Location: Plant Genetic Resources Unit (PGRU)
2025 Annual Report
Objectives
Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, apply them to priority apple, grape, and tart cherry genetic resources to avoid backlogs in plant genetic resource and information management, and to support genetic enhancement of apple and grape.
Sub-objective 1.A: Investigate the applicability of orchard and vineyard management systems, which include integrated pest management practices, for modernizing and improving maintenance of priority apple, grape, and tart cherry genetic resources.
Sub-objective 1.B: Develop or adapt existing and emerging genotypic and phenotypic methods to characterize and evaluate genetic resources for priority traits and to support identification and development of superior breeding lines and populations possessing priority traits for genetic enhancement of apple and grape.
Sub-objective 1.C: Update and expand standard operating procedures to decrease backlogs in germplasm maintenance, characterization, and data management, including backup preservation, pathogen screening, and upload of genetic markers and other relevant information to public repositories.
Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority apple, grape, and tart cherry genetic resources and associated descriptive information.
Sub-objective 2.A: Identify and fill genetic diversity gaps by acquiring new genetic resources of apple, grape, and tart cherry through exchanges and explorations, and restoring priority genetic resources through regeneration or reintroduction.
Sub-objective 2.B: Develop and implement crop-specific plans for backup preservation including seed conservation of crop wild relatives (CWR) and cryopreservation of priority accessions.
Sub-objective 2.C: Identify bottlenecks and improve processes in genetic resource distribution and management of descriptive information for apple, grape, and tart cherry genetic resources by updating and expanding standard procedures and collaborating closely with other NPGS genebanks, Crop Germplasm Committees, GRIN-Global, and other stakeholders.
Approach
The interconnected objectives above aim to improve the health and accessibility of the apple, grape, and tart cherry collections maintained by The Plant Genetic Resources Unit (PGRU). Above all else, maintenance of healthy trees and vines is paramount to PGRU’s mission. IPM practices for apple, grape, and tart cherry will be implemented following updated guidance specific to New York State. This includes monitoring for known and emerging pests, utilization of modeling systems for pesticide application timings, soil testing and planting cover crops for appropriate erosion and nutrient control, management of weeds and vertebrate pests (including chemical and non-chemical controls), and crop growing systems. Adoption of modern orchard and vineyard systems would improve our capacity to safeguard our genetic resources and ensure future growth. Diverse genetic resources serve as the basis for genetic improvement, with comprehensive evaluation and documentation acting as limiting factors for utilization. As such PGRU will focus on collecting data for key traits of interest for customers, including fruit quality, cold-hardy adaptations, disease resistance, and genetic characterization of key traits for apple and grape breeding. Results from this effort will also identify germplasm with unique traits and desirable allele combinations to support genetic enhancement. Gaps will also be identified in connection with genotyping and phenotyping efforts as we identify missing genotype combinations or unique phenotypic variants. Collection gaps may also be identified by reviewing taxonomic representation, geographic distribution, or missing allelic or phenotypic variation. Key backlogs identified in the NPGS Plan for the PGRU collections include propagation/regeneration and backup preservation of germplasm, pathogen screening, and deposition of relevant information into GRIN-Global. New approaches will be explored to update and expand standard operating procedures (SOPs) to effectively decrease these backlogs. Virus testing of priority germplasm will help identify well characterized accessions which meet phytosanitary conditions and can be readily distributed. Finally, long-term storage of biological material through cryopreservation provides a way to preserve clonal material free from environmental pressures and serves as a backup to replace field accessions lost to disease or catastrophic events.
Progress Report
Maintenance of apple, grape, and tart cherry resources is the highest priority (Objective 1). Over the course of three years nearly 1,000 apple accessions were replanted to revitalize the orchard in response to disease outbreak. Enhanced management practices, including more diverse chemical applications, have contributed to increased orchard health. Cryopreservation techniques to propagate apple trees infected with fire blight bacteria were evaluated over the past two years. Through there is an indication of reduced fire blight bacteria, the change of viability through the cryopreservation process (ranging from 0-100%) makes this approach ineffective compared to traditional grafting. As such, we have not incorporated cryopreservation into our standard practices for apple preservation. New orchard and trellis systems are being established to enhance our maintenance practices and improve space utilization. Data logging technology has continued to streamline field observations and inventory management, which include QR labeled trees and vines for quick access. The new core collection of 250 apple accessions were screened for viruses prior to initiating propagation later this year. An additional 80 apple and 7 cherry accessions were cryopreserved for long-term preservation.
Characterization of genetic resources significantly increases their value and accessibility for stakeholder use (Subobjective 1B). Nearly 100 cherry, 200 apple, and 500 grape accessions were evaluated for metabolite diversity using gas and liquid chromatography in a multiyear evaluation. The genetic diversity of the fruit selected for these studies represents the nutritional and aromatic potential across all apple, cherry, and grape cultivars. Sequencing for more detailed genetic evaluations is being completed summer 2025 to better understand the unique traits under evaluation. Phenotypic evaluation of grapevine accessions to powdery mildew and downy mildew infection was completed for 1,200 grapevine accessions. AI data analysis is ongoing for disease phenotyping along with curating genetic resistance markers to powdery mildew. Grapevine bud cold hardiness is continuing to be evaluated, along with predictive model development for cold tolerance and observations of spring frost damage within 1 month after bud break.
Acquisitions, data management, and distribution are critical to the clonal germplasm project (Objective 2). An additional 6 apple, 105 grapevine, and 10 cherry accessions were included in the collections, representing important historic cultivars, industry standards, pre-breeding material, and wild resources from underrepresented species. Explorations for wild North American apples and cherries are in development but seasonal challenges and fruit availability has limited this effort. Explorations for wild North American grapevines (V. labrusca and V. aestivalis) occurred in Fall of 2024, adding 53 of the 105 grapevines listed above via cuttings. Additional grapevine accessions may be added from seed material collected on the same trips. An additional 8 cold-hardy cultivars were added to the grapevine collection after being released from quarantine (a donation from 2010). Genetic fingerprints are being developed for all new material to confirm identities, along with intake characterizations (pictures, initial observations). 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. A plum and cherry nursery of nearly 200 California adapted accessions was established to evaluate cold hardiness and develop a pipeline for routine cryopreservation. Use of this technology will facilitate integration of collected data into public databases to better serve genebank stakeholders. Nearly 2,000 samples were distributed to stakeholders for research, breeding, or commercial development.
Cherry preserves associated with American President George Washington were discovered at his home in Mount Vernon in Virginia. It is estimated that these remains are pre-Revolutionary War (1775) and were preserved for the family’s consumption. ARS researchers in Geneva, New York, contributed to the sterile recovery and documentation of these preserves, with the aims of long-term preservation of the samples for scientific research, and identification of the cherry cultivar preserved.
Accomplishments
1. Critical apple, grape, and tart cherry resources maintained and distributed. Delays in access to genetic resources hinder the advancement of American agriculture and development of high-quality cultivars. This is especially important in fruit breeding, where healthy and well-characterized germplasm improves stakeholder accessibility. ARS researchers in Geneva, New York, maintained high quality apple (n=4,952), grape (n=1,415), and tart cherry (n=154) genetic resources, along with their wild relatives. These collections are primarily field-based and require substantial maintenance and protection from disease and pests. Close to 1000 accessions were regenerated to revitalize plant health. About 50 apple and cherry accessions were backed up cryogenically to prevent field losses. 2,223 samples, including leaves, fruit, scions, and seeds, were distributed to stakeholders for breeding, research, and commercial development.