Progress 10/01/23 to 09/30/24
Outputs
PROGRESS REPORT Objectives (from AD-416): Objective 1: Conduct research to develop regulatory compliant genetic resource maintenance, evaluation, testing, and characterization methods and, in alignment with the overall NPGS Plan, apply them to priority hemp genetic resources. Record and disseminate hemp evaluation and characterization data via GRIN-Global and other data sources. Sub-objective 1.A: Develop and apply genomic, phenotyping, and tissue culturing tools that facilitate research and management of regulatory compliant hemp genetic resources. Sub-objective 1.B: Establish efficient data collection and documentation protocols to ensure that data associated with germplasm resources are recorded and disseminated to all stakeholders via GRIN-Global, appropriate public databases, and hyperlinking or searches. Objective 2: Acquire and maintain the safety, genetic integrity, health, and viability of priority hemp genetic resources, and distribute them and associated descriptive information worldwide. Sub-objective 2.A. Identify and fill gaps in the hemp genetic resource collection through acquisition, germplasm exchange, and cooperator donations of regulatory compliant materials. Sub-objective 2.B. Ensure long-term availability of regulatory-compliant hemp genetic resources and associated information and distribute them to NPGS stakeholders. Incorporating associated information into GRIN-Global and appropriate online databases. Sub-objective 2.C. Ensure the long-term safety of hemp genetic resource collections by systematically completing regeneration, pathogen and viability testing, completing backups at National Laboratory for Genetic Resource Preservation and other appropriate seedbanks. Objective 3: With other NPGS genebanks and Crop Germplasm Committees, formulate, update, document, and implement best management practices and Crop Vulnerability Statements for priority hemp genetic resource and information management. Sub-objective 3.A. Strengthen and implement best management practices for research and management of hemp germplasm resources through cooperation and consultation with appropriate Crop Germplasm Committees and other NPGS genebanks. Sub-objective 3.B. Work closely with other NPGS genebanks, Crop Germplasm Committees, and other stakeholders to develop and update Crop Vulnerability Statements for priority hemp genetic resources and information management. Objective 4: Devise and apply research tools, knowledge of hemp genetics and of the genetic control of priority hemp traits to create genetically enhanced hemp germplasm that broadens the diversity available for hemp production. Sub-objective 4.A: Develop genomic information, molecular markers, biotechnology, and high throughput phenotyping tools and apply them to characterize and elucidate genetic control of priority traits. Sub-objective 4.B. Investigate the genetic control of priority traits and apply pre-breeding methods to accelerate identification of valuable hemp germplasm accessions and the development of breeding lines with superior traits across market classes. Approach (from AD-416): Hemp genetic resources will be obtained and stored under controlled conditions in Geneva, NY for long-term availability and distribution to stakeholders. Routine regenerations, pathogen and viability testing, and backups at National Laboratory for Genetic Resource Preservation will be completed to ensure long-term viability of hemp germplasm. Hemp accessions will be evaluated for plant architecture, secondary metabolites, fiber, and seed quality in randomized and replicated field trials. Accessions with total �-9-tetrahydrocannabinol levels less than 0. 3% will be listed as available for distribution. Regulatory compliant germplasm will be grown in field trials in at least six states throughout the U.S. to quantify genetic and environmental interactions that influence critically important traits. Characterization information will be uploaded to GRIN-Global. Best management practices and Crop Vulnerability Statements for priority hemp genetic resource and information management will be formulated with other NPGS genebanks and Crop Germplasm Committees. Plants with complementary traits will be hybridized and the resulting populations will be advanced to the F2 generation. Accessions and populations will be genotyped with a high- density genotyping platform. Genotypes will be utilized to understand population structure within the hemp collection. Gaps in the collection and sources to fill these gaps will be identified. Genotypes and trait phenotypes will be used for genome-wide association analysis, and generating linkage maps for F2 populations. Molecular markers that are tightly linked with genetic loci that control important traits will be validated with PACE assays and the resulting primer sequences will be published. Important F2 populations will be advanced through single seed descent to determine if inbred lines can be developed. In Fiscal Year 2024, efforts by USDA-ARS researchers in Geneva, New York, substantially increased the genetic resources and associated information available to the hemp research community. The USDA-ARS Plant Genetic Resources Unit Hemp collection grew to 609 accessions from 34 countries and distributed 2,906 seed samples to the hemp scientists. New accessions were tested for tetrahydrocannabinol and tetrahydrocannabinolic acid with high performance liquid chromatography to verify regulatory compliance. Over 70 accessions have been regenerated in Geneva, New York, and 28 accessions have been regenerated by collaborators. Ten hemp accessions are backed up at National Laboratory for Genetic Resource Prevention (NLGRP) for long-term storage. A coordinated multi-state NIFA Supplemental and Alternatives Crops supported effort to characterize newly acquired hemp germplasm across diverse field environments was continued in Davis, California; Geneva, New York; Klamath Falls, Oregon; Baton Rouge, Louisiana, Hazel Green, Alabama, and Othello, Washington. At the Geneva trial location, 3,975 plants were evaluated for a suite of phenotypic traits including flowering, sex, architecture, secondary metabolite, and grain and fiber quality. A new evaluation protocol using high-density small plots to better estimate yield and agronomic quality was implemented at these six trial locations. In addition, genome sequencing is being conducted on approximately 500 accessions via collaborators at the HudsonAlpha Institute in Huntsville Alabama; approximately 1,725 low-coverage phased genomes will be generated from this work and the sequence will be made publicly available on National Center for Biotechnology Information (NCBI) . Plant phenotypic data was recorded using a suite of digital agricultural tools including Field Book and other tools developed in collaboration with USDA-ARS Breeding Insight, including high-throughput leaf morphometric analysis and preliminary testing of DeltaBreed. Flower, stem, and grain samples were collected for the evaluation of secondary metabolite profiles, seed, and fiber quality. Hemp germplasm field trial information including 100,000 datapoints of hemp accession information was summarized and added to the Germplasm Resource Information Network GRIN-Global. Pollination tents using ultra fine pollen-exclusion mesh were developed, constructed, and evaluated in-house by ARS researchers in Geneva, New York. Prebreeding and inbred line development progressed with over 20 populations undergoing selfing and selection for low THC content. Artificial Intelligence (AI)/Machine Learning (ML) Machine learning/computer was applied to evaluate the leaf morphology of approximately 500 USDA NPGS hemp accessions using tools developed in collaboration with USDA-ARS Breeding Insight. In addition, ML tools to evaluate drone data capture during hemp trails are under development. ACCOMPLISHMENTS 01 Substantially increased and characterized hemp genetic resources. For hemp to achieve a central role in the future of domestic and international agricultural production (e.g., as a grain, fiber, and secondary metabolite crop), plant breeders and biologists require a genetically and geographically diverse collection of hemp genetic resources. Until recently, such a collection of materials has not been available. USDA-ARS researchers in Geneva, New York, have characterized approximately 500 accessions for critical agronomic traits for breeding and downstream genetic mapping. This work has substantially intensified and accelerated hemp breeding and research efforts by providing access to well characterized resources and allowing public and private sector breeders to develop high-value and locally adapted genetic resources.
Impacts
(N/A)
Publications
- Chiwina, K., Bhattarai, G., Xiong, H., Joshi, N., Dickson, R.W., Phiri, T. M., Alatawi, I., Chen, Y., Stansell, Z.J., Ling, K., Shi, A. 2024. Evaluation of drought tolerance in USDA tomato germplasm at seedling stage. Agronomy. 14(2):380. https://doi.org/10.3390/agronomy14020380.
- Chowdhury, R.N., Gordon, T.C., Babar, A., Harrison, S.A., Kianian, S., Esvelt Klos, K.L. 2024. Mapping crown rust resistance in the oat diploid accession PI 258731 (Avena strigosa). PLOS ONE. 19(2). https://doi.org/10. 1371/journal.pone.0295006.
- Ehn, M., Michel, S., Morales, L., Gordon, T.C., Dallinger, H.G., Burstmayr, H. 2022. Genome-wide association mapping identifies common bunt (Tilletia tritici/laevis) resistance loci in bread wheat (Triticum aestivum) accessions of the USDA National Small Grains Collection. Theoretical and Applied Genetics. Available: https://doi.org/10.1007/s00122-022-04171-3.
- Ford, T., Gordon, T.C., Ellison, S., Ainu, A., Stansell, Z.J. 2024. Utilizing digitized occurrence records of midwestern feral Cannabis sativa to develop ecological niche models. Ecology and Evolution. https://doi.org/ 10.1002/ece3.11325.
- Grunwald, D., Wijesinghege, C.W., Gordon, T.C., Stansell, Z.J., Ellison, S. 2024. First report of Tobacco Streak Virus in Cannabis sativa in New York. Plant Disease. https://doi.org/10.1094/PDIS-09-23-1810-PDN.
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Progress 10/01/22 to 09/30/23
Outputs
PROGRESS REPORT Objectives (from AD-416): Objective 1: Conduct research to develop regulatory compliant genetic resource maintenance, evaluation, testing, and characterization methods and, in alignment with the overall NPGS Plan, apply them to priority hemp genetic resources. Record and disseminate hemp evaluation and characterization data via GRIN-Global and other data sources. Sub-objective 1.A: Develop and apply genomic, phenotyping, and tissue culturing tools that facilitate research and management of regulatory compliant hemp genetic resources. Sub-objective 1.B: Establish efficient data collection and documentation protocols to ensure that data associated with germplasm resources are recorded and disseminated to all stakeholders via GRIN-Global, appropriate public databases, and hyperlinking or searches. Objective 2: Acquire and maintain the safety, genetic integrity, health, and viability of priority hemp genetic resources, and distribute them and associated descriptive information worldwide. Sub-objective 2.A. Identify and fill gaps in the hemp genetic resource collection through acquisition, germplasm exchange, and cooperator donations of regulatory compliant materials. Sub-objective 2.B. Ensure long-term availability of regulatory-compliant hemp genetic resources and associated information and distribute them to NPGS stakeholders. Incorporating associated information into GRIN-Global and appropriate online databases. Sub-objective 2.C. Ensure the long-term safety of hemp genetic resource collections by systematically completing regeneration, pathogen and viability testing, completing backups at National Laboratory for Genetic Resource Preservation and other appropriate seedbanks. Objective 3: With other NPGS genebanks and Crop Germplasm Committees, formulate, update, document, and implement best management practices and Crop Vulnerability Statements for priority hemp genetic resource and information management. Sub-objective 3.A. Strengthen and implement best management practices for research and management of hemp germplasm resources through cooperation and consultation with appropriate Crop Germplasm Committees and other NPGS genebanks. Sub-objective 3.B. Work closely with other NPGS genebanks, Crop Germplasm Committees, and other stakeholders to develop and update Crop Vulnerability Statements for priority hemp genetic resources and information management. Objective 4: Devise and apply research tools, knowledge of hemp genetics and of the genetic control of priority hemp traits to create genetically enhanced hemp germplasm that broadens the diversity available for hemp production. Sub-objective 4.A: Develop genomic information, molecular markers, biotechnology, and high throughput phenotyping tools and apply them to characterize and elucidate genetic control of priority traits. Sub-objective 4.B. Investigate the genetic control of priority traits and apply pre-breeding methods to accelerate identification of valuable hemp germplasm accessions and the development of breeding lines with superior traits across market classes. Approach (from AD-416): Hemp genetic resources will be obtained and stored under controlled conditions in Geneva, NY for long-term availability and distribution to stakeholders. Routine regenerations, pathogen and viability testing, and backups at National Laboratory for Genetic Resource Preservation will be completed to ensure long-term viability of hemp germplasm. Hemp accessions will be evaluated for plant architecture, secondary metabolites, fiber, and seed quality in randomized and replicated field trials. Accessions with total �-9-tetrahydrocannabinol levels less than 0. 3% will be listed as available for distribution. Regulatory compliant germplasm will be grown in field trials in at least six states throughout the U.S. to quantify genetic and environmental interactions that influence critically important traits. Characterization information will be uploaded to GRIN-Global. Best management practices and Crop Vulnerability Statements for priority hemp genetic resource and information management will be formulated with other NPGS genebanks and Crop Germplasm Committees. Plants with complementary traits will be hybridized and the resulting populations will be advanced to the F2 generation. Accessions and populations will be genotyped with a high- density genotyping platform. Genotypes will be utilized to understand population structure within the hemp collection. Gaps in the collection and sources to fill these gaps will be identified. Genotypes and trait phenotypes will be used for genome-wide association analysis, and generating linkage maps for F2 populations. Molecular markers that are tightly linked with genetic loci that control important traits will be validated with PACE assays and the resulting primer sequences will be published. Important F2 populations will be advanced through single seed descent to determine if inbred lines can be developed. Fiscal Year 2023 efforts substantially increased the genetic resources available to the hemp research community. Plant Genetics Resources (PGRU) has acquired over 500 unique hemp accessions spanning feral, landrace, fiber, grain, and chemical classes. The collection is expected to grow significantly with contributions from several private breeding programs and contributions from two Supplemental and Alternative Crop (SAC) Grants. Seven hemp accessions were backed up at National Laboratory for Genetic Resource Preservation (NLGRP) for long-term storage. In collaboration with University of California Davis, Oregon State University, Washington State University, Louisiana State University, Alabama A&M, USDA Cotton Quality Laboratory in New Orleans, Louisianna, the USDA Agricultural Utilization Laboratory in Peoria, Illinois, a diverse collection of 48 accessions were planted in a randomized, replicated field trial to obtain secondary metabolite, plant architecture, fiber, and seed quality phenotypes. Plant architecture, flowering date, and sex traits were recorded in the field using FieldBook. Flower, stem, and grain samples were collected for the evaluation of secondary metabolite profiles, seed, and fiber quality. Hemp accession field trial information including 75,000 datapoints of hemp accession information was added to Germplasm Resource Information Network (GRIN)-Global. Small plot trials of 23 hemp accessions were direct seeded with a grain drill at 1-million and 500,000 live seeds per acre planting densities in early June to obtain secondary metabolite, plant architecture, fiber, and seed quality phenotypes in these densely planted stands. PGRU is applying new curatorial techniques and approaches to increase genebank operational efficiency and is approximately 30 % ahead of schedule to regenerate and make available diverse genetic resources. Small plot pollination exclusion tents are being trialed to determine if they will work to increase accessions in the field. Blackout tents were assembled to induce flowering in photoperiod sensitive hemp plants inside a greenhouse. Literature indicated that sprays of silver thiosulfate would induce male flowering in female plants. Using this technique, six female plants were sprayed with a silver thiosulfate solution to start inbred line development. Two hemp crosses were made between accessions with complementary priority traits. ACCOMPLISHMENTS 01 Substantially increase and characterize hemp genetic resources. For hemp to achieve a central role in the future of domestic and international agricultural production (e.g., as a grain, fiber, and secondary metabolite crop), plant breeders and biologists require a collection of highly genetically and geographically diverse collection of hemp genetic resources. Until recently, such a collection of materials has not been available. USDA-ARS researchers in Geneva, New York, have substantially increased the genetic resources available to the hemp research community. The USDA-ARS hemp germplasm collection is now the largest hemp germplasm collection in the world, and the only hemp collection with substantial associated phenotypic data (cannabinoid profile, plant architectural traits, and other critical agronomic characters). Characterization of newly acquired diverse hemp germplasm occurred in five unique environments resulting in over eleven- thousand data points being associated with the Germplasm Resource Information Network (GRIN)-Global. Data was collected in accordance with the Hemp Phenotyping Handbook published by USDA and is being used by over 10 university research programs. Additional phenotyping efforts were accomplished at the USDA Cotton Quality Laboratory in New Orleans, Louisianna, the USDA Agricultural Utilization Laboratory in Peoria, llinois, and three state universities for fiber, secondary metabolite, and seed fatty acid/protein. As an example, USDA-ARS researchers have significantly supported the development of this first Cannabis Pangenome, which will allow much deeper characterization of priority traits in hemp. This work will substantially intensify and accelerate hemp breeding and research efforts by providing access to highly characterized resources and allow public and private sector breeders to develop high-value and locally adapted genetic resources.
Impacts
(N/A)
Publications
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