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ARS Home » Midwest Area » Ames, Iowa » Plant Introduction Research » Research » Research Project #434242

Research Project: Plant Genetic Resource Management and Information System Development

Location: Plant Introduction Research

2022 Annual Report

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.

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 (255) included transfer of 80 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 9 accessions of Chenopodium, 14 accessions of amaranth, 5 accessions of flax, 7 accessions of wild sunflowers, and miscellaneous legumes, 7 accessions from the Germplasm Enhancement of Maize (GEM) Project, 26 accessions of maize inbreds, 80 accessions with expired Plant Variety Protection certificates, 22 accessions of Cucumis melo, and 54 medicinal, herbaceous, and woody landscape accessions. 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 748 accessions which require insect pollination for reproduction. These include honeybees, bumblebees, Osmia (mason) bees, Alfalfa Leafcutter bees, and two species of flies. Use of designated “permanent” pollination control cage fields enhanced productivity and reduced labor costs in 2022. Elimination of the field layout mapping and cage frame construction activities have kept labor needs to a minimum and enhanced the ability to provide proper social distancing of employees in field operations. Specialized equipment for field tillage operations within the cages provide excellent soil preparation and fertilizer incorporation. Seeding of grass between cages provides improved weed control and improves access to cages during the growing season. Two new fields will be established in 2022 for use in 2023. New fields will allow for rotation of crops and fields for optimal disease control. The standard germination testing using 200 seed samples to monitor condition and viability of 2,709 accessions was conducted in 2021. Interruptions in part-time labor schedules caused by the Covid-19 pandemic forced the cancelation of additional germination testing to address the backlog of germination testing needed to monitor accession seed condition. Regeneration plans must address accessions with declining viability. Viability testing was focused on the Brassica, Crucifers, maize, Cucurbita, and Amaranthus collections. Regeneration of portions of the Brassica collection and the flax collection is needed due to declining viability. Pandemic restrictions and concerns about availability of labor in summer 2021 delayed regeneration plans for accessions of several crops until 2022. 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 relatives and maize. Focus was placed on uploading of images to GRIN-Global for genebank accessions. Loading of accession images continued in 2021 to enhance collection characterization. The images are important for stakeholder/researchers who search the public GRIN database to verify and/or select materials based on visual seed or plant images, as well as phenotypic and genetic information. Accession evaluation information (milestone 2B) was provided for 460 accessions, 76% of which was associated with maize inbreds, populations, and expired Plant Variety Protected (PVP) inbred lines. The backlog of accession images awaiting release was reduced with 33,776 images of 15,541 accessions provided. Efforts to identify methods to reduce seedborne Acidovorax citrulli, the causal agent of bacterial fruit blotch, in Cucumis melo seeds using dry heat did not prove effective and have been discontinued. Heat treatment of seeds degraded germination of the seeds but failed to eliminate the pathogen. Research into use of antibiotics showed promise in early tests but also proved to be unsuccessful. Antibiotic seed treatment trials with 12 different compounds showed pathogen sensitivity to Doxycycline, Trimethoprim, Sulfamethoxazole, and Ceftazidime, but further investigation coupled with use of ELISA tests could not confirm bacteria elimination from infected seeds. Field and greenhouse plantings of 687 seed increases were inspected for plant pathogens; no diseases of phytosanitary concern were observed Seed health testing and treatment programs ensure seed health and support utilization. In addition, nearly 142 plots were inspected for the Germplasm Enhancement of Maize breeding project. Additional declarations were written in support of phytosanitary certificates for 117 orders. Obj 2 Related: Evaluation of 391 of the 675 NCRPIS Brassica rapa accessions was conducted to properly classify the collection into spring and winter flowering groups. Proper classification is essential for regeneration of the accessions and an important trait for stakeholders. Winter flowering accessions require vernalization to induce flowering. These accessions can be planted in the greenhouse to establish initial growth and transferred to a vernalization growth chamber. After vernalization, the established plants are transplanted to the field. Flowering classification data was then added to the GRIN-Global database. Obj 3 Related: Virtual meetings with Crop Germplasm Committees representing the NCRPIS collection species were conducted in 2021. Collection management and distribution information was shared with committees. Germination and viability of the Brassica and Linum (flax) accessions is falling, and regeneration of these accessions is an increasing priority. Long term, stable storage of these oilseed species requires -20 oC conditions. The main NCRPIS storage chamber is maintained at 4 oC. 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 was released. GRIN-Global interoperability with the Maize Genetics and Genomics Database (MaizeGDB), Soybean Genetics and Genomics Database (SoyBase), Peanut Genetics and Genomics Database (PeanutBase), and Legume Information System (LIS) 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. Ames, Iowa ARS personnel 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.

1. Plant genetic resource distribution. Plant genetic resources (germplasm) were distributed for research and educational objectives. In 2021, more than 840 public and private sector researchers received 41,690 packets of seeds of 21, 132 accessions. Domestic recipients (70% of requestors) received 54% of the packets, and 46% of the packets were distributed to international recipients (30% of requestors). Demand remains strong 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. 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.