Location: Plant Genetic Resources Unit (PGRU)
2021 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
This project addressed NP301 Action Plan Component 2 “Plant and microbial genetic resource and information management”, 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. 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 Germplasm Resources Information Network (GRIN)-Global and other data sources. Objective 3: Work with other National Plant Germplasm System (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.
ARS researchers in Geneva, New York, preserve the genetic diversity of apples, grapes, and tart cherries, including their crop wild relatives (Objective 1). USDA collections are utilized for genetic improvement and basic research. Maintenance and distribution of clonal germplasm are the greatest priorities as well as the most significant challenges. ARS researchers in Geneva, New York, maintain 7,637 accessions of Malus (apple), Vitis (grape), and Prunus (cherry) accessions as field (n=6,193) and seed collections (n=1,444). In 2020, there was an outbreak of fire blight in the USDA apple collection. Fire blight is a bacterial disease in apple which can kill mature trees within a season and quickly spread through an orchard. Antibiotics are the primary control of fire blight in conventional orchards, however, in 2020, an antibiotic resistant strain was identified that did not respond to chemical applications. Through pruning, extensive chemical control, and accession repropagation, the impact of this pathogen was reduced in the USDA apple collection. In response, the chemical application program and management practices for the apple collection were updated to mediate future outbreaks (Objective 3). In collaboration with ARS researchers in Fort Collins, CO, an additional 100 Malus and 27 tart cherry accessions were cryopreserved. Events, such as disease outbreaks, highlight the need for increased cryopreservation of NPGS Clonal collections.
For the 2020 and 2021 distribution seasons, ARS researchers in Geneva, New York, restricted distribution of apple germplasm to reduce spread of antibiotic-resistant fire blight; apple represents the largest clonal collection and the most requested crop for distribution in Geneva, New York. In 2020, ARS researchers in Geneva, New York, distributed 3,537 Malus samples in 215 orders, 471 Vitis samples in 63 orders, and 84 Prunus samples in 17 orders, for a total of 4,092 samples and 295 orders. This is a substantial reduction from the four-year average of 7,206 items and 469 orders annually across all crops. Challenges due to COVID19 did not impact operations related to distribution during the 2020-2021 season. However, the number of samples distributed for the curated crops was lower for all crops in 2020 and 2021, with number of samples distributed reduced to 55%, 72%, 51% of the four-year average for apples, grapes, and tart cherry, respectively. Number of orders for apple (56%) and tart cherry (69%) reduced, whereas grape (98%) did not significantly decrease relative to the four-year average.
ARS researchers in Geneva, New York, continually seeks new genetic resources to add to its collections. Recently, 30 Malus accessions, representing 18 Malus doumeri from an exploration in Vietnam, and 12 heirloom cultivars with potential for cider research and development were added to the collection. In addition to new accessions, 117 individuals were propagated from a seedling evaluation for permanent maintenance. These seedlings represent genetic and species diversity missing from the collection. Additionally, 14 Prunus accessions representing 4 cold-hardy species previously missing from the collection were added (Objective 1).
ARS researchers in Geneva, New York, evaluated the USDA apple, grape, and tart cherry collection for key traits and genetic diversity (Objective 2). In response to the fire blight outbreak, the apple collection was evaluated for disease susceptibility. In the grape collection, genetic markers were used to explore relationships between accessions and wild species. Finally, in the tart cherry collection, diversity of bloom and fruit quality was documented.
ARS researchers in Geneva, New York, updated the draft of Best Management Practices, primarily for its chemical application program to manage the apple collection, in consultation with stakeholder groups, including the Crop Germplasm Committees. Additionally, ARS researchers in Geneva, New York, worked with Crop Germplasm Committees update Crop Vulnerability Statements (Objective 3).
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, maintain 7,637 accessions of apple, grape, and tart cherry genetic resources, and their wild relatives. These collections are primarily field-based and require substantial maintenance and protection from disease and pests. This effort ensures USDA fruit crop collections are accessible for distribution, evaluation, and research to advance American horticulture.
2. Evaluation of fire blight in the USDA Apple Collection. Fire blight is a severe disease that impacts apple trees. In response to a fire blight outbreak in the USDA apple collection, ARS researchers in Geneva, New York, evaluated fire blight susceptibility across 2,525 accessions and 48 apple species. This work represents one of the largest documented natural fire blight studies in apple, in terms of number of accessions and species evaluated. From this evaluation, ARS researchers in Geneva, New York, identified potential sources for disease resistance for future fire blight resistance studies and apple breeding.
3. Classification of grape hybrids. Between two or more grape (Vitis) species and incorporate unique fruit qualities, cold- hardiness, and disease resistance from wild and cultivated grapes, expanding where grapes can be sustainably grown in the United States. Nearly half the USDA grape collection in Geneva, New York, consists of grape hybrids, and the lack of more descriptive terminology limits the accessibility of the collection to stakeholders. Using genetic markers, ARS researchers in Geneva, New York, estimated the genomic ancestry of the cultivated grape, Vitis vinifera, which ranged from 0-100%. This classification will help stakeholders better select material for research and improvement of cold-hardy grapes.
4. Phased diploid and pan-genomes of cultivated and wild apples. Molecular characterization of apple genomes can help understand apple's genetic diversity and identify useful traits for breeding new cultivars. ARS researchers in Geneva, New York, in collaboration with researchers from other research institutions, sequenced, assembled and compared the full reference genomes for three species, Gala, a top commercial cultivar of M. domestica; and apple's two main wild progenitors, the European crabapple (M. sylvestris) and the central Asian wild apple (M. sieversii). The results significantly contribute to the understanding of genetic basis of apple domestication and provide apple breeders with detailed genomic roadmaps that could help them build a better apple.
Review Publications
Thapa, R., Singh, J., Gutierrez, B.L., Arro, J., Khan, A. 2021. Genome-wide association mapping identifies novel loci underlying fire blight resistance in apples. The Plant Genome. https://doi.org/10.1002/tpg2.20087.
Dougherty, L.E., Wallis, A., Cox, K., Zhong, G., Gutierrez, B.L. 2021. Phenotypic evaluation of fire blight outbreak in the USDA Malus collection. Agronomy Journal. https://doi.org/10.3390/agronomy11010144.
Migicovsky, Z., Gardner, K., Richards, C.M., Chao, T., Schwaninger, H., Fazio, G., Zhong, G., Myles, S. 2021. Genomic consequences of apple improvement. Horticulture Research. https://doi.org/10.1038/s41438-020-00441-7.
Sun, X., Jiao, C., Schwaninger, H., Chao, T., Ma, Y., Duan, N., Khan, A., Xu, K., Cheng, L., Zhong, G., Fei, Z. 2020. Phased diploid and pan-genomes of cultivated and wild apples unravel genetic basis of apple domestication. Nature Genetics. https://doi.org/10.1038/s41588-020-00723-9.
