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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

2023 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
This is the final report for the Project 5030-21000-064-000D, which has been replaced by new Project 5030-21000-070-000D. For more information, see the new project report. Objective 1 related progress: New germplasm acquisitions (336) in 2022 included transfer of accessions from Ft. Collins, Colorado, of many of the species we curate, as well as from exploration and other transfers. These include two Chenopodium accessions, three amaranth accessions, three Aster accessions, five Brassica accessions, 35 crucifer accessions, 45 cultivated sunflower accessions, two wild sunflower accessions, one miscellaneous legume accession, seven Germplasm Enhancement of Maize (GEM) Project accessions, 76 maize inbred accessions, 46 expired Plant Variety Protection (PVP) accessions, two Cucumis melo accessions, three Cucurbita accessions, one Daucus accession, two Ocimum accessions, and 71 medicinal, herbaceous, and woody landscape accessions. Over the 5 years of the project, 1,789 germplasm acquisitions were added to the collection and accession availability increased from 76% to 80%. Beneficial insects are used in both the field cages and greenhouse rooms to control pest insects which include rove beetles, ladybug beetles, and beneficial nematodes. Six species of pollinator insects were used to pollinate 765 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 has enhanced productivity and reduced labor costs over the plan's 5-year cycle. 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 continues to provide improved weed control and access to cages during the growing season, reduced field tillage operations, and limited soil compaction. The standard germination testing to monitor condition and viability of 5,075 accessions was conducted in 2022. Easing COVID-19 pandemic restrictions allowed germination testing to increase to near pre-pandemic levels. The increased testing was targeted to the backlog of germination testing needed to monitor accession seed condition. Part-time labor availability continues to be the challenge which limits germination testing capacity. Efforts to monitor the condition of collection accessions in storage have been improved over the plan cycle. Development of small sample germination tests and targeted tracking of seed viability have increased the effectiveness of the seed viability team efforts. 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. Remaining pandemic restrictions and shortage of labor in summer 2022 delayed regeneration plans for accessions of several crops until 2023. 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. Regeneration efforts over the project cycle have been significantly impacted by pandemic restrictions, limited labor availability, and budget considerations. Accession selection for regeneration required careful review to target items that remain in high demand and those that are critical for preservation of species diversity. Limited regeneration capacity has created a substantial backlog of accessions that will be in danger of either inactivation or loss in coming years. Focus was placed on uploading accession images to Germplasm Resource Information Network (GRIN-Global) in 2022 to enhance collection characterization. The images are important for stakeholder/researchers who search the public GRIN-Global database to verify and/or select materials based on visual seed or plant images, as well as phenotypic and genetic information. Accession evaluation information was provided for 873 accessions, 56% of which were associated with maize inbreds, populations, and expired PVP inbred lines. Over the project cycle, substantial progress has been achieved in reducing the backlog of data and images that need to be uploaded to GRIN-Global. All curation projects within the research unit leveraged increased levels of telework to address the backlog. Field and greenhouse plantings of 828 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 692 plots were inspected for the GEM breeding project. Additional declarations were written in support of phytosanitary certificates for 85 orders. Objective 2 related progress: Substantial progress was made over the five years of the project. Accessions from several collections were characterized for flowering habit, maturity, disease resistance, climate condition sensitivity, and disease resistance. The resulting data was then added to the GRIN-Global database and used to enhance regeneration success and provide valuable information to seed requesting research scientists and breeders. Objective 3 related progress: Virtual and in person meetings with Crop Germplasm Committees (CGC) representing the Ames, Iowa, collection species were conducted in 2022. 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. Availability of virtual meetings allowed work with the respective CGCs to stay on track and make substantial progress over the project cycle. This meeting format sustained committee activity during the years of pandemic restriction and served to improve communication within the committees by expanding the attendance beyond individuals who could travel to a designated site. The format provided for more direct frequent interaction and fostered the exchange of ideas and actions. Objective 4 related progress: 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 extract, transform and load (ETL) processing. To address this, a software prototype using a representational state transfer (RESTFUL) interface has been developed to facilitate pulling data from GRIN-Global to use in conjunction with data from other providers. We 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. Progress on enhancement of the GRIN-Global system continued over the duration of the program cycle.

1. Grain amaranth germplasm distributed from the collection improve survival of children and increase the income of Uganda farmers. Accessions from the amaranth germplasm collection are frequently requested by researchers in the United States and countries around the world for basic research and crop improvement. The germplasm collection curators seldom receive information on the use and impact of these seed distributions. The amaranth collection curator at Ames, Iowa, provided grain amaranth accessions that were introduced and evaluated for grain production in Uganda by Makerere University through their Iowa State University collaboration. Several of the accessions proved to be well adapted and highly productive. The produced grain was added to locally consumed porridge to increase the nutritional value. The produced grain also acted as a cash crop that small local farmers could sell to increase their income. The enriched porridge has improved the nutrition and survival of children in rural Uganda and increased the income of small local land holders. A collaborative project has now been funded for a plant breeding project to increase grain amaranth production in Uganda.

2. Carrot germplasm identified for drought tolerance improvement. Accessions from the carrot germplasm collection are frequently requested by researchers in the United States and countries around the world for basic research and crop improvement. The accessions provide a set of genetically diverse lines and populations that are well suited for basic plant research studies. Drought is one of the major environmental challenges restricting the production of agricultural crops, including carrots. Studies to understand the impact of drought on crop germination and the response of genetically diverse materials to this major crop production challenge. The carrot germplasm curator at Ames, Iowa, provided seed of 250 carrot lines and wild relatives for germination response evaluation under drought conditions to researchers at the University of Wisconsin-Madison, ARS, and the University of Sargodha in Pakistan. Studies found a wide range of seed germination response to drought conditions. Several accessions from the collection were identified as promising sources for improvement of germination response under drought conditions. This information was published in recent scientific articles and the information added to the GRIN-Global database which will allow plant breeders to use these accessions in future plant breeding programs to improve carrot response to drought.

Review Publications
McCoy, J., Martinez-Ainsworth, N.E., Bernau, V.M., Scheppler, H., Hedblom, G., Adhikari, A., McCormick, A., Kantar, M., McHale, L., Mercer, K., Baumler, D. 2023. Population structure in diverse pepper (Capsicum spp.) accessions. BMC Research Notes. 16. Article 20.