Research Project: Plant Genetic Resource Management and Information System Development

Location: Plant Introduction Research

2020 Annual Report

Objectives
Objective 1: Efficiently and effectively acquire and maintain the safety, genetic integrity, health, and viability of priority maize, vegetable, oilseed, minor grain crop, medicinal, and ornamental genetic resources, and distribute them and associated information worldwide. Sub-objectives: 1A. Expand, regenerate and conserve collections of priority maize, vegetable, oilseed, minor grain crop, medicinal, and ornamental genetic resources. 1B. Enhance genetic integrity of genetic resources maintained. 1C. Backup accessions at second sites, increasing the proportion of accessions backed up to more than 83% of 2016 holdings. 1D. Distribute germplasm and associated information to support research objectives. 1E. Monitor accessions for viability and phytosanitary health to ensure availability of healthy propagules and to preserve their genetic integrity. 1F. Develop and/or refine diagnostic methods to detect seed-borne pathogens. Objective 2: Develop more effective genetic resource maintenance, evaluation, or characterization methods and apply them to maize, vegetable, oilseed, minor grain crop, medicinal, and ornamental genetic resources. Record and disseminate evaluation, characterization, and adaptation data via GRIN-Global (GG) and other data sources. Sub-objectives: 2A. Enhance capacities to increase collection availability. 2B. Evaluate crop collections for phenotypic, morphological, composition, and productivity related traits such as biotic/abiotic stress resistance and yield. 2C. Apply and utilize genetic marker technologies to better characterize key collections. 2D. Provide information and findings that facilitate germplasm utilization via GG, other data sources, and publications. Objective 3: With other National Plant Germplasm System (NPGS) genebanks and Crop Germplasm Committees (CGCs), develop, update, document, and implement best management practices and Crop Vulnerability Statements (CVSs) for priority maize, vegetable, oilseed, minor grain crop, medicinal, and ornamental genetic resources and information management. Sub-objectives: 3A. Modify, document and implement best management practices, and share them publicly. 3B. Provide input for annual/periodic updates of CVSs. Objective 4: Continue to expand the capacity and capabilities of the GRIN-Global (GG) plant genetic resource (PGR) information management system to meet the needs of crop curators and genetic resource users, and to ensure smooth integration of its data with information from other sources, such as model organism databases (MODs). Sub-objectives: 4A. Cooperate with GG users and developer communities to identify and develop wizards and applications to improve system utility, information delivery, and genebank workflow efficiency. 4B. Provide technical leadership to the NPGS for GG evolution to meet genebank information and workflow needs.

Approach
Obj 1: Plant genetic resource (PGR) regeneration/management priorities are determined in response to PGR demand, external pressures such as stakeholder needs, or the status of resources, i.e. threatened or endangered, and inventory quantity, viability, and quality status. Genetic integrity will be assured through use of best management practices and monitoring to detect contamination. Seed lots will be backed up at the NCGRP in Ft. Collins, CO, and an international seed vault. Periodic testing to assess collection quality and health will assure their security, and new protocols will be developed. Quality PGR and associated information are distributed to support research objectives based on criteria which may govern their distribution or use. Seeds/plantings will be monitored for disease and assayed for pathogen identity, with phytosanitary precautions implemented at several points to preclude seedborne pathogens. New methods for detection of seed-borne pathogens will be evaluated and implemented. Obj 2: Collaborations with other NPGS site personnel or tropical nursery providers are required to grow certain accessions where they are adapted, including facilities that support quarantine grow-outs of maize originating from some countries. In-house facilities will be improved to handle accessions with challenging growth requirements. Phenology and basic morphological descriptors are captured during seasonal activities. High priority evaluation traits will be determined. Woody ornamental germplasm will be evaluated via the NC7 Ornamental Trial system to determine adaptation and survival across the North Central US. Evaluations will be conducted using established protocols, and findings published on the GRIN-Global website or suitable fora. Genetic marker technologies will be utilized to assess maize accession relationships. Sunflower genetic marker information will be assessed to determine whether valid associations can be made with habitat/geographic information, and used to determine how well crop wild relatives are represented in the collection. Obj 3: Best management practices for collection management and standard operating procedures that govern genebank workflows will be reviewed, modified, and documented periodically. Crop Germplasm Committee chairs and members will be provided information on the status of the collections and specific issues that threaten the security and/or availability and backup status of the collections, and opportunities to mitigate threats. Personnel will assist in development of Crop Vulnerability Statements. Obj 4: The capabilities of the GRIN-Global PGR information management system will be expanded to meet crop curator and genetic resource user needs. Wizards and applications to improve system utility, information delivery, and genebank workflow efficiency will be identified and developed. Improvements necessary to support system adoption will be made. Use of improved communications technologies will be facilitated. Interoperability of GRIN-Global with multiple information providers will be supported.

Progress Report
Obj 1 Related: New germplasm acquisitions (437) included transfer of 121 accessions from the National Laboratory for Genetic Resources Preservation (NLGRP) in Ft. Collins, Colorado, of many of the species we curate, as well as from exploration and transfer. These include the first cytoplasmic male sterile amaranth and a dwarf breeding line of Amaranthus cruentus, both developed in Ames, Iowa, by an Iowa State University Curator; a group 34 of psuedocereal accessions that provide triazine herbicide-tolerant and -susceptible examples for weed physiology research; 124 medicinal, herbaceous, and woody landscape accessions; transfers of crop wild relatives from the Seeds of Success Program, administered by the Bureau of Land Management; vegetable and maize resources with expired Plant Variety Protection certificates; and cultivated and wild sunflower resources. Use of cover crops is being tested in caged regeneration fields for improvement of soil health and weed control. Beneficial insects are used both in the field cages and greenhouse rooms to control pest insects; these include rove beetles, ladybug beetles, green lacewings, beneficial nematodes, and Encarsia formosa, a beneficial wasp. Our entomology team provided six species of pollinator insects to pollinate 989 accessions which require insect pollination for reproduction. These include honeybees, bumblebees, Osmia (mason) bees, Alfalfa Leafcutter bees, and two species of flies. The team produced documentation and videos of the processes involved in sources, managing, and use of pollinators at the station for education and training purposes. Equipment was improved in the vernalization rooms (first used in February, 2019) to reduce humidity and were successfully used a second season to vernalize Brassica seedlings for six weeks at less than 40 F. Methods to increase germplasm that does not respond to normal, temperate conditions are being tested. More than 1,100 accessions were harvested and processed in 2020. Regeneration plans must address accessions with declining viability. Viability was tested for 10% of collection holdings, focused on Brassica, flax, foxtail millet, Setaria, maize, cultivated sunflower, Cucurbita, and Daucus. Regeneration of portions of the Brassica collection and the flax collection is needed due to declining viability. Due to concerns about availability of labor in summer 2020, flax regeneration was postponed until 2021 as a high oilseed priority. Samples of Salix (willow) and Quercus (oak) were shared with the NLGRP to support collaborative research to better understand optimum storage variables that support retention of seed viability. ARS personnel in Parlier, California, supported regeneration of specific wild Helianthus taxa that need a longer growing season than Ames, Iowa, can provide, and mountain and desert species that do not thrive in midwestern humidity and heavy soils. ARS personnel in Salinas, California provided support for spinach seed increases, which require use of positive pressure growth chambers. Private sector collaborators provided support for regeneration of Daucus relative and maize. A strong focus was placed on enabling uploading of images to GRIN-Global for genebank accessions. With the new protocol, image mass-loading will continue in 2020, important for researchers who search the public GRIN database in order to verify and/or select materials for research based on visual seed or plant images, as well as phenotypic and genetic information. Newly available crop accession evaluation information (milestone 2B) was provided for 1,853 accessions, 72% of which was associated with maize inbreds, populations, and expired Plant Variety Protected (PVP) inbred lines. Collector/source information for Daucus since 2009 was loaded, and progress made for acquisitions dating back to 1987. Passport information was improved; geographic collection coordinates locations and improvement status entered, and more than 1,580 older, pathology-related inspection notes loaded to facilitate selections to fill seed requests. Soil sampling protocols were developed and implemented for all station fields; information will facilitate actions to improve soil health. New diseases were observed in Ames, Iowa, a phytoplasmal disease affecting flax, and an anthracnose disease of quinoa. First reports of these diseases have been submitted. Effort to identify methods to reduce seedborne Acidovorax citrulli, the causal agent of bacterial fruit blotch, in Cucumis melo seeds now focus on chlorine gas treatment. While previous treatment methods testing the efficacy of use of streptomycin were not effective, chlorine gas did appear to reduce symptom development. Research into use of other antibiotics is ongoing. Further investigation coupled with use of ELISA tests is required to verify whether bacteria are consistently detected in seeds. Field and greenhouse plantings of 914 seed increases were inspected for plant pathogens; the only disease of significance observed was black rot of Brassica. Vegetable plantings were inspected weekly, no diseases of significance observed. Seed health testing and treatment programs ensure seed health and support utilization. In addition, nearly 4,100 plots were inspected for the maize breeding project (Germplasm Enhancement of Maize). Additional declarations were written in support of phytosanitary certificates for 138 orders. Obj 2 Related: A collaboration with University of Arkansas researchers entitled "Evaluation and Association Analysis of Stemphylium Leaf Spot Resistance for USDA Spinach Germplasm", has resulted in evaluation of more than 100 spinach germplasm accessions in greenhouse testing for this leaf spot disease. More evaluations are pending due to pandemic-related delay; the phenotypic data will be used in conjunction with genetic marker for genome wide association studies in order to conduct marker assisted and genomic selection in a breeding program for Stemphylium leaf spot resistance. Obj 3 Related: Crop Vulnerability Statement updates were completed or are in process for the Root and Bulb, Cucurbit, Leafy Vegetable, and Sunflower Crop Germplasm Committees, in collaboration with their members. Documentation of best management practices and standard operating protocols are modified frequently. Virus testing protocols were updated. Plant/seed protection practices were reviewed and re-evaluated. A new pre-plant treatment for control of Brassica black rot is being tested. Brassica rapa accessions are being evaluated to determine flowering type, and a flowering stimulation test is being evaluated prior to field planting. Obj 4 Related: Protocols were developed to detail how applications can appropriately be shared and vetted between U.S. and international GRIN-Global collaborating institutions. This will advance evolution of the system, facilitate genebank workflows and information objectives, and extend the lifecycle of the system. Following security code scanning, the Office of the Chief Information Officer approves all new versions for release. New Order, Cooperator and Viability wizard versions of GRIN-Global were completed in response to evolving genebank personnel users desired enhancements. Curator Tool (CT) build version 1.9.9.4 was released. GRIN-Global interoperability with the Maize Genetics and Genomics Database and Legume Information System information providers was inspected; routine information updating is currently limited to ETL (extract, transform and load) processing. To address this, a software prototype using a RESTFUL interface has been developed to facilitate pulling data from GRIN-Global to use in conjunction with data from other providers. ARS personnel in Ames, Iowa, participated in virtual weekly development team meetings with ARS personnel in Beltsville, Maryland, twice monthly with the GRIN-Global Advisory Committee to work on priorities for developers and the database administrator, and monthly with the International Developer’s Advisory Committee.

Accomplishments
1. Plant genetic resource distribution. Plant genetic resources (germplasm) were distributed for research and educational objectives. Crop improvement and production is dependent on sources of plant genetic diversity to introduce new genetics and new or improved traits. Information on plant genetic resource collections and access to the germplasm is provided via the GRIN-Global website, and via direct contact with curatorial personnel. Samples are maintained and distributed by personnel from the North Central Regional Plant Introduction Station in Ames, Iowa. In 2019, more than 900 public and private sector researchers received 54,232 packets of seeds of 22,271 accessions, representing 41% of the entire collection. Domestic recipients (73% of requestors) received 67% of the packets, and 33% of the packets were distributed to international recipients (27% of requestors). In the first five months of 2020, 33,182 packets were distributed of 18,089 accessions. Demand continues to escalate for our collections of maize, vegetables, oilseeds (Brassica, crucifers, and sunflower), woody and herbaceous ornamentals, and miscellaneous crops such as quinoa, amaranth, spinach, panicum, and several others. These resources contribute to sustaining agricultural productivity, and to research findings devoted to understanding genetic diversity and inherent value of the germplasm.

2. Use of high altitude site to regenerate Andean highland maize germplasm. Many plants, especially landrace cultivars and crop wild relatives, are uniquely adapted to the specific environmental conditions associated with their origins. Through experience it is known that Andean tropical highland accessions held by the maize collection can only be regenerated in highland tropical conditions. ARS scientists in Ames, Iowa, collaborated with scientists at the International Center for Maize and Wheat Improvement (CIMMYT) to increase seed of 25 Peruvian highland accessions at their Tolucca, Mexico site and were very successful as measured by seed quantity, vigor, and quality. Additional collaborations with CIMMYT scientists to increase seed of highland maize are planned. Collaborative opportunity greatly enhances our capacity to ensure we can fulfill our mission in preserving these unique and highly valuable maize genetic resources.