Location: Plant Genetic Resources Unit (PGRU)
2020 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 evlaute our Malus collection for hard cider characteristics; we will determine polidy levels of selected Malus accessions; and we will evelop 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” with the following three objectives: 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 1); 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 (Objective 2); and 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 (Objective 3).
Maintenance and distribution of clonal germplasm are the two primary functions of ARS researchers in Geneva, New York, (Objective 1). During FY2020 we maintained 7,618 accessions of apples (Malus), grapes (Vitis), and tart cherry (Prunus). The number of requests for germplasm and volume of samples distributed continues to increase each year. During the FY2019 distribution period we completed 498 requests for germplasm, primarily as scion and cuttings, including 7,255 Malus, 535 Vitis, and 160 Prunus samples, representing 31% of the distinct accessions maintained in Geneva, New York. We continued to work with ARS researchers in Fort Collins, Colorado, to cryopreserve clonal germplasm, providing 24 tart cherry samples to evaluate a new cryopreservation technique.
ARS researchers in Geneva, New York, maintain one of the world’s largest and most diverse collections of wild and cultivated apples. Acquisition of wild Malus is a critical focus for apple germplasm conservation, particularly for wild North American apple species (Objective 1). We received new seed accessions from the Royal Botanic Gardens, Kew, Millennium Seed Bank Partnership, including 43 accessions from 5 wild Malus species from 7 countries. Malus chitralensis (n=4) from Pakistan and Malus crescimannoi (n=1) from Italy are new species added to the collection. Additionally, we are collaborating with ARS researchers in Beltsville, Maryland, to index viruses in the apple collection, and sampled approximately 350 apple accessions and 110 tart cherry accessions in FY2019 (Objective 2).
Grapevine is one of the most valuable fruit crops worldwide. ARS researchers in Geneva, New York, continued to evaluate chemical diversity of grapevine, with an emphasis on chemistry associated with fruit quality in hybrid grapevines in Geneva, New York, and table and wine grapes from Davis, California, (Objective 2). Additionally, we are collaborating with researchers in Montpellier, France to evaluate fruit chemistry diversity in wild grapevines. In collaboration with USDA-ARS researchers and collaborators in Geneva, and Ithaca, New York, the Davis and Geneva grape collections were genotyped using rhAMPseq markers. This method has become a standard platform through VitisGen for genotyping grapevines and will allow us to better leverage the genetic diversity found in both collections and infer pedigree information for our accessions. In 2019, we collected samples and extracted DNA from the entire Geneva collection. Initial data processing suggests high success rate for the Geneva samples (Objective 2).
To evaluate flowering time in the apple and tart cherry collections, we used aerial photography and image analysis, in collaboration with ARS researchers in Beltsville, Maryland (Objective 2). In the FY2019 season, we recorded bloom date with field observations and drone images for tart cherry, determined flight and camera parameters, integrated GPS data for the cherry collection, and explored analysis software to record flowering time for the apple and tart cherry collections in 2020. Utilization of these technologies will enhance our capacity to evaluate collections, with fewer personnel hours during observation times.
Accomplishments
1. Maintenance of clonal germplasm. The preservation and availability of healthy genetic resources to breeders and researchers, is critical to crop improvement. During FY2019, we maintained 6,073 apple (Malus), 1,414 grape (Vitis), and 131 tart cherry (Prunus) accessions. Occasional loss of field inventory due to disease or environmental conditions requires the repropagation of clonal germplasm. As such, we regenerated 240 accessions during FY2020.
2. Distribution of clonal germplasm. In FY2019, ARS researchers in Geneva, New York, distributed 7,950 samples (including dormant budwood, leaf, fruit, pollen, seed, and DNA) from 498 requests for germplasm, primarily as scion and cuttings. We distributed 7,255 apple, 535 grape, and 160 tart cherry samples, representing 31% of the distinct accessions maintained in Geneva. The average number of orders and samples distributed over the past five years was 450 and 6,995, respectively. The international distribution of clonal germplasm, is challenging due to restrictions on importing scion and cuttings in receiving countries. However, in FY2019, we distributed 225 samples to 7 countries. We are collaborating with authorities in Kazakhstan to repatriate 119 accessions of Malus sieversii, the wild progenitor of modern apple, collected by ARS researchers in the 1990s. Samples distributed supported research and breeding efforts for apple, grapes, and tart cherry, and provided the genetic diversity necessary for future crop improvement.
Review Publications
Yang, Y., Cuenca, J., Wang, N., Liang, Z., Sun, H., Gutierrez, B.L., Xi, X., Arro, J., Wang, Y., Fan, P., Londo, J.P., Cousins, P., Li, S., Fei, Z., Zhong, G. 2020. A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’. Horticulture Research. 7(67). https://doi.org/10.1038/s41438-020-0304-6.
Brewer, E., Cao, M., Gutierrez, B.L., Bateman, M., Li, R. 2020. Discovery and molecular characterization of a novel trichovirus infecting sweet cherry. Virus Genes. https://doi.org/10.1007/s11262-020-01743-7.
