Location: Plant Genetic Resources Unit (PGRU)
2024 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 two years nearly 1000 apple accessions were replanted to revitalize the orchard in response to disease outbreak. New orchard and trellis systems are being established to meet Objective 1 goals to enhance our maintenance practices and improve space utilization. Data logging technology was implemented to streamline field observations and inventory management. A high-density apple orchard was delayed to allow additional time for stakeholder feedback and genetic analysis. A list of 250 apple accessions have been selected and they are being screened for viruses prior to initiating propagation later this year. An additional 38 apple and 13 cherry accessions were cryopreserved. 20 apple, 3 grapevine, and 1 cherry accessions were added to the collections, representing important historic cultivars, industry standards, and wild resources from underrepresented species from collaborators. Explorations for wild North American apples are in development but seasonal challenges and fruit availability has limited this effort. Explorations for wild North American grapevines are occurring in Fall of 2024. A technique to evaluate fire blight bacteria contamination during cryopreservation was developed and tested, with data supporting cryopreservation minimizes risk of spreading infection.
Characterization of genetic resources significantly increases its value and accessibility for stakeholder use (Objective 2). Due to fruit damage from a late spring frost in 2023 in the apple collection, fruit was not evaluated in the fall at the beginning of FY24. Characterization for apple will resume in the fall of 2024 (FY25). 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. Nearly 500 grape accessions were evaluated for metabolite diversity using gas and liquid chromatography across two seasons. The genetic diversity of the grapes selected for this study represents the nutritional and aromatic potential across all grapevine cultivars. The next phase will include more detailed genetic evaluations to better understand the unique traits under evaluation. Some of the techniques developed for this analysis will work well across multiple crops, including apple and tart cherry. Phenotypic evaluation of grapevine accessions to powdery mildew infection was completed for 800 accessions. Data analysis is ongoing along with screening the accessions for genetic resistance markers to powdery mildew. 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. 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. 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. Delays in access to genetic resources hinder the advancement of American agriculture and development of new climate adapted, 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. Breeders’ desired grape traits characterized. Grapevine breeders seek high-quality genetic resources to incorporate into their research programs to develop new cultivars that will be more resistant to diseases, improve yields, and discover new flavors. Genetic markers enable researchers to shorten the timeline of making a new cultivar from decades to years. USDA-ARS researchers in Geneva, New York, characterized grapevines for fruit quality, disease resistance, and genes related to each trait. Over 100 vines have fruit flavor and aroma profiles built. Over 800 vines have disease resistance determined for powdery mildew, along with 20 genetic markers that are related to resistance. Curating these traits will enable breeders seeking specific traits to request material more efficiently, enabling their ability to produce new cultivars on a shorter timeline.
