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Research Project: Management of the National Collection of Carya Genetic Resources and Associated Information

Location: Crop Germplasm Research

2019 Annual Report

1a. Objectives (from AD-416):
Objective 1: Efficiently and effectively acquire Carya genetic resources; maintain their safety, genetic integrity, health and viability; and distribute them and associated information worldwide. Sub-objective 1A: Acquire high priority Carya genetic resources, characterize them using molecular profiling methods, integrate them into secure, temporary maintenance systems, and distribute associated information and appropriate propagules worldwide. Sub-objective 1B: Revise diagnostic methods for detecting Xylella fastidiosa in Carya. Sub-objective 1C: Screen ex situ and in situ Carya populations for Xylella fastidiosa. Sub-objective 1D: Confirm efficacy of remediation methods to eliminate Xylella fastidiosa from nuts and/or scions of Carya. Objective 2: Develop more effective genetic resource conservation, evaluation, and characterization methods and apply them to priority Carya genetic resources. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources. Objective 3: With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices for Carya genetic resource and information management.

1b. Approach (from AD-416):
This project represents one of the eight National Clonal Germplasm Repositories in the National Plant Germplasm System. It shares the common mission of all clonal repositories to collect, maintain, evaluate, document, and distribute valuable plant genetic resources. It is unique in its focus on the Carya genus, which includes the most valuable nut tree native to North America, the pecan [Carya illinoinensis (Wangenh.) K. Koch]. This project is a sister project of the Pecan Breeding Program (3091-21000-039-00D) and furnishes diverse Carya germplasm for use as parents within that program, as well as to other domestic and international breeding programs. Other North American species of Carya do not provide economic incentive for commercial nut production, but are valuable components of their ecosystems and are represented for use in breeding, with increasing interest on endemic and microbiotic associations. All diploid Carya, including commercially valuable Asian species, hybridize with pecan. Some Carya species exist only as fragmented populations in threatened habitats. Strategies for the appropriate characterization and utilization of those species are addressed in this project. Molecular genetic tools have been developed by the precursor project. These tools will continue to be cooperatively developed, refined, and applied by the current project in order to understand genetic diversity and gene flow in native populations, to verify identity of individual cultivars, to confirm parentage in controlled crosses, and to facilitate management of the Collection and its knowledgeable deployment.

3. Progress Report:
Significant progress was achieved in FY 2019 in assuring maintenance of the critical pecan germplasm curated/maintained by the project, in digitally managing critical data associated with the collection, and in better defining the physical and genetic characteristics associated with critical gerplasm types. Under Objective 1, graftwood of two early cultivars ('Kennedy' and 'Randall') significantly linked to the domestication history of the pecan were located, obtained, and grafted at both worksites of the National Clonal Germplasm Repository for Pecans and Hickories (NCGR-Carya). Tender leaf tissue of those (and 496 other diverse living accessions) were sampled, DNA was extracted, and is being resequenced (ref. sister project 3091-21000-039-00D, Pecan Breeding and Genomic Resource Development). Phenotypic observations of symptom expression related to Xylella fastidiosa (causal agent of an important pecan disease) were made on repository accessions, with some samples being submitted to state diagnostic labs for analysis, and others being sampled, extracted, and stored using appropriate methods (Objective 1). In work under Objective 3, a prototype initiated by the U.S. National Arboretum, using a relational database (BG-Base) developed for use by that organization with both living and voucher type specimens, was obtained and installed on ARS computers. The digital asset manager AssetBank was obtained, installed, and coordinated with BG-Base. Hundreds of inventory specific images were uploaded and indexed. A cooperative project was initiated in which remote images were obtained and developed into ArcGIS georeferenced mosaic images at each worksite, and a prototype linking relational and image data to spatial maps was developed (Objective 3). The georeferencing work will provide much-needed spatial characterization of orchard composition and will facilitate health monitoring and other aspects of orchard maintenance going forward.

4. Accomplishments
1. Collaborative detection of Xylella in pecan. Xylella is a pecan pathogen that embeds itself in woody plant tissues and is difficult to control in long-lived organisms such as pecan. The disease distribution is primarily located in the continental U.S., and phytosanitary restrictions prevent at the present time the repository from fulfilling germplasm requests. Assessment of the pathogen distribution is the first step to understanding the scale of the problem. ARS scientists at College Station, Texas, working with a national team of researchers, used coordinated methods and samples to confirm widespread presence of Xylella fastidiosa in Georgia pecan orchards, consistent with previous reports from this program concerning presence of the disease in Texas Repository orchards. This assessment provided a much needed perspective on the distribution of the pathogen and confirmed the continued need for research related to methods of remediation in order to distribute disease free germplasm.

Review Publications
Bock, C.H., Olive, J.E., Chen, C., Hotchkiss, M.W., Stevenson, K.L., Wang, X., Grauke, L.J., Hilton, A.E., Jo, Y., Randall, J.J. 2018. Pecan bacterial leaf scorch, caused by Xylella fastidiosa, is endemic in Georgia pecan orchards. Plant Health Progress. 19:284-287.
Bentley, N., Grauke, L.J., Klein, P. 2019. Genotyping by sequencing (GBS) and SNP marker analysis of diverse accessions of pecan (Carya illinoinensis). Tree Genetics and Genomes. 15:8.