Location: Plant Genetic Resources Unit (PGRU)
2019 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 NPGS (National Plant Germplasm System) 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 FY2019 we maintained 7,613 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 FY2018 distribution period we completed 540 requests for germplasm, primarily as scion and cuttings, including 7,267 Malus, 760 Vitis, and 193 Prunus samples, representing 29% of the distinct accessions maintained in Geneva, New York. We continued to work with ARS researchers in Fort Collins, Colorado, to cryopreserve clonal germplasm. Seeds from 33 apomictic Malus accessions were collected apomictic for preservation. An average of 2,500 seeds were preserved from 15 Vitis accessions. We will conduct germination tests to determine appropriate handling and storage conditions for grape seeds.
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). A domestic exploration for Malus coronaria in Ohio was completed in August 2018 by ARS researchers in Geneva, New York. An additional exploration is scheduled in fall 2019 to collect Malus angustifolia and M. coronaria in Kentucky, Tennessee and Arkansas. A foreign exploration for Malus doumeri in Vietnam was completed through a joint effort between ARS researchers and foreign collaborators in Hanoi, Vietnam. Germplasm for this species was extremely limited in the United States and Europe prior to this exploration. Due to the cold-sensitivity of this species, accessions will be maintained by ARS researchers in Corvallis, Oregon. Approximately 270 permanent accessions were added to the collection following the evaluation of a wild apple seedling orchard in collaboration with ARS researchers in Fort Collins, Colorado. Additionally, we are collaborating with ARS researchers in Beltsville, Maryland, to index viruses in the apple collection. We sampled 20 accessions and identified a novel apple virus using High Throughput Sequencing of virus genomes (Objective 2). Additional apple and cherry samples are under evaluation in FY2019.
Grapevine is one of the most valuable fruit crops worldwide. ARS researchers in Geneva, New York, initiated studies to evaluate chemical diversity of grapevine, with an emphasis on chemistry associated with fruit quality (Objective 2). We are evaluating fruit chemistry in hybrid grapevines in Geneva, New York, and table and wine grapes from Davis, California. Additionally, we are collaborating with researchers in Montpellier, France, to evaluate fruit chemistry diversity in wild grapevines. We are collaborating with ARS researchers in Geneva, New York, and Davis, California, and researchers in Ithaca, New York, to genotype 1,400 and 3,500 accessions from the Geneva, New York, and Davis, California, grapevine collections, respectively, using rhAMPseq (Objective 2). This method has become a standard platform for genotyping grapevines and will allow us to better leverage the genetic diversity found in both collections and will better enable us to understand relationships and pedigrees among the accessions (Objective 3).
Tart cherry is valued around $90.8 million within the United States with actively expanding markets based on its nutritional qualities. ARS researchers in Geneva, New York, completed a fruit quality evaluation for 103 accessions from the tart cherry collection in Geneva, New York (Objective 2). We identified promising accessions with superior nutritional quality than those commonly grown within the United States. These results will be added to our germplasm database and will assist stakeholders in selecting tart cherry germplasm from our collection.
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). This 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. Preservation and availability of healthy genetic resources to breeders and researchers is critical to crop improvement. During FY2019 we maintained 7,613 accessions of apples (Malus), grapes (Vitis), and tart cherry (Prunus). Occasional loss of field inventory due to disease or environmental conditions requires repropagation of clonal germplasm. As such, we regenerated 114 accessions during FY2019, including 75 from cryopreserved material.
2. Distribution of clonal germplasm. Distribution of plant material is the largest service we provide to our stakeholders. The samples distributed supported research and breeding efforts for apple, grapes, and tart cherry, and provided the genetic diversity necessary for future crop improvement. During FY19, ARS researchers in Geneva, New York, processed 417 requests and distributed 8,206 samples, in the form of cuttings for propagation, vegetative tissues, fruit, pollen, seeds, and DNA. Additional requests for fruit and dormant cuttings are anticipated during the fall and winter 2019.
Review Publications
Gutierrez, B.L., Zhong, G., Brown, S., Arro, J. 2018. Linkage and association analysis of Dihydrochalcones Phloridzin, Sieboldin, and Trilobatin in Malus. Tree Genetics and Genomes. 14:91. https://doi.org/10.1007/s11295-018-1304-7.
Gutierrez, B.L., Zhong, G., Brown, S. 2018. Increased Phloridzin content associated with russeting in apple fruit. Genetic Resources and Crop Evolution. 65(8):2135-2149.
Zong, X., Zhang, Y., Walworth, A., Tomaszewski, E.M., Callow, P., Zhong, G., Song, G. 2019. Constitutive expression of an apple FLC3-like gene promotes flowering in transgenic blueberry under nonchilling conditions. International Journal of Molecular Sciences. 20(11):2775. https://doi.org/10.3390/ijms20112775.
Arro, J., Yang, Y., Song, G., Zhong, G. 2019. RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines. Biomed Central (BMC) Plant Biology. 9(1):80. https://doi.org/10.1186/s12870-019-1675-4.
