NE9: Conservation and Utilization of Plant Genetic Resources

(Multistate Research Project)

Status: Active


The Need: Agriculture in the United States contributes to both national and global food security, and supports many diverse industries (e.g., food, ornamental, textile, medicine). Sustainability and diversification of agricultural industries depend on the development of genetically enhanced 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. However, diverse genetic resources are at risk due to reduced diversity in large-scale cultivation, changes in environmental conditions, degradation of native habitats, and international inaccessibility. These resources are difficult or can even be impossible to reconstitute if lost. This is especially true for fruit genetic resources, where preservation clonal identity is paramount.

The mission of the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Plant Germplasm System (NPGS) is to acquire, safeguard, document, and distribute plant germplasm, which is accomplished through a cooperative effort with State, Federal, and non-profit partners. NPGS serves research, breeding, and higher education as a public source of plant genetic diversity. The composition of NPGS collections includes landraces, older commercial cultivars, pre-breeding, elite breeding material, and crop wild relatives. As of 2022, more than 16,000 plant species in the form of more than 605,000 accessions were actively held by NPGS. An average of 296,488 samples per year were distributed during the five-year period 2018 – 2022; typically, 70% of these were domestic and 30% were foreign distributions.

The NPGS Plant Genetic Resources Unit (PGRU) located on the campus of Cornell AgriTech at the New York State Agricultural Experiment Station (NYSAES) in Geneva, NY is comprised of the Northeast Regional PI Station for seed crop collections, the National Clonal Germplasm Repository-Geneva, as well as the Apple Rootstock Breeding Program. In 2021, PGRU initiated the new NPGS Hemp (Cannabis sativa) collection. Major collections conserved are tomato, onion, celery, winter squash, brassica vegetable crops, radish, hemp, apple, cold-hardy grape, and tart cherry, including crop wild relatives. The Seed, Hemp, and Clonal repositories hold 12,723, 301, and 6,504 active NPGS accessions, respectively.

Safeguarding these genetic resources is critical to meeting future stakeholder demands, including states in the Northeast US, where many of these crops are principal sources of economic activity and potential commercial growth. The Northeast Regional Multistate Research Project, NE9, brings together representatives from 12 states (CT, DE, ME, MD, MA, NH, NJ, NY, PA, RI, VT, WV) and Washington DC to address mutual interests in plant breeding, research, and extension/education. Members of the Regional Technical Advisory Committee (RTAC) represent state universities, State Agricultural Experiment Stations (SAESs), and the USDA-ARS; the duty of Project Administrative Advisor is assigned to the director of Cornell AgriTech at the New York SAES. Breeding, research, and extension within the NE9 region are supported and strengthened by services and activities performed by PGRU and NPGS. Funding from the NE9 Project has been critical for the realization and sustainability of PGRU germplasm activities. PGRU Seeds and Clonal germplasm projects rely heavily on collaborations for evaluation trials and cultivar development, which are largely beyond the scope of NPGS.

Proposed Objectives: Objectives of this project are directed towards providing the required germplasm to assure stable and sustainable production of vegetable, hemp, and fruit crops in the Northeast USA and worldwide:

  1. Efficiently and effectively acquire and maintain the safety, genetic integrity, health, and viability of priority genetic resources, and distribute them and their associated information worldwide. 

  1. Develop more effective germplasm maintenance, evaluation, and characterization methods and apply them to priority genetic resources. Record and disseminate evaluation and characterization data via the Germplasm Resources Information Network (GRIN-Global) and other data sources. 

  1. With other NPGS gene banks and Crop Germplasm Committees (CGCs) develop, update, document, and implement best management practices and Crop Vulnerability Statements (CVSs) for priority vegetable, hemp, and fruit genetic resources and information management. 

  1. Actively engage in and support the development of novel priority vegetable, hemp, and fruit germplasm that integrates diverse, useful genes from various resources and breed, release, maintain, and evaluate improved and regulatory compliant germplasm and cultivars. Devise and apply research tools, knowledge of genetics, and of the genetic control of priority traits to broaden the diversity available for agricultural production systems. The role of the PGRU staff in the development of novel priority germplasm will vary across different crops and projects, and can range from providing germplasm resources to projects, advising project planning and implementation, to direct action on data collection and analysis.

Note: Objectives 3 and 4 require collaboration. Developing strong collaborative relationships among PGRU staff and reliable and productive cooperators are viewed as part of these objectives.

Importance of the Work:  The vegetable genetic resources, which includes tomato, onion, brassica, winter squash, celery, and asparagus, managed by this project represent approximately 36% of the combined dollar value of fresh and processing vegetables in the USA. The average production annual value from 2016-2021 in the US for PGRUs major vegetable collections was $5.145 billion (Appendix A, Table 1). During the past five years, PGRU maintained more than 12,600 accessions of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, other brassica crops, celery, tomatillo, asparagus, other vegetables, and buckwheat, representing 29 genera, 151 species and 1,999 taxa. Approximately 150 – 200 seed crop accessions were regenerated per year to replenish stocks. In addition, 285 distinct inventories were acquired since 2017. 

In 2021, the hemp germplasm repository achieved all federal and state compliance to initiate germplasm acquisition, characterization, evaluation, and distribution of regulatory compliant genetic stocks. This collection has grown rapidly to include over 300 accessions and is now the largest international public hemp germplasm collection. The collection contains feral, fiber, grain/oilseed, secondary metabolite, landrace, breeding lines, and other classes of diverse germplasm. Distribution of regulatory compliant materials began in 2022. Work is planned for 2023 to genotype the entire collection and to conduct population structure analysis. These genotyping efforts will guide collection and conservation priorities, development of mapping populations, and provide higher stakeholder utility as inputs into breeding programs.

PGRU maintains 4,940 accessions of Malus, 1,415 accessions of Vitis, and 149 accessions of tart cherries. Through introductions, explorations, and exchanges, PGRU acquired 104 Malus, 1 Vitis, and 13 Prunus accessions since 2017. The fruit crops maintained by PGRU account for about 49% of the value of US fruit and vine crop production (Appendix A, Table 1). Apples, grapes, and tart cherries contribute significantly to the US economy, with average annual values of $3.129, $5.908, and $0.062 billion from 2016-2021, respectively (Appendix A, Table 1). 

Historically, the NE9 Project has made substantial contributions to the vegetable and fruit industries through distribution of germplasm and associated information for developing improved varieties with higher and more stable yield, disease and insect resistance, and improved quality. From 2017 – 2022, PGRU distributed 52,612 seed lots (47% domestic and 53% foreign) comprising 11,155 unique seed accessions. PGRU distributed 24,399 clonal crop samples (97% domestic and 3% foreign) comprising 3,790 unique accessions. In NE9 states, there were 4,930 seed samples from 3,788 accessions distributed and 8,778 clonal samples from 2,8236 unique accessions distributed (Appendix A, Tables 2-7). Close to 40% of distribution of PGRU fruit germplasm is directed to NE9 states. The collections have been extensively used worldwide to develop new cultivars and for other research purposes, such as genetic analysis of disease resistance, fruit quality, 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 NE9 region and other regions in the USA and abroad. Research into quality and health-beneficial traits was initiated at the request of partners in various CGCs and has become increasingly emphasized.

Technical Feasibility and Value of a Multi-state Project:  

:  Acquisition, conservation, and characterization of germplasm collections are more efficient at a central location than through individual state organizations, which would result in unnecessary duplication of efforts. A cooperative approach among state partners and the PGRU allows for an efficient conservation of vegetable, hemp, and fruit germplasm while plant breeders and other researchers can take the lead in characterization and evaluation, especially for quantitative traits that require replicated field trials. Utilization of germplasm for crop improvement by geneticists and breeders at individual SAESs capitalizes on the genetic resources and the characterization/evaluation information maintained by the NPGS.

PGRU is primarily supported by appropriated funds authorized by Congress, which provides long term stability for performing basic genebank activities. It is located within a vibrant agricultural region at Cornell AgriTech on the NYSAES campus and is well suited to take maximum advantage of additional multi-state funds from the NE9 project for conservation and characterization/evaluation of vegetable, hemp, and fruit germplasm of important crops to the Northeast region.

Funding from NE9 provides critical resources for better management of the collections and quality service of germplasm distribution. It also supports major efforts in supplying germplasm to screen for high-priority traits, such as important disease and pest resistances and traits important to human health, much of which is done in collaboration with scientists from SAESs. The budget allocated to NE9 over the last 5 years was kept constant, even though salaries and expenses kept increasing. To retain skilled staff and maintain our current operational levels with the addition of a high-value crop, a 7% increase in the budget is requested, matching the 7% increase the Northeast region received during the last 5 years for Hatch and Multistate federal allocations. The budget will stay constant for the 5-year project. This increase will allow NE9 to maintain resources for a growing, valuable genetic resource.

Impact: Genetic resources in the PGRU repository will continue to prove useful in developing improved cultivars of vegetable, hemp, and clonal crops while supporting and stabilizing agricultural production. Expansion of global trade and complex food systems, increases the risk of introduction of exotic pests and diseases to the United States.  Agricultural research in the United States has intensified efforts to improve the sustainability of national food production while reducing its deleterious impacts. For example, crops with genetic resistance to pests and diseases reduces dependency on pesticides and preventative chemical sprays and reduces risks for agricultural workers and impact on the environment. In response to changing environmental conditions, PGRU collections will be used as sources of resistance to environmental stresses to increase the range of adaptation of crops. The Northeastern United States is particularly well suited to embrace emerging agricultural opportunities, to which PGRU can provide well documented germplasm for our growing conditions.

Finally, maximizing the use of available germplasm at PGRU will help domestic producers thrive in a competitive global marketplace. For example, within the current NE9 project, PGRU has provided accessions of tomatillo and cabbage as sources of natural pigments for breeding programs aimed at emerging markets; screened the tomato collection for biotic and abiotic resistances; identified a wild tomato accession used for late blight resistance in cultivated tomatoes. In 2021-2022 PGRU has assembled the world’s largest public hemp germplasm collection, collected approximately 100,000 data points for priority horticultural and agronomic traits, and these materials have been used to develop five long-read whole genome sequences to be deposited in the National Center for Biotechnology Information. The hemp germplasm collection has been used to develop fiber quality standards that will underpin an emerging domestic fiber industry. Apple germplasm has been utilized to develop new rootstocks with multiple disease resistances and improved plant architecture. Both apple and grape accessions have been screened for biotic and abiotic resistances, leading to new scion cultivars being developed in large, multi-state projects.

Germplasm from PGRU has proven useful in developing improved cultivars of vegetable and fruit in the Northeast region, the USA, and the world:

  • Genes from wild tomatoes have been exploited to increase ease of harvesting, disease resistance, and for stress and drought tolerance.

  • More than 20 genes from the PGRU tomato collection for bacterial speck, spotted wilt virus, tobacco mosaic virus, leaf mold, fusarium wilt, verticillium wilt, late blight, and nematode resistance have been bred into modern varieties.

  • Phylloxera resistant grape rootstocks and hybrids derived from North American wild Vitis germplasm were instrumental in rescuing the European grape and wine industry.

  • The recent spread of grape cultivation throughout the USA, especially in the northeast, has been made possible by use of the germplasm collection for breeding of new cultivars of Vitis vinifera and Vitis vinifera Vitis species hybrids that are adapted to environments where vinifera could not previously be grown.

  • Genetic resources for resistance to apple scab, fire blight, and wooly apple aphids maintained in the germplasm collection have been deployed in disease resistant apple rootstocks and cultivars. Insect and disease resistant apple cultivars can be traced back to the PGRU apple collection.

  • PGRU apple germplasm, especially historic cultivars, has been used directly by growers to expand the US apple cider industry.

Germplasm maintained at PGRU is currently or will be used for crop improvement of fruits, hemp, and vegetables:

  • Tomato accession are being tested for resistance to race 1 strains of Rs5 bacteria, ToBrFV virus, salt, and drought tolerance in growth chamber facilities. These phenotypic characterizations of the PGRU tomato germplasm collection will identify genomic regions controlling pathogen and stress tolerances and add significant value to our long-term breeding effort and cultivar development.

  • Cucurbit accessions have been evaluated for resistance to the oomycete pathogen Phytophthora capsica, which result in outbreaks that are challenging to manage and can result in huge yield loss.

  • Specialty cucurbit accessions from PGRU and other NPGS collections will be screened for powdery and downy mildew resistance, and critical agronomic traits as novel specialty crops to serve historically underserved communities in the Northeast.

  • Hemp germplasm from PGRU has been used to create five of the highest-quality cannabis sativa reference genomes and will likely contribute to the development of a cannabis pan-genome.

  • PGRU’s hemp collection has been screened for plant architectural traits, fiber and grain agronomic characteristics, and secondary plant metabolite composition and profile. This data will enhance subsequent curation, distribution, and evaluation efforts.

  • PGRU’s vegetable, hemp, and fruit germplasm collections are being screened for medicinal and nutraceutical properties for development of cultivars that will improve the health benefits of consumption.

  • Genomic resources developed for major apple progenitors from Central Asia and other wild Malus are key to accelerating breeding programs to introduce resistance and adaptability traits in modern apple cultivars.

  • Grape germplasm will continue to be used in developing new grape cultivars for better resistance to disease and climate change.

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