Location: Plant Genetic Resources Unit (PGRU)
2023 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 2023, apple fruit quality was again significantly reduced due to heavy use of pesticides to manage fire blight. Heavy russeting, spotting, and smaller than typical fruit was observed on most accessions. As such, Plant Genetics Resources Unit (PGRU) did not do routine fruit characterization of the apple collection. Fruit size of 100 tart cherry accessions were documented using image analysis, as part of a pilot study adopting seed analysis equipment to evaluate small fruits. To increase the utility of the USDA Apple collection, 200 accessions were selected as part of a new diversity core. These apples were selected based on genetic information and needs of key stakeholders of the USDA Apple Collection and will be used for in-depth characterization and genetic studies. Targets for specific North American Malus explorations were set with for northern species M. coronaria and southern species M. angustifolia using genetic information from recent explorations. These North American species show high value for breeding and genetic research, particularly for disease resistance and climate adaptations. In collaboration with ARS Researchers in Kearneysville, West Virginia, a high-quality genome for M. fusca, the Pacific crabapple, was developed. Similar genomic resources are underway for M. angustifolia.
In FY23, grapes were collected from 150 accessions in the Geneva collection and 350 accessions in the Davis grapevine collection for in-depth fruit analysis (terpenes, phenolics, sugars, nitrogen, titratable acidity). New protocols have been developed in the lab for these processes. This project analyses will continue, and a second year of grapes will be collected. Maintenance continues to improve with replacing trellis and growing patterns of vines in the primary block along with moving larger vines into a T-trellis system to enable better management of foliage. 250 accessions are being regenerated along with full digitization of inventory tracking. An initial exploration trip was completed from Maine to Virginia to search for two species: Vitis labrusca and Vitis aestivalis. Both are native to North America, have desirable fruit qualities and high disease resistance. After genetic evaluation to confirm true species vs wild hybrids, collaborators will send woody cuttings and seeds from vines geo-tagged.
In FY23, germplasm was acquired through exchanges including 21 apple cultivars, 5 Vitis accessions, and 1 cold-hardy Prunus accession. The incoming apple accessions represent cider cultivars previously unavailable within the United States and are of special interest to U.S. stakeholders. Routine cryopreservation covered 100 apple accessions in FY23, further securing the collection. A collaboration was developed with ARS researchers in Davis, California, with the National Clonal Germplasm Repository to relocate the national collection of cherries and plums to Geneva, New York, for routine cryopreservation. So far approximately 150 plum cultivars were propagated in Geneva, New York.
Cold hardiness in fruit crops could be used to accommodate various growing regions and shifting climate norms. Through winter 2022-2023, cold tolerance in cherry and grape was measured 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 de-acclimation during the dormant season. ARS Researchers in Geneva, New York, continued a cold-hardy study of 64 tart cherries, to better understand the capacity of cultivars to withstand freezing damage during winter and frost avoidance during spring bloom. This included weekly monitoring of 64 tart cherry cultivars through winter and recording bloom during spring. A second-year evaluation of 90 Vitis accessions in the collection, focused on V. labrusca cultivars, for cold hardiness descriptors was completed.
From 2018-2023, ARS researchers in Geneva, New York, maintained diversity collections of apples (n=4,940), grapes (n=1,406), and tart cherries (n=153). Maintenance practices included annual pruning, chemical applications for weed and pest management, and regeneration of germplasm. The operations manual for PGRU and Crop Vulnerability Statements for apple and cherry were updated, which include clear priorities and guidelines for acquisition based on genetic information to prevent accession redundancy. The operations manual for PGRU and Crop Vulnerability Statement for grape are currently being updated. Distribution was documented in GRIN-Global and accessible to the U.S. National Plant Germplasm System (NPGS) staff. From FY2018 to FY2023, PGRU distributed 22,992 samples across 1,523 requests. During this period, we served 1,055 stakeholders. Apple germplasm is the highest requested crop; an average of 4,249 apple samples across 246 requests were distributed annually during the five-year period. Years 2020 and 2021 represent a significant reduction in apple germplasm distribution related to a severe fire blight outbreak in 2020. Through pruning, extensive chemical control, and accession repropagation, ARS researchers in Geneva, New York, were able to reduce the impact of this pathogen in our apple collection and have updated our chemical application program and management practices to mediate future outbreaks. Additionally, ARS researchers in Geneva, New York, are developing cryotherapy techniques for sanitary regeneration of severely infected trees.
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=4,940), Vitis (n=1,406), and Prunus (n=153) genetic resources, including their wild relatives. These collections are primarily field-based and require substantial maintenance and protection from disease and pests. Close to 250 accessions were regenerated to revitalize plant health. About 100 apple accessions were backed up cryogenically to prevent field losses. Continued practices minimized the effect of apple fire blight disease following the 2020 outbreak. New genetic resources for apple stakeholders were added to the collection. These efforts ensure USDA fruit crop collections are accessible for distribution, evaluation, and research to advance American horticulture.
