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

2021 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
In support of Objective 1, research continued on the implementation of best management strategies for the acquisition, maintenance, and distribution of the genetic resources of the National Clonal Germplasm Repository Unit for tree fruits, nut crops, and grapes (NCGRU-Davis). Field space continues to be limited and the University of California, Davis, which hosts the NCGRU-Davis, has not been able to allot more land to the collections. Although the Repository is not actively collecting new germplasm to fill gaps due to limited field space, Prunus germplasm (mainly apricots and plums) continue to slowly clear USDA Animal and Plant Health Inspection Service quarantine in Beltsville, Maryland. Therefore, there is a backlog of new acquisitions arriving yearly, expanding the collections and addressing part of Objective 1. During fiscal year (FY) 2021, the Repository received 266 Prunus trees (P. cerasifera, P. avium, and P. spp.) representing five new clonal accessions as grafted trees (total of 15 trees) and seven new seedling family accessions as trees (251 trees of which 84 were planted in the Repository orchards due to space limitations). Four Vitis (grape) accessions and one fig accession were also received. Among the grape accessions was the hybrid ‘Wine King’, a cultivar bred by Thomas Volney Munson, a famous historical figure in American grape breeding. Propagations of the various collections including but not limited to Prunus (almonds, apricots, cherries, peaches, and plums), persimmon, olives, figs, and grapes. Tree and vine maintenance in the field and nursery continue to be the major emphasis and are year-round activities. This year, a new pruning crew for the grape collections was identified and significant progress was made in getting the vineyard maintenance back on track although limited resources (i.e., personnel) remain a challenge. 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 or tolerance in the persimmons. New equipment in the form of a hedger and a brush chipper were employed together to mechanically prune and remove the resulting brush (trimmed branches) from several of the collections with small to medium-sized trees including apricots, peaches, as well as the younger growth from recently pruned pistachios and walnuts. Employing both equipment will increase the efficiency of maintaining the collections and reduce or eliminate the need to clean up and dispose of branches/brush from the orchards by burning. Larger trees (older walnuts and pistachios) could not be pruned due to issues in identifying a suitable contractor with large enough hedging equipment. Resolution of this issue will be a major concern going forward. Manual pruning of trees and removal of weedy trees and suckers was performed for the collections as needed including Prunus, kiwifruit, and others. 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. Distribution of all forms of genetic materials including dormant and green cuttings/budwood, pollen, and leaves continued. As of July 2021, 2925 items (2455 domestic, 470 international) have been shipped to 200 customers/stakeholders (194 domestic, siz international). 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 addition to fulfilling requests from genebank customers, pollen and cuttings were collected and shipped to ARS AGRPRU in Fort Collins, Colorado, for cryopreservation. For FY2021, these included pollen from 23 Prunus accessions, budwood of 14 Prunus accessions, budwood of 2 walnut accessions, and green cuttings of 30 Vitis accessions. Backing up the collections through approaches such as cryopreservation is necessary where maintenance fails, or plants do not thrive. 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. Knowledge of the 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. Work continued on updating the GRIN-Global database. As of July 2021, three accessions were added and 81 accession records were modified this year. In addition, 588 inventory records were added and 3362 were modified. In July and August 2020, peach data (1156 records) were upload to the database, fig genetic data (15 records) and Prunus data (1117 records) were edited. In addition, 123 walnut images were added, and 518 image attachment files were modified. 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. In FY2021, 645 pistachio trees across 11 Pistacia species were genotyped using 16 microsatellite loci with some gaps in the data. These gaps will need to be filled and uploaded on to the GRIN database. In addition to this pistachio genotyping work, the collection inventory in GRIN is being updated to remove duplicates and provide explanatory comments. A total of 180 pistachio records have been updated so far. Other genotyping work included the evaluation of 800 cultivated grape accessions using the rhAmpSeq genotyping platform in a collaborative effort between the Davis and Geneva repositories. Two manuscripts describing Frequentist and Bayesian approaches to genomics prediction of economic traits in walnut and grape are in preparation. In support of Objective 3, work continued on developing updated and documented best management practices for collection management and evaluation in both the field (orchards and vineyards) and nursery operations. A pest control advisor is now routinely consulted about pest and other management issues in the orchards and vineyards. This has helped address a zinc deficiency issue in some of the collections. In June 2021, a new management practice of simultaneously deploying a mechanical hedger (i.e., tree pruning equipment) and a brush chipper to prune and shred the resulting branches within the orchards was implemented for the first time. This practice cuts the amount of labor and fuel required and improves on the old, unsustainable practice of removing the brush from the orchards after pruning and burning it. In the nursery, routine evaluation of greenhouse/screenhouse management practices such as propagation techniques continued to be performed. Training and certification in pesticide/herbicide application of our new nursery manager was completed. Standard operating procedures for the repository operations continued to be updated as warranted.

Accomplishments
1. Crop germplasm distribution. ARS scientists and staff in Davis, California, shipped crop germplasm, including 2,925 items to 200 stakeholders (six international and 194 domestic) to research and education entities that require genetic diversity or genetic standards. The germplasm collections were assembled and managed by ARS scientists to be made available to scientists, especially geneticists and breeders who develop new cultivars to address the needs of growers and consumers. Most germplasm requests were shipped in late winter/early spring as three to five cuttings per accession. Leaves, pollen, and fruit were also sent as requested.

Review Publications
Preece, J.E., Balunek, E., Volk, G.M. 2021. Pistachio collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/pistachios/
Preece, J.E. 2020. The USDA-ARS National Clonal Germplasm Repository for tree fruit, nut crops, and grapes, Davis, CA. Journal of American Pomological Society. 74(2): 111-116.
Preece, J.E., Karp, D. 2020. Fig. HortScience. p.1183-1184.
Volk, G.M., Preece, J.E. 2021. Overview of the National Clonal Germplasm Repository in Davis, California. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/introduction/
Gasic, K., Preece, J.E., Karp, D. 2020. Register of new fruit and nut cultivars list 50. HortScience. 55(7)1164-1201. https://doi.org/10.21273/HORTSCI50register-20.
Sanchez, A., Volk, G.M., Preece, J.E. 2021. Fig collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/figs/
Smith, J., Volk, G.M., Preece, J.E. 2021. Persimmon collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/persimmons/
Smith, J., Volk, G.M., Preece, J.E. 2021. Walnut collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/walnuts/
Smith, J., Volk, G.M., Preece, J.E. 2021. Mulberry collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/mulberries/
Prins, B., Volk, G.M., Preece, J.E. 2021. Grape collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/grapes/
Diaz-Lara, A., Golino, D., Preece, J.E., Rwahnih, M. 2020. Development of RT-PCR degenerate primers to overcome the high genetic diversity of grapevine virus T. Journal of Virological Methods. 282. Article 113883. https://doi.org/10.1016/j.jviromet.2020.113883.
Sanchez, A., Volk, G.M., Balunek, E., Preece, J.E. 2021. Kiwifruit collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/kiwifruit/
Smith, J., Volk, G.M., Balunek, E., Preece, J.E. 2021. Olive collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/olives/
DeBuse, C., Volk, G.M., Balunek, E., Preece, J.E. 2021. Prunus collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/prunus-collection/
Moersfelder, J., Volk, G.M., Balunek, E., Preece, J.E. 2021. Pomegranate collection. In: Volk, G.M., Preece, J.E., editors. Field tour of the USDA National Clonal Germplasm Repository for Tree Fruit, Nut Crops, and Grapes in Davis, California. Fort Collins, Colorado: Colorado State University. Available: https://colostate.pressbooks.pub/davisrepositoryfieldtour/chapter/pomegranates/
Chater, J.M., Jia, Z., Qin, G., Liu, C., Li, J., Merhaut, D.J., Preece, J.E. 2020. Pomegranate. HortScience. p.1197-1199.
Ramasamy, R.K., Luo, M., Leslie, C.A., Velasco, D.M., Ott, N.J., McClean, A.E., Dandekar, A.M., Aradhya, M.K., Brown, P.J., Browne, G.T., Kluepfel, D.A., Westphal, A., Dvorak, J. 2021. Co-located quantitative trait loci for resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrid rootstock. Horticulture Research. 8. Article 111. https://doi.org/10.1038/s41438-021-00546-7.
Salman, M., Kluepfel, D.A., Greenhut, R., Preece, J.E., Ferguson, L. 2020. Field evaluation of olive (Olea europaea) genotypes for resistance to Pseudomonas savastanoi pv savastanoi. Journal of Plant Pathology. 102:663-670. https://doi.org/10.1007/s42161-020-00549-8.
Milczarek, R.R., Woods, R., Lafond, S.I., Smith, J.L., Sedej, I., Olsen, C.W., Vilches, A.M., Breksa III, A.P., Preece, J.E. 2020. Texture of hot-air-dried persimmon (diospyros kaki) chips: instrumental, sensory, and consumer input for product development. Foods. 9(10). Article 1434. https://doi.org/10.3390/foods9101434.