Location: Plant Genetic Resources Unit (PGRU)
2022 Annual Report
Objectives
The long-term overall objectives of this project are to acquire and conserve a broad spectrum of genetic diversity of apples (Malus), cold-hardy grapes (Vitis) and tart cherries (Prunus), to characterize and distribute these genetic resources and associated information to breeders and others for research and crop
improvement, and to increase public awareness of the value of these crop genetic resources. During this project period, our objectives are as follows:
Objective 1: Efficiently and effectively acquire apple, cold-hardy grape, and tart cherry genetic resources, maintain their safety, genetic integrity, health and viability, and distribute them and associated information worldwide. [NP301, C2, PS2A; C1, PS1A]
Sub-objective 1.A.: Conserve, back up, regenerate, and distribute apple, cold-hardy grape, and tart cherry genetic resources and associated information.
Sub-objective 1.B.: Acquire apple, cold-hardy grape, and tart cherry genetic resources through exploration, collection, and/or exchange to fill the gaps in the collections.
Objective 2: Develop more effective genetic resource characterization and evaluation (especially for phenotyping trees and vines) methods and applying them to priority apple, cold-hardy grape, and tart cherry genetic resources. Record and disseminate characterization and evaluation data via GRIN-Global and other data sources. [NP301, C2, PS2A; C1, PS1A]
Sub-objective 2.A.: Characterize and evaluate key morphological, horticultural, genetic, and biochemical attributes of apple, cold-hardy grape, and tart cherry genetic resources. Record all the characterization and evaluation data via GRIN-Global and other databases.
Sub-objective 2.B.: Develop or adapt new methods and apply them for characterizing priority apple, cold-hardy grape, and tart cherry genetic resources.
Objective 3: Work with other NPGS gene banks and Crop Germplasm Committees to develop, update, document, and implement curatorial best management practices and Crop Vulnerability Statements for apple, cold-hardy grape, and tart cherry genetic resources and information management. [NP301, C2, PS2A]
Sub-objective 3.A.: Work with other clonal repositories to develop and implement best management practices for apple, cold-hardy grape, and tart cherry genetic resources.
Sub-objective 3.B.: Update the Crop Vulnerability Statements of apple, grape, and Prunus (tart cherry).
Approach
To accomplish the objectives above, effective project planning, implementation and management are required. Innovative and sustained scientific efforts are needed to provide scientific foundation for better managing the germplasm resources and making the resources and associated information readily available to the users.
To meet Objective 1, we will maintain the collection in a good healthy condition through effective field cultivation, cryopreservation and seed storage; we will continue to increase the back-up coverage of the Malus and tart cherry collection using cryopreservation and other methods in collaboration with the National Center for Germplasm Resources Preservation (NCGRP); information about accessions will be made available in easily understandable and accessible formats via GRIN-Global; we will regenerate and distribute our collections and associated information timely and effectively; we will continue filling collection gaps through germplasm exploration and exchanges. Vitis and Malus will be our primary foci. To meet Objective 2, we will characterize and evaluate key morphological, horticultural, genetic, and biochemical attributes of apple, cold-hardy grape, and tart cherry genetic resources; we will record all the characterization and evaluation data via GRIN-Global and other databases; we will continue collecting basic Malus and Vitis descriptor information such as fruit size and cluster attributes; we will work with collaborators to evalaute our Malus collection for hard cider characteristics; we will determine policy levels of selected Malus accessions; and we will develop or adapt new methods, such as aerial phenotyping and new virus testing technologies, and apply them for characterizing priority apple, cold-hardy grape, and tart cherry genetic resources. To meet Objective 3, we will work closely with other clonal repositories to develop and implement best management practices for apple, cold-hardy grape, and tart cherry genetic resources and will update the Crop Vulnerability Statements of apple, grape, and Prunus (tart cherry). In addition, we will enhance the germplasm management effectiveness and utilization efficiencies by characterizing and evaluating the collection through various genetic and molecular approaches. We will work closely with Crop Germplasm Committees to implement the priorities they define for collection and evaluation. The major impact of the project is to preserve genetic resources of apples, grapes, and tart cherries for future improvement of these crops worldwide.
Progress Report
In 2022, Plant Genetic Resources Unit (PGRU) maintained diversity collections of Malus (n=6,073), Vitis (n=1,415), and Prunus (n=149). In 2022 germplasm was acquired through exchanges including 16 Malus accessions, 13 cold-hardy Prunus accessions, and 3 Vitis accessions. The PGRU Apple collection is one of the most diverse collections in the world, containing close to 1,500 unique cultivars, and 3,493 accessions representing 55 taxa. A seedling block representing diverse wild apples seedlings was evaluated over the past several years using taxonomic, geographic, morphological, and genetic data. Approximately, 250 selections of 1,600 individuals were propagated for permanent maintenance, and the rest destroyed. This will drastically reduce the maintenance burden and expand the space for permanent accession maintenance. Maintenance practices included annual pruning, chemical applications for weed and pest management, and regeneration of germplasm. Close to 800 apple, cherry, and grape accessions were regenerated. Routine cryopreservation resumed in 2021, securing close to 150 additional Malus and Prunus accessions. An outbreak of fire blight in the apple collection in that started in 2020 continued through 2021 and 2022, requiring extensive intervention to rescue infected trees, including regeneration of 528 apple accessions. The operations manual for PGRU and Crop Vulnerability Statements for apple and cherry were updated. Distribution was documented in Germplasm Resource Information Network (GRIN)-Global and accessible to U.S. National Plant Germplasm System (NPGS) staff. From 2021 to 2022, PGRU distributed 1,000 samples across 284 requests. Years 2021 and 2022 represent a significant reduction in apple germplasm distribution related to severe fire blight and limited access to reduce spread of disease.
Apple fruit quality was significantly reduced this season due to heavy use of copper, Apogee, and sulfur to better manage fire blight. Heavy russeting, spotting, and smaller than typical fruit was observed on most accessions. As such, PGRU did not do routine fruit characterization. Fruit weights and images of 367 accessions from wild and hybrid species unimpacted by pesticides were collected to fill gaps in documentation and aid in taxonomic identification. First-year evaluation of 90 Vitis accessions in the core collection for cold hardiness descriptors was completed. A screen of 90 Vitis accessions in the core collection for presence of trunk diseases was completed. Fruit quality traits in 149 tart cherry and wild Prunus accessions were characterized across 5 years. Traits included total soluble solids, titratable acidity, and phenolic composition, including 10 prominent metabolites in cherry. We identified broad phenotypic variation across traits and identified distinctive chemical fingerprints that distinguish tart and sweet cherries. Genetic variation was characterized using genotyping by sequencing (GBS). Data will be published and uploaded to GRIN-Global.
Cold hardiness in fruit crops could be used to accommodate various growing regions and shifting climate norms. Through winter 2021-2022, ARS researchers in Geneva, New York, measured cold tolerance in cherry and grape using differential thermal analysis (DTA) by collecting dormant buds throughout the winter season and recording the lethal bud temperature to build a model of cold-hardy acclimation and deacclimation during the dormant season. In cherry, ARS researchers in Geneva, New York, also monitored budbreak as an indicator of fulfillment of the chilling requirement. This included two types of sampling populations: first, for fine-scale monitoring of bud sensitivity to seasonal temperature changes, four species for weekly sampling were selected: Prunus cerasus (‘Montmorency’), the P. cerasus progenitors P. avium (‘Black Gold’) and P. fruticosa (‘Dwarfrich’), and the early-blooming Japanese species P. nipponica. Second, monthly sampling was conducted using 64 diverse accessions, including 42 P. cerasus, 8 P. fruticosa, 4 P. avium, 1 P. maackii, 1 P. pennsylvanica, and 8 hybrid accessions to capture broader genetic diversity. In grape, ARS researchers in Geneva, New York, selected 90 accessions from the grape core collection, representing the diversity of the collection. Grape assays were completed monthly. This project will continue through winter 2022 and winter 2023.
Accomplishments
1. Critical apple, grape, and tart cherry resources maintained. Research and breeding of fruit crops relies on availability of genetic diversity. ARS researchers in Geneva, New York, maintained Malus (n=6,073), Vitis (n=1,415), and Prunus (n=149) genetic resources, including their wild relatives. These collections are primarily field-based and require substantial maintenance and protection from disease and pests. Close to 500 accessions were regenerated to revitalize plant health. About 50 apple and cherry accessions were backed up cryogenically to prevent field losses. Continued practices minimized the effect of apple fire blight disease following the 2020 outbreak. To improve farmland, 5,000ft of drainage tile was installed to reduce water logging. Additionally, a new deer fence was installed to prevent substantial herbivory and protect collections. These efforts ensure USDA fruit crop collections are accessible for distribution, evaluation, and research to advance American horticulture.
Review Publications
Brillouet, J., Romieu, C., Bacilieri, R., Nick, P., Trias-Blasi, A., Maul, E., Solymosi, K., Szelak, P., Jiang, J., Sun, L., Ortolani, D., Londo, J.P., Gutierrez, B.L., Prins, B.H., Reynders, M., Vancaekenberghe, F., Maghradze, D., Marchal, C., Sultan, A., Thomas, J., Scherberich, D., Fulcrand, H., Roumeas, L., Billerach, G., Salimov, V., Musayev, M., Ul Islam Dar, H., Peltier, J., Gaudeul, M., Grisoni, M. 2022. Tannins phenotyping in the Vitaceae reveals constellations of compositions intimately linked to genera and species. Annals Of Botany. https://doi.org/10.1093/aob/mcac077.
Gutierrez, B.L., Schwaninger, H.R., Meakem, V.M., Londo, J.P., Zhong, G. 2021. Phenological diversity in wild and hybrid grapes (Vitis) from the USDA-ARS cold-hardy grape collection. Planta. https://doi.org/10.1038/s41598-021-03783-x.
