NE9: Conservation and Utilization of Plant Genetic Resources

(Multistate Research Project)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[01/09/2025] [01/29/2026]

Date of Annual Report: 01/09/2025

Report Information

Annual Meeting Dates: 12/18/2024 - 12/18/2024
Period the Report Covers: 10/01/2023 - 09/30/2024

Participants

Clark, Matt-University of Minnesota; Frances, Anne-USDA ARS; Galarneau, Erin-USDA ARS; Gasic, Ksenija-Clemson; Gordon, Tyler-USDA ARS; Gottschalk, Chris-USDA ARS; Griffiths, Phillip-Cornell University; Gutierrez, Ben-USDA ARS; Hernandez, Chris-University of New Hampshire; Khan, Awais-Cornell University; Kothari, Neha-USDA ARS; Mazourek, Michael-Cornell University; Mykala, Robertson-USDA ARS; Oravec, Maddy-Cornell University; Povilus, Becky-USDA ARS; Rhodes, Rick-University of Rhode Island; Shade, Jessica-NIFA; Shanower, Tom-USDA ARS; Smart, Chris-Cornell University; Stansell, Zach-USDA ARS; Tobias, Christian-NIFA; Vogel, Greg-Cornell University; Volk, Gayle-USDA ARS; Zhong, Gan-Yuan-USDA ARS

Brief Summary of Minutes

Chris Smart (Director of Cornell AgriTech and NE9 Advisor), gave welcome to the group and provide brief overview of budget – spending is on track; 7% budget increase helps, but only keeps up with inflation for employee salaries. Gayle Volk and Neha Kothari (new National Program Leaders over National Plant Germplasm System, (NPGS)) gave updates from the NPGS. NPGS budget overall has been steady but not keeping up with inflation; some targeted increases within NPGS to specific crops, including hemp. Emphasized need to better highlight our work to stakeholders. One outlet is Impact Statements which highlight the commercial/research benefits of accessions from the NPGS genebanks. NE9 stakeholders encouraged to contribute to these. Proposal to have 2025 NE9 meeting combine with other RTACs in Texas. Group was supportive. Christian Tobias provided an overview of NIFA grant opportunities. Anna Frances requested NE9 stakeholders, in addition to the United States Department of Agriculture (USDA) curators, to review plant exploration and exchange proposals. Stakeholders provided updates on their individual research, with an emphasis on their need for diverse genetic resources. The need for pre-breeding material that incorporates desirable wild traits into a more accessible forms to accelerate breeding. Curators provided update on the status of the vegetable, hemp, and fruit collections associated with this project. Their highlights are provided in more detail below.

Accomplishments

The USDA Agricultural Research Service (ARS) Plant Genetic Resources Unit (PGRU) in Geneva, NY maintains diversity collections of select vegetables (12,762 accessions), hemp (640 accessions), and fruit (6,521 accessions). Targeted acquisitions over the past year have filled gaps (phenotypic, genotypic, and geographic) within the collections, expanding the resources available to stakeholders. Funding from NE9 provides critical resources for management and distribution of these collections. NE9 supports major efforts in supplying germplasm to screen and map high-priority horticultural and agronomic traits, such as important disease and pest resistances and traits contributing to human well-being. Many of these efforts are done in collaboration with scientists from SAESs. In 2024 the NE9 project received a vital 7% budgetary increase which significantly supports ongoing germplasm conservation efforts, maintenance of equipment, and staffing limitations. However, additional expenses including renewing land/facility leases with Cornell University and matching farm support salaries to keep pace with inflation will decrease our research capacity and purchasing power. Additional increases in the overall budget must be considered to maintain project integrity. Maintenance of these collections requires substantial effort and regeneration of each accession is a rate limiting step, impacting the ability to distribute material to stakeholders. In 2024, 261 vegetable, 121 hemp, and 112 grape accessions were at various stages of the regeneration pipeline. The apple collection has gone through a period of orchard rejuvenation with the repropagation of close to 1,000 accessions in the past 3 years. Disease status is a primary concern for the distribution of clonal collections, particularly virus status. This reporting period, 300 apple accessions were tested for multiple viruses, which identified several that should be quarantined and treated before reintroduction. Plans for additional testing and virus remediation are underway for apple. Methods for high throughput testing of grapevine viruses is in discussion. In 2024, PGRU distributed 8,337 distinct units (seed lots, propagules, fruit, etc.) to requestors. The collections have been extensively used worldwide to develop new cultivars and for other research purposes, including disease resistance, fruit quality traits, genetic diversity, and population structure. PGRU scientists characterize germplasm for priority traits to make the material more readily accessible. Much of this characterization and evaluation is performed in collaboration with scientists from the Northeastern US, other regions in the USA, and abroad. Activities: <ul> <li>Near completion of two large high-tunnel/greenhouses which will serve all NE9 crops.</li> <li>Led pollinator efficiency study comparing the quality of pollinator services provided by flies, honeybees, and bumble bees on winter squash to improve pollinator management decisions.</li> <li>Received ARSx funding for a project to crowdsource vegetable accession phenotyping. This is a multi-site, multi-collection project.</li> <li>Continued sample collection for whole-genome-scale sequencing for the entire USDA Physalis (tomatillo) collection.</li> <li>Investment in equipment resulted in doubling of squash seed collection/processing capacity; producing higher quality seed.</li> <li>Adjustments to tomato seed collection/processing protocols resulted in faster collection of tomato seed and higher seed quality.</li> <li>Two parallel seed inventory management projects were initiated to improve the accuracy of information between physical seed lots and information in the GRIN-Global database.</li> <li>Conducted genotyping/phenotyping project of most of the hemp collection. Samples were collected for sequencing, cannabinoid analysis, protein analysis, and fiber analysis.</li> <li>Initiated work for development of a stakeholder-driven low-cost mid-coverage hemp genotyping platform to help conserve and characterize diverse germplasm, develop mapping populations for priority traits, and identify critical candidates for pre-breeding populations.</li> <li>Ongoing research with high-density hemp plantings and selection for regulatory compliant germplasm.</li> <li>Received ARSx funding to develop pipeline for rapid introgression of wild apple germplasm into publicly available apple pre-breeding lines.</li> <li>Propagation of 140 plum cultivars for maintenance from Davis, CA to Geneva for cold hardy evaluation and cryopreservation.</li> <li>Exploration for Vitis aestivalis and labrusca resulted in 70 new accessions from new geographic regions to be incorporated for new flavors and disease resistances. 15 accessions returned to the collection from cooperators.</li> <li>Over 900 accessions of grape screened for powdery and downy mildew resistances with 40 resistance markers being characterized through NIFA-SCRI funding.</li> <li>1200 accessions of grapevine sequenced using the rhAmpSeq platform with 2000 markers.</li> <li>Fruit quality metabolic evaluations continued for apple, grape, and cherry, covering over 600 accessions. Focus has been on phenolics, aromatics, and sugar and acid ratios.</li> <li>Collaborated with archeologists to evaluate and identify preserve fruit specimens found at Mount Vernon in Virginia.</li> </ul> Milestones for 2025: <ul> <li>Regenerate seed for 150 vegetable accessions.</li> <li>Backup up 100 vegetable and hemp accessions at NLGRP.</li> <li>Rescue 50 jeopardized vegetable accession in greenhouse regeneration.</li> <li>Continue to refine regeneration protocols of seed crops.</li> <li>Improve soil and assess onion bulb production.</li> <li>Develop parents for hemp MAGIC populations with collaborators.</li> <li>Regenerate 25 hemp accessions in controlled-environment conditions.</li> <li>Upload 10,000 phenotypic data points to describe hemp germplasm collection.</li> <li>Acquired over 20 novel hemp genetic resources.</li> <li>Backup of clonal accessions and test viability of cryo-treated buds.</li> <li>Evaluate apple nursery for rootstock compatibility.</li> <li>Retrain vines to enable mechanical management.</li> <li>Re-evaluate set 1 of apple cultivars for fruit quality. Complete evaluation of 470 accessions for grape juice metabolites.</li> <li>Evaluated abiotic and biotic phenotypes in grape.</li> </ul>

Publications

Arro J, Yang Y, Song G, Cousins P, Liu Z, Zhong G-Y, et al. (2024) Transcriptome analysis unveils a potential novel role of VvAP1 in regulating the developmental fate of primordia in grapevine. F 4. <a href="https://doi.org/10.48130/frures-0024-0004">https://doi.org/10.48130/frures-0024-0004</a> Chiwina K, Bhattarai G, Xiong H, Joshi N, Dickson R, Phiri R, Alatawi I, Chen Y, Stansell Z, Ling K-S (2024). Evaluation of Drought Tolerance in USDA Tomato Germplasm at Seedling Stage. Agronomy, 14(2), 380.https://doi.org/10.3390/agronomy14020380 Ford T, Aina A, Ellison S, Gordon T, Stansell Z (2024) Utilizing digitized occurrence records of Midwestern feral Cannabis sativa to develop ecological niche models. Ecology and Evolution 14:e11325. <a href="https://doi.org/10.1002/ece3.11325">https://doi.org/10.1002/ece3.11325</a> Grunwald D, Wijesinghege CW, Gordon T, Stansell Z, Ellison S (2024) First Report of Tobacco Streak Virus in Cannabis sativa in New York. Plant Disease 108:1407. <a href="https://doi.org/10.1094/PDIS-09-23-1810-PDN">https://doi.org/10.1094/PDIS-09-23-1810-PDN</a> Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, et al. (2023) A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. The Plant Journal n/a. <a href="https://doi.org/10.1111/tpj.16433">https://doi.org/10.1111/tpj.16433</a> Sinclair G, Galarneau ER, Hnizdor JF, McElrone AJ, Walker MA, Bartlett MK (2024) Grape cultivars adapted to hotter, drier growing regions exhibit greater photosynthesis in hot conditions despite less drought-resistant leaves. Annals of Botany 134:205–218. <a href="https://doi.org/10.1093/aob/mcae032">https://doi.org/10.1093/aob/mcae032</a> Yang Y, Wheatley M, Meakem V, Galarneau E, Gutierrez B, Zhong G-Y (2024) Editing VvDXS1 for the creation of muscat flavour in Vitis vinifera cv. Scarlet Royal. Plant Biotechnology Journal 22:1610–1621. <a href="https://doi.org/10.1111/pbi.14290">https://doi.org/10.1111/pbi.14290</a>

Impact Statements

Impacts: Sustainability and diversification of agricultural industries depend on the development of superior cultivars to combat emerging pests and diseases, climate and environmental changes, and shifting consumer demands. Germplasm, or genetic resources (sources of genetic diversity), provides the foundation for crop improvement and genetic enhancement. However, genetic resources are at risk due to reduced diversity in large-scale cultivation, changes in environmental conditions, degradation of native habitats, and international inaccessibility. The mission of the USDA ARS NPGS is to acquire, safeguard, characterize, document, and distribute plant germplasm, which is accomplished through a cooperative effort with State, Federal, and non-profit partners. Activities: • Participated in over a dozen outreach events to educate the public about the mission of seed/gene banks. Altogether, thousands of people were interacted with during these events. • Mentored six undergraduate interns in germplasm evaluation and maintenance. • Held the first USDA-ARS Hemp Germplasm Laboratory Stakeholder meeting on Sept 11, 2024. Approximately 80 people attended this all-day meeting. Initial conversations were initiated to establish a Hemp Crop Germplasm Committee. • Contributed to Crop Germplasm Committee discussions to inform stakeholders on the status of our collections. Indicators: Key indicators for program success and impact include number of accessions distributed, number of accessions maintained and acquired, and number of observations (genetic or phenotypic) recorded.

Date of Annual Report: 01/29/2026

Report Information

Annual Meeting Dates: 12/02/2025 - 12/02/2025
Period the Report Covers: 01/01/2025 - 12/31/2025

Participants

Clark, Matt-University of Minnesota; Frances, Anne-USDA ARS; Gasic, Ksenija-Clemson; Gottschalk, Chris-USDA ARS; Griffiths, Phillip-Cornell University; Gutierrez, Ben-USDA ARS; Herzeelle, Peter-Cornell University; Kinard, Gary-USDA-ARS; Kothari, Neha-USDA ARS; Mazourek, Michael-Cornell University; Povilus, Becky-USDA ARS; Rich, Joe-USDA ARS; Shade, Jessica-NIFA; Smart, Chris-Cornell University; Smith, Margaret-Cornell University; Stansell, Zachary-USDA ARS; Vogel, Greg-Cornell University; Zhong, Gan-Yuan-USDA ARS

Brief Summary of Minutes

Chris Smart (Director of Cornell AgriTech and NE9 Advisor), gave welcome to the group and provided brief overview of budget – spending is on track. Neha Kothari (National Program Leader over National Plant Germplasm System, (NPGS)) gave updates from the NPGS. NPGS budget overall has been steady but not keeping up with inflation; some targeted increases within NPGS to specific crops, including hemp. NPGS is exploring new initiatives to improve management and emphasized the need to highlight our work to stakeholders. Jessica Shade provided an overview of NIFA grant opportunities and encouraged participants to apply. Stakeholders provided updates on their individual research, with an emphasis on their utilization and need for diverse genetic resources. There is a need for pre-breeding material that incorporates desirable wild traits into a more accessible forms to accelerate breeding. Curators provided update on the status of the vegetable, hemp, and fruit collections associated with this project. Their highlights are provided in more detail below. Meeting emphasized value of in-person meetings. We will target the next meeting for July 2026. Also discussed a joint meeting with other RTACs (NC7, W6, and S9) before our next project renewal.

Accomplishments

The USDA Agricultural Research Service (ARS) Plant Genetic Resources Unit (PGRU) in Geneva, NY maintains diversity collections of select vegetables (12,801 accessions), hemp (743 accessions), and fruit (6,521 accessions). Targeted acquisitions over the past year have filled gaps (phenotypic, genotypic, and geographic) within the collections, expanding the resources available to stakeholders. Funding from NE9 provides critical resources for management and distribution of these collections. NE9 supports major efforts in supplying germplasm to screen and map high-priority horticultural and agronomic traits, including disease and pest resistances, and traits contributing to profitability and nutrition. Many of these efforts are done in collaboration with scientists from SAESs. In , PGRU distributed 7,432 distinct units (seed lots, propagules, fruit, etc.) to requestors. The collections have been extensively used worldwide to develop new cultivars and for other research purposes, including disease resistance, fruit quality traits, genetic diversity, and population structure. PGRU scientists characterize germplasm for priority traits to make the material more readily accessible. Much of this characterization and evaluation is performed in collaboration with scientists from the Northeastern US, other regions in the USA, and abroad. Over the past year, the USDA PGRU focused on its core goals of conserving genetic diversity, strengthening germplasm characterization, and increasing the accessibility of plant genetic resources. Expanded genomic and phenotypic efforts enhanced the scientific value of multiple collections, including whole-genome–scale genotyping of the USDA Physalis (tomatillo) collection, large-scale genotyping and phenotyping of hemp, skim-sequencing of cherry and grape accessions, disease resistance screening of grape accessions, and continued metabolic profiling of apple, grape, and cherry germplasm. We also improved efficiency within our programs, including a multi-year winter squash pollinator efficiency study to better inform pollinator management. An ARSx crowdsourced phenotyping initiative expanded national characterization capacity, producing more than 6,000 datapoints across diverse squash and tomato accessions. Targeted improvements to PGRU operations and infrastructure enhanced germplasm stewardship and resource availability to stakeholders. Squash seed collection and processing capacity was doubled, tomato seed processing protocols were streamlined to improve efficiency and quality, and plum cultivars were propagated for cold-hardiness evaluation and cryopreservation. Progress on high-tunnel greenhouse infrastructure expanded capacity for hemp breeding and characterization. Outreach, interdisciplinary collaborations reinforced stakeholder engagement and ensured NPGS priorities remain aligned with user needs.  Activities: <ul> <li>Completed year two of a pollinator efficiency study in three winter squash varieties, comparing fly, honeybee, and bumble bee pollination to inform squash pollinator management.</li> <li>Completed year one of an ARSx crowdsourced phenotyping project, expanding capacity to characterize USDA collections across multiple sites; 25 squash and 25 tomato accessions generated 6,000+ datapoints nationwide.</li> <li>Generated whole-genome–scale genotyping data for the entire USDA Physalis (tomatillo) collection.</li> <li>Increased squash seed collection and processing capacity twofold through targeted equipment investments, improving seed quality.</li> <li>Streamlined tomato seed collection protocols, resulting in faster processing and higher seed quality.</li> <li>Conducted genotyping and phenotyping of most of the NPGS Hemp Germplasm Collection; ongoing 2025 work produced 1,000+ long-read, low-pass genomes.</li> <li>Continued development of a stakeholder-driven, low-cost mid-coverage genotyping platform (DArT-Tag) to support germplasm conservation, trait mapping, and pre-breeding efforts.</li> <li>Scheduled the first Hemp Crop Germplasm Committee meeting for February 2026.</li> <li>Advanced development of two large high-tunnel greenhouses to support hemp breeding and characterization.</li> <li>1200 accessions of grape screened for powdery and downy mildew resistances with 35 resistance markers being screened through NIFA-SCRI funding.</li> <li>WGS genotyping of 250 accessions of cherry using the SkimSeq platform.</li> <li>WGS genotyping of 480 accessions of grapevine using the SkimSeq platform.</li> <li>Fruit quality metabolic evaluations continued for 600 apple, grape, and cherry accessions.</li> <li>Propagation of 140 plum cultivars for maintenance from Davis, CA to Geneva for cold hardy evaluation and cryopreservation.</li> <li>Collaborated with archeologists to evaluate and identify preserve fruit specimens found at Mount Vernon in Virginia.</li> <li>Participated in numerous public outreach events highlighting the mission, and the value of seed and gene banks.</li> </ul> Milestones for 2026: <ul> <li>Regenerate seed for 150 vegetable accessions.</li> <li>Backup up 100 vegetable and hemp accessions at NLGRP.</li> <li>Rescue 50 jeopardized vegetable accession in greenhouse regeneration.</li> <li>Continue to refine regeneration protocols of seed crops.</li> <li>Improve soil and assess onion bulb production.</li> <li>Develop parents for hemp MAGIC populations with collaborators.</li> <li>Regenerate 25 hemp accessions in controlled-environment conditions.</li> <li>Upload 10,000 phenotypic data points to describe hemp germplasm collection.</li> <li>Acquired over 20 novel hemp genetic resources.</li> <li>Backup of clonal accessions and test viability of cryo-treated buds.</li> <li>Evaluate apple nursery for rootstock compatibility.</li> <li>Retrain vines to enable mechanical foliar management.</li> <li>Re-evaluate apple cultivars for fruit quality.</li> <li>Complete evaluation of 480 accessions for grape juice metabolites.</li> <li>Complete disease phenotypes of powdery and downy mildews in grapevine.</li> </ul>

Publications

Carey, S.B., Bentz, P.C., Lovell, J.T., Akozbek, L.M., Myers, Z.A., Korani, W., Havill, J.S., Padgitt-Cobb, L., Lynch, R.C., Allsing, N., 2025. An X-linked sex determination mechanism in cannabis and hop. bioRxiv 2024–12. Lukach, M.E., Yeti̇şi̇r, H., Kanchana-Udomkan, C., Stansell, Z., Sheehan, M.J., Jannink, J.-L., 2025. A Unified Crop Ontology for Standardizing Phenotypic Data Collection in Bottle Gourd [Lagenaria siceraria (Molina) Standl.]. HortScience 60, 1655–1664. MacWilliams, J., Padimi, V., Carter, O., Brownstein, K., Stansell, Z., Gordon, T., Nachappa, P., 2025. Assessing the adaptive role of cannabidivarinic acid (CBDVA) in aphid defense in Cannabis sativa. J Cannabis Res 7, 34. <a href="https://doi.org/10.1186/s42238-025-00291-x">https://doi.org/10.1186/s42238-025-00291-x</a> Schwartz, J.A., Vignale, L., Gordon, T., Stansell, Z., Smart, L.B., Smart, C.D., 2025. Screening of Cannabis sativa germplasm for susceptibility to Septoria leaf spot. Plant Disease PDIS-07-25-1367-RE. <a href="https://doi.org/10.1094/PDIS-07-25-1367-RE">https://doi.org/10.1094/PDIS-07-25-1367-RE</a> Sehgal A, Deys K, Szewc-McFadden A, Duplais C, Gutierrez B, Meakem V, Galarneau E, Londo J, Turner B, Cadle-Davidson L, Zhong GY, Gouker F, and Kirubakaran S. Plant Physiology and Biochemistry Effect of Grapevine Rootstock and Foliar Biostimulants in Regulating Scion Physiology, Secondary Metabolites, and Root Architectural Adaptation to Drought Stress. <a href="https://ssrn.com/abstract=5125249">https://ssrn.com/abstract=5125249</a> Vignale, L., Schwartz, J.A., Stansell, Z., Gordon, T., Smart, C.D., Smart, L.B., 2025. Screening diverse Cannabis sativa germplasm for resistance to Golovinomyces ambrosiae. Plant Disease. Whitt L, Bennett JS, Collum TD, Evans B, Raines D, Gutierrez B, Janisiewicz WJ, Jurick WM, Gottschalk C (2025) Genome-wide associations within diverse wild apple germplasm for postharvest blue mold resistance to Penicillium expansum. Postharvest Biology and Technology 225:113513. <a href="https://doi.org/10.1016/j.postharvbio.2025.113513">https://doi.org/10.1016/j.postharvbio.2025.113513</a>

Impact Statements

The mission of the USDA ARS NPGS is to acquire, safeguard, characterize, document, and distribute plant germplasm to support the sustainability and diversification of agricultural industries which depend on the development of superior cultivars to combat emerging pests and diseases, climate and environmental changes, and shifting consumer demands.