Research Project: Plant Genetic Resource Management and Information System Development

Location: Plant Introduction Research

2019 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: 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 field cages and greenhouse rooms to control pest insects; these include rove beetles, ladybug beetles, beneficial nematodes, and Encarsia formosa. Vernalization rooms with controlled lighting and temperature conditions were constructed and used to vernalize Brassica seedlings for six weeks at less than 40 F. Following transplant, flowering was successful. A new technician and plant pathologist filled positions vacated in early 2016, and a maize geneticist filled another vacancy, providing needed support. Methods to increase germplasm that does not respond to normal, temperate conditions were tested; a Glyceria striata increase succeeded following exposure of 20-month-old plants to 22-hour day conditions (through harvest) in the greenhouse. Agar use helped establish extremely small, difficult to handle Salix seedlings. Regeneration plans were adjusted to address accessions with declining viability. Viability testing focused on Brassica, flax, foxtail millet, maize and cultivated sunflower, previously delayed for lack of personnel. Viability of portions of the Brassica collection and 38% of the flax collection have declined, and regeneration needed. Maize viability testing used a new strategy, two replications of 25 seeds instead of 100. Lots with questionable viability were retested using 200 seeds, enabling testing of more accessions while conserving seed and resources. Five new viability testing protocols were created for germinating umbel crops. 2019 spring planting in Ames was challenging due to excessive rain and exceptionally cool temperatures. The earliest planted block of maize suffered water damage and losses, second planting was delayed, and the third planting reduced due to prolonged wet conditions. Vegetable transplanting, caging and screening activities were delayed. Distribution: One thousand recipients received a total of 61,124 packets of seeds of 23,230 accessions, or 42% of the collection. Of these distributions, 48% of the packets went to 292 foreign recipients and 52% went to 708 domestic recipients (29% and 71% of all requestors, respectively). To date, FY2019 domestic distributions are approximately equal and foreign distributions are 40% of this point last year, when demand was exceptionally high. Seasonal variability is not unusual; activity may reflect demand for urgent food security related research and possibly efforts to secure plant genetic resources prior to U.S. implementation of the Standard Material Transfer Agreement associated with the International Treaty for Plant Genetic Resources for Food and Agriculture. About 780 accessions were transferred to ARS researchers in Ft. Collins, Colorado for backup and 300 to Svalbard; currently 81% of 2016 holdings are backed up. Significant sunflower distributions included pre-breeding lines to Argentina, California, Canada, India and Uganda for evaluation of biotic and abiotic stress tolerance, and association mapping lines to Genome Canada for genotyping. Carrot and cucurbit distributions were made to support research initiatives focused on disease, insect, nematode and/or abiotic stress evaluations, genetic and molecular investigations, and genomic-assisted breeding. Aronia accessions were rooted and provided to the University of Illinois for breeding and commercial potential evaluation. Recently published Crop Wild Relatives volumes provide gap-analysis information, informing collection development needs. Nearly 300 new accessions were acquired, including five Cichorium cultivars donated by Nunhems Netherlands, BV; Ft. Collins, Colorado ARS researchers provided cucumber and melon accessions received from Cucurbit Coordinated Agricultural Project participants, a basil accession with expired plant variety protection, and a new wild Daucus accession. ARS researchers in Fargo, North Dakota provided 56 cultivated sunflower pre-breeding lines with introgressions from 21 different wild annual or perennial sunflower species and wild Helianthus to fill geographic gaps in the species representation in North Dakota and Minnesota. Wild accessions of six taxa were from the Tampa, Florida area, including Chenopodium with sub-tropical winter adaptation. New ornamentals included 23 woody landscape, 38 medicinal and eight herbaceous accessions, Yellowwood from Kansas and Oklahoma, and several 'firsts' for the collection, including the first diploid Ulmus americana (Kansas) and a Salix serissima. Erygium leavenworthii was collected near Winfield, Kansas, and Dalea purpurea near Guthrie Center, Iowa, both with ornamental potential. The Arnold Arboretum contributed Betula fargessii. Dyrmocallis arguta was donated from the Chicago Botanic Garden Dixon National Tallgrass Prairie Seed Bank and by the University of Northern Iowa Tallgrass Prairie Center. Obj 2 Related: A contract seed increase nursery was grown by the International Center for Maize and Wheat Improvement of 25 Peruvian highland maize landraces at their high-altitude location near Tolucca, Mexico in 2018. Seed quality of these specialized, rare materials was excellent and a second contract issued. Seed from Thailand was grown in the Ames, Iowa winter greenhouse under quarantine permit with limited success due to harsh weather. ARS personnel in Parlier, California regenerated wild Helianthus taxa that need a longer growing season than Ames can provide, and mountain and desert species that do not thrive in midwestern humidity and heavy soils. More than 13,150 observations were entered in the GRIN-Global database (Germplasm Resource Information Network) (GG) for 1,853 accessions, including pedigree records extracted from Plant Variety Protection certificates and adaptation and seed maturity evaluations of Panicum and Setaria in Ames, Iowa. 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 1580 older, pathology-related inspection notes loaded to facilitate selections to fill seed requests. Protocols for image naming/renaming, data loading and for use new equipment such as the optical seed sorters are in development. Protocols for regeneration, pathogen assessment, plant/seed protection from diseases/pests for all vegetable crops, specific cucurbit pathogens, and pre-plant Brassica seed treatments are being re-evaluated. Grow out assays were used to determine contamination of Cucumis melo accessions with the Bacterial Fruit Blotch pathogen, based on seedling symptoms and enzyme linked immunosorbent assay (ELISA) testing. Cotyledons, hypocotyls and roots of positive seedlings tested positive, indicating systemic pathogen presence. All field and greenhouse plantings were inspected; the only significant disease observed was black rot of Brassica. Vegetable plantings were inspected weekly and infected plants removed. More than 2,130 seed health testing records and phytosanitary documents were uploaded to GG. Seed health testing and treatment programs ensure seed health and support utilization. Obj 3 Related: Crop Vulnerability Statement updates were completed or in process for the Root and Bulb, Cucurbit, Leafy Vegetable, and Sunflower Crop Germplasm Committees, in collaboration with members. Best management practices are documented and standard operating protocols adjusted 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. B. rapa accessions are being evaluated to determine flowering type, and a pre-field planting, flowering stimulation tested. Obj 4 Related: Since international GRIN-Global developers met in 2018, a thorough analysis of international and U.S. development needs for GG enhancements, features and functionalities was developed. Protocols are in development to detail how applications can appropriately be shared and vetted between 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. In order to serves genebank users' workflow and information management needs, 'Pocket Pollinator' and 'Pocket Actions' applications used with GG were replaced. An interim Pocket Pollinator application was migrated from personal computer devices to Windows tablets to facilitate field data entry of specific pollinator insects and timing requests for pollination. This version fulfills user needs until an Android version is developed. Prototype applications were developed for Android applications that safely communicate with the GG middle tier. The Order Wizard, used to manage/process germplasm distributions, was optimized to ensure functions in conjunction with the Public Website. Six Curator Tool (CT) builds (currently V 1.8.30) were released, all provided Order Wizard enhancements/optimizations. HTTP compression enabled faster data transmission between client and middle tier. The new Attachment Wizard enables batch loading of thousands of images in a single step. GG 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. Ames, Iowa ARS personnel participated in virtual weekly development team meetings with ARS personnel in Beltsville, Maryland, twice monthly with the GG Advisory Committee (Ad Com) on developer and database administrator priorities, and monthly with the International Developer's Ad Com.

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 germplasm is provided via the GRIN-Global website, and via direct contact with curatorial personnel. Samples are maintained and distributed by North Central Regional Plant Introduction Station personnel in Ames, Iowa. One thousand public and private sector researchers received a total of 61,124 packets of seeds of nearly 23,230 accessions, or 42% of the entire collection. Foreign recipients (29% of all requestors) received 48% of the packets, and 52% of the packets were distributed to domestic recipients (71% of all requestors). Demand continues to escalate for our collections of maize, oilseeds (Brassica, crucifers, and sunflower), woody and herbaceous ornamentals, miscellaneous crops (which include amaranth, quinoa, 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. Optical sorting technologies were implemented for seed sorting. Excellent seed quality is of high importance to users of USDA plant genetic resources. Processing small seed lots is laborious, resource intensive, expensive, and does not produce knowledge, only quality as measured by key criteria. Complicating this, many curated crop collections are heterogeneous in nature and training is required to discriminate between acceptable, normal variation and abnormalities for discard. Use of two companies' high speed optical seed sorting machines was explored. ARS researchers in Ames, Iowa, collaborated to apply their technologies to our objectives, rapid and accurate sorting of a various crop seeds. The first outcome proved that one company's machine was highly successful for sorting maize, soybean, sorghum and millet seeds for properties including size, shape, color, weight, and abnormals. A recipe was created to remove pre-germed maize kernels, improving the viability and quality of seed lots, and selected maize kernels for optimum size and shape for use in modern research planters. The second outcome showed using the other company's machine enabled capture of both vision-based images and near infrared spectra of seeds; their algorithm to discriminate between haploid and diploid maize kernels was more than 94% accurate, compared to 80% by manual sorting. Rapid development of algorithms for a variety of properties is a goal. The potential benefits of applying non-destructive machine learning to plant genetic resource characterization and seed sorting are far-reaching. Immediate benefits include improved quality of seed lots provided to scientific stakeholders, enhancing their ability to acquire high quality experimental data, and improved genebank efficiency. Combining vision, spectra, and morphological characteristics to develop new insights and knowledge of germplasm traits and properties will contribute to addressing challenges to food security.

Review Publications
Pal, N., Gardner, C.A., Block, C.C. 2019. A real-time PCR differentiating Pantoea stewartii subsp. stewartii from P. stewartii subsp. indologenes in corn seed. Plant Disease. https://doi.org/10.1094/PDIS-06-18-0936-RE.
Block, C.C., Shepherd, L., Mbofung, G., Sernett, J., Robertson, A. 2019. Re-evaluation of seed transmission of Clavibacter michiganensis subsp. nebraskensis in Zea mays. Plant Disease. 103:110-116. https://doi.org/10.1094/PDIS-02-18-0292-RE.