FY23, 19 vials of pistachio pollen and 44 vials of walnut pollen were collected and transferred for preservation.
Some material is only distributed in spring/summer, including pollen, leaves and green budwood. From 03/01/2023 - 07/05/2023: Staff shipped 40 orders (Domestic requesters: 36 total (11 Federal, 13 State, four Commercial, eight individuals. International: four). The 40 orders consisted of 810 inventories that were shipped during that time period. 567 inventories were collected as bud sticks/cutting with a total of 2,455 sticks. 134 inventories were collected for packets of leaves. 95 inventories were collected as vials of pollen. Five inventories were collected as packets of seed. Some international requests could not be sent because of stringent phytosanitary requirements for shipping to the European Union, specifically for those crops that are hosts of Xylella fastidiosa.
In support of Objective 2, research continued on the evaluation of the collections and posting of those results in the Germplasm Resources Information Network (GRIN) Global database so that stakeholders can better understand and use the collections in their research. Staff at the Repository participated in collaborative efforts with the GRIN-Global Development Team to improve the capacity of the software for managing clonal inventory, which will lead to improvements in germplasm management and utilization at multiple germplasm repositories. In collaboration with USDA-ARS researchers in Geneva, New York, scientists at Davis began a project to develop segregating mapping populations of grape to identify new sources of powdery mildew resistance. This year the first cross was made, and pollen collected and preserved to allow for crosses to diverse species next year. The bulk of the grape collection (over 3200 vines) were sampled and shipped to ARS researchers in Geneva, New York for in-depth genotyping and allele mining for known traits of interest. The remainder of the collection is currently being sampled. Leaves of just over 100 accessions of sweet cherry were collected for genotyping by ARS researchers in Geneva, NY. Phenology observations (timing of budbreak, first leaf, full leaf, first bloom, and full bloom) were recorded for the main persimmon collection (150 inventories) by weekly monitoring from March – May 2023. These observations were directly requested from users and will improve utilization of this unique collection.
In support of Objective 3, work continued developing updated and documented best management practices for collection management and evaluation in both the field (orchards and vineyards) and nursery operations. Crop Germplasm Committees (CGC) are critical sources of stakeholder feedback and collaborative development of new management strategies. This year, staff from Davis participated in meetings with the grape and Prunus CGC’s, where multiple management and evaluation projects were discussed. A committee was formed to begin updating the Crop Vulnerability Statement for grape. Staff developed documentation for the collection and extraction of walnut and pistachio pollen, including photos and videos. In the nursery, routine evaluation of greenhouse/screenhouse management practices such as propagation techniques continued to be performed. Staff documented protocols for germinating seeds of persimmon rootstock. Standard operating procedures for the repository operations continued to be updated as warranted.
Accomplishments
1. Critical nut tree diversity is backed up through pollen cryopreservation. The living collections of nut trees maintained in Davis, California, represent critical genetic diversity for growers and researchers worldwide, yet many of these collections lack a secure backup in case of an environmental disruption in the field. Research to develop effective methods of cryopreservation of dormant budwood for pistachio and walnut is still ongoing. In the meantime, researchers in Davis, California, and in Fort Collins, Colorado, have developed effective methods to collect, store, and preserve pollen of these species to serve as an emergency backup. This year, 44 additional accessions of walnut were preserved by pollen, and 19 vials of pistachio pollen were also collected for testing.
