Location: Crop Germplasm Research2017 Annual Report
1a. Objectives (from AD-416):
The long-term goals of this project are to conserve a broad spectrum of the genetic diversity of Carya, develop analytical tools to characterize that diversity, use those tools in the evaluation of the horticultural merit of the materials, maintain the permanent collection appropriately within resource constraints, and encourage the use of these genetic resources and associated information in research and crop genetic improvement. The existing ex situ collection of germplasm in the National Collection of Genetic Resources (NCGR) for Pecans and Hickories provides a broad representation of the diversity of the genus. NCGR collections will be augmented and strategically expanded by addition of accessions, and by qualifying in situ populations in cooperation with federal and state conservation programs. Molecular genetic tools have been developed and will be refined, extended, and used on NCGR collections, in conjunction with standardized phenological descriptors, to define the relationships between genetic diversity, phenotypic expression and geographic distribution. Data will be entered into the Germplasm Resources Information Network (GRIN-Global), making a wealth of information available to an international, multi-disciplinary audience. Over the next 5 years we will focus on the following objectives: Objective 1: Elucidate patterns of genetic divergence and diversity in Carya (pecan and related taxa) and apply that knowledge to genetic resource management and ultimately to pecan genetic improvement. Sub-objective 1A: Determine ploidy level and comparative genome size in Carya using flow cytometry. Sub-objective 1B: Profile NCGR Carya accessions with selected genetic markers. Objective 2: Effectively manage and conserve Carya genetic resources and associated information. Sub-objective 2A: Manage ex situ collections at College Station and Brownwood worksites. Sub-objective 2B: Designate in situ reserves based on regional characterizations of diversity. Objective 3: Evaluate ("phenotype") pecan genetic resources for their horticultural merit. Sub-objective 3A: Summarize existing phenological data and refine descriptors in consistency with uniform ontologies to facilitate cross-database queries and the comparative analysis of gene expression and phenotypes. Sub-objective 3B: Establish a phenotypic "core subset", monitor phenology. Objective 4: Transfer pecan germplasm, genetic marker technology, and descriptive information to accelerate pecan research and genetic improvement.
1b. Approach (from AD-416):
In order to better elucidate patterns of genetic divergence and diversity in Carya (pecan and related taxa) and apply that knowledge to genetic resource management and to pecan improvement (Objective 1A), the ploidy level and genome size will be determined in selected accessions. Work will stress species whose ploidy level is not currently known and species whose subgeneric placement has been disputed. For more broadly represented species, accessions representing different areas of origin will be checked. Data on ploidy and genome size will be combined with genetic marker data being developed for routine profile determination of NCGR accessions (Objective 1B). Using sequence information generated in cooperative work, single nucleotide polymorphic sites (SNPs) will be selected to represent known genic regions that are well distributed across chromosomes in homologous species, as well as SNPs representing organelles. SNPs will be validated for information content using a panel of diverse species of Carya as well as geographically and phenotypically diverse pecan accessions. Validated SNPs will be used in analyses designed for cost efficiency. DNA will be extracted from remaining NCGR accessions to be profiled. The resulting datasets will contribute to effective ongoing management of ex-situ collections maintained at worksites in College Station and Brownwood, TX (Objective 2A) and will help in the identification of in situ reserves based on regional characterization of diversity (Objective 2B). Phenological records of the NCGR will be summarized and refined in consistency with uniform ontologies to facilitate cross-database queries and comparative analysis of gene expression and phenotype (Objective 3A). Based on previous observations of diversity, a phenotypic "core subset" will be established and used to monitor phenology (Objective 3B). Historical data will be examined to select a small group of cultivars that represent geographic diversity of origin and manifest broad diversity in phenology but which can be sampled at both the Brownwood and College Station worksites. Inventories of those accessions will be visited weekly to rate patterns of growth inception, flowering, nut development, nut quality, leaf condition, and leaf drop using revised descriptors (from sub-objective 3A). This will provide a framework onto which other Carya accessions will be integrated and their variability interpreted by comparison over a broad geographic range. The initial effort will be the aerial characterization of budbreak, which differs by over a month across accessions in provenance orchards. Observations of the progression of budbreak in the diverse phenotypic core cultivars at Burleson and Brown Counties in Texas will be entered into the budbreak protocol on Pecan ipmPIPE. In order to facilitate the transfer of pecan germplasm, genetic marker technology, and descriptive information and accelerate pecan research and genetic improvement (Objective 4), the historic origination records and all inventory-specific evaluation records will be made publicly available on GRIN-Global, with appropriate summaries on the Unit website.
3. Progress Report:
In FY 2017, project objectives to effectively manage and conserve Carya (pecan and hickory) genetic resources and associated information were addressed in cooperation with researchers at Texas A&M University, New Mexico State University, The University of Arizona, Louisiana State University, Mississippi State University, and ARS researchers in Byron, Georgia. Portions of the work focused on improving detection methods for Xylella fastidiosa (pecan bacterial leaf scorch), improving sampling protocols for diagnosing the disease, and the use of the improved techniques to screen repository collections. The presence of the bacteria was confirmed in inventories of the National Collection of Genetic Resources for Pecan and Hickory (NCGR-Carya). Distribution of graftwood has been stopped to international cooperators until efficacy of remediation treatments in graftwood is confirmed. Bacterial transmission via seed is currently being studied, with focus on the development of methods to eliminate contamination detected in seed and seedlings (Objective 2). Genomic profiles of historic cultivars used by the pecan industry and their controlled cross progeny, plus selected wild relatives with interspecific hybrids, were developed using a molecular biology technique known as genotype by sequencing in on-going efforts to deliver cultivar verification and nursery certification procedures to the industry (Objective 1).
1. Xylella fastidiosa verified in pecans in the Southwestern United States. Requests coming to the USDA ARS National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya) for international distribution of pecan graft wood often require documentation that the wood is free of Xylella fastidiosa, a causal agent of pecan bacterial leaf scorch (PBLS). ARS researchers at College Station, Texas, working with colleagues at Texas A&M University, New Mexico State University, and The University of Arizona, screened 79 pecan samples from Arizona, New Mexico, California, and Texas, for X. fastidiosa using a technique known as enzyme-linked immunosorbent assay (ELISA); all samples tested positive. The molecular technique, polymerase chain reaction (PCR), was used to confirm X. fastidiosa in a number of samples; when amplified PCR products were sequenced, they aligned closely with reference sequences from known subspecies of the Xylella disease organism. This is the first report of the presence of X. fastidiosa in pecan in the southwest region of the U.S. and in NCGR-Carya, and has implications for international distribution of pecan germplasm, as well as pecan nursery and orchard management.