Location: Plant Introduction Research
2024 Annual Report
Objectives
Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall National Plant Germplasm System (NPGS) Plan, then apply them to priority maize, vegetable, oilseed, ornamental, medicinal plant, protein grain, and crop wild relative (CWR) genetic resources to avoid backlogs in plant genetic resource (PGR) and information management.
1.A: Develop and/or refine methodology and protocols to enhance and optimize site capacity for regeneration and availability of collections.
1.B: Develop and/or refine bioinformatic and program capacity for devising algorithms and machine learning to capture data from spectral imaging.
1.C: Develop and evaluate methods to utilize genetic marker technologies to better characterize collections and identify collection gaps.
1.D: Develop and/or refine efficient and effective methods for timely germination/viability testing to meet demand in current collection accessions.
1.E: Investigate, implement, or develop laboratory methods to detect or eradicate seedborne pathogens to increase accession availability.
1.F: Develop software tools for the GRIN-Global (GG) software suite to expand user flexibility and options for descriptive information collection and upload, data management, and seed distribution.
Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of maize, vegetable, oilseed, ornamental, medicinal plant, protein grain, and CWR genetic resources and associated descriptive information.
2.A: Expand, regenerate, and conserve collections of priority maize, vegetable, oilseed, protein grain, medicinal, and ornamental genetic resources.
2.B: Protect genetic integrity of maintained seed and plant materials.
2.C: Incrementally increase percentage of North Central Plant Introduction Station (NCRPIS) genebank accessions backup at alternate sites to more than 85% of 2021 holdings.
2.D: Monitor accessions for viability and phytosanitary health to ensure availability of healthy propagules for regeneration and distribution.
2.E: Evaluate crop collections for phenotypic, morphological, composition, and productivity related traits such as biotic resistance or abiotic stress tolerance and yield.
2.F: Distribute germplasm and associated information to support stakeholder research objectives.
Approach
1.A: Regeneration protocols will be reviewed for accessions within species and germplasm types each year prior to planning annual regeneration efforts and after harvest in reflection of seed returns to ensure maximization of return for the effort.
1.B: Individual seed data capture capabilities of equipment located at the NCRPIS will allow effective data capture within heterogeneous populations. Results will provide enhanced accession phenotypic evaluation information for inclusion in GG.
1.C: The Maize Genetics/Genomics Database (MaizeGDB) and Panzea Project genotyping tools will be utilized to calculate genetic relationships between maize lines and assess differences or duplication among seed lots of a given accession within and across a collection. Trait association studies conducted by collaborators and stakeholders will be noted and linked to individual collection accessions.
1.D: Specialized germination methods will be developed to determine the germination/viability status of species with dormancy or other restrictions that do not allow the application of standard methods.
1.E: Investigation of methods to render unviable (non-infective the seed borne Acidovorax citrulli bacteria (bacterial fruit blotch [BFB] pathogen) infesting Cucumis melo seed) without adversely affecting seed viability will be a priority. Results of research to develop real-time polymerase chain reaction (PCR) detection methods capable of discriminating between Pantoea stewartii subsp. stewartii (Pss), and other Pantoea species have been developed at the NCRPIS and will be implemented.
1.F: NCRPIS staff will continue to expand the capacity and capabilities of the GG PGR information management system to meet the needs of crop curators and genetic resource users.
2.A: Germplasm acquisition and conservation objectives based on input from stakeholders and curators' scholarly efforts will be used to determine sources of unique, potentially useful genetic variation for crops and CWR.
2.B: Best management practices will be maintained according to protocols developed by NCRPIS personnel and hosted on local servers; modify and document processes and changes.
2.C: With regeneration activities in Ames, Iowa, Parlier, California, commercial winter nurseries, and collaborator locations, backup of collection holdings will be increased to 85%, even with an expected annual collection growth of 0.9%.
2.D: Viability and germination testing of collection holdings will be conducted to ensure the security of the accessions using Association of Official Seed Analysts (AOSA) protocols. Phytosanitary precautions will be implemented at multiple points in the production cycle to protect plant health and guard against seedborne pathogens.
2.E: Information related to phenotypic trait performance, adaptation, source habitat, and application of crop specific marker technologies to better characterize key collections enable the research community to target germplasm to meet current and future production challenges or needs.
2.F: Germplasm distributions are made to researchers and educators in accordance with NPGS distribution policies.
Progress Report
Objective 1 related progress: The entomology team has assisted with providing both beneficial insects to control pest insect and pollinator insects to pollinate greenhouse and field increases of germplasm accessions. A total of 748 insect pollinators were supplied throughout the 2023 pollination season. The entomologist, in collaboration with the curators, are continually improving best management practices associated with pairing pollinators with different taxa under various weather conditions. Best management practices are also evolving for the maintenance of beneficial insects to control pests in the greenhouse. The maize curation team has been adopting practices to control spider mites in the greenhouse with predatory insects. Significant gains have been made with the introduction of pepper plants as hosts to provide habitat for the minute pirate bugs.
Maize seed health testing was the primary pathology testing activity in 2023. All germplasm distributions to the European Union (EU) require testing for Pantoea stewartii subsp. stewartii (Stewart's wilt) at levels sufficient to meet a detection standard of 0.5% level of infestation with a 99% level of confidence. Because few existing lots in storage meet this new 2022 standard, a substantial increase in maize seed health testing was needed to fulfill international orders in addition to de novo testing of new seed increases prior to storage.
During the past year the farm staff initiated and completed multiple projects which enhanced the efficiency and safety of site operations. These projects ranged from the installation of rolling greenhouse tables to repairing field tile washouts. A large project involving the replacement of the South Cold room cooling system finally started at the end of 2023 and is still in progress. Routine maintenance of equipment and emergency repair needs continuously change based on field and laboratory activities.
Objective 2 related progress: A total of 322 accessions were added to the NCRPIS collection, including targeted collections of wild Amelanchier (serviceberry), Baptisia (baptisia), Chenopodium (lamb's quarters), Fraxinus (ash), Delphinium (delphinium), Monarda (bee-balm) and others. Additional accessions collected through the Bureau of Land Management (BLM) program, Seeds of Success, were transferred to Ames. A further 68 accessions with expiring Plant Variety Protection certificates were transferred to Ames from NLGRP in Fort Collins, Colorado for regeneration.
Curatorial teams, along with their collaborators, harvested more than 900 regenerations in the field and greenhouse. With processing of previous harvests, a total of 1,058 accessions were made available for distribution. This contributed to a net increase of 188 accessions available for distribution, while the number of accessions in the collection increased by 450, to a total of 55,152 accessions.
Viability tests continue to be routinely performed on newly increased seed lots prior to storage and on available distribution seed lots on a maintenance testing schedule. This routine testing identifies accessions with declining viability and provides curators with information to prioritize regenerations. This year, 12% of the collection was tested (6,840 accessions), including 20% of the maize collection (4,020 accessions).
Backup samples of 968 accessions were sent to NLGRP. This increased the percentage of accessions with backup samples to 84%. There has been a significant focus on increasing the backups of the maize collection, as funding has not been available for regenerations to be conducted at contract nurseries in Mexico for tropically adapted germplasm.
Crop accession evaluation information was provided for 11,013 accessions, most of which were associated with amaranth, setaria, and panicum accessions. Images of 2,814 of accessions were uploaded to GRIN-Global, so more than half of the accessions in the NCRPIS collection now have associated images available through the public database.
Accomplishments
1. Essential plant genetic resources (germplasm) were provided to researchers worldwide to support continued improvement of cultivated crops and national and global ecosystem restoration goals. ARS researchers in Ames, Iowa, distributed plant germplasm to stakeholders to accomplish research and educational objectives around these themes. In 2023, more than 800 public and private sector researchers around the world received 44,295 packets of seed representing 20,989 unique accessions. Domestic recipients (75% of requestors) received 64% of the packets distributed. Furthermore, these distributions supported the research objectives of 45 scientists from USDA and other federal agencies, and hundreds of recipients of federal research grants. These resources contribute to sustaining agricultural productivity while addressing national and global agricultural challenges.
2. Brassica rapa collection characterized for flowering type. Characterizing flowering type is important both for the efficient conservation of the collection, and to facilitate utilization of the germplasm by stakeholders engaged in cultivar development. Winter-type accessions require vernalization, or a cold treatment, to induce flowering and seed production. ARS scientists in Ames, Iowa, along with colleagues from Iowa State University, completed the characterization of the 674 varieties in the Brassica rapa oilseed germplasm collection. Brassica rapa collection contains accessions with both winter and spring flower types. For assessment, 12 plants for each accession were seeded in the greenhouse in late fall. An accession was determined to be winter flowering type if no plants had flowered by the end of February. After five years of evaluating around 120 accessions each year, approximately 75% of the collection was determined to be spring-type. With this information, the crop curator will be able to more effectively regenerate seed for distribution, and plant breeders will be able to make better selections for advancing their cultivar development objectives.
Review Publications
Yu, P., Li, C., Li, M., He, X., Wang, D., Li, H., Marcon, C., Tegethof, H., Perez-Limón, S., Chen, X., Delgado-Baquerizo, M., Koller, R., Metzner, R., Van Dusschoten, D., Borisjuk, L., Plutenko, I., Resende, M.R., Bernau, V.M., Salvi, S., Akale, A., Abdalla, M., Ahmed, M., Bauer, F.M., Schnepf, A., Lobet, G., Heymans, A., Suresh, K., Schreiber, L., Mclaughlin, C.M., Li, C., Sawers, R.J., Wang, T., Hochholdinger, F. 2024. Seedling root system adaptation to water availability during maize domestication and global expansion. Nature Genetics. 56:1245-1256. https://doi.org/10.1038/s41588-024-01761-3.
Martinez-Ainsworth, N.E., Scheppler, H., Moreno-Letelier, A., Bernau, V.M., Kantar, M.B., Jardón-Barbolla, L., Mercer, K.L. 2023. Fluctuation of ecological niches and geographic range shifts along chile pepper's domestication gradient. Ecology and Evolution. 13(11):e10731. https://doi.org/10.1002/ece3.10731.
