NE9: Conservation and Utilization of Plant Genetic Resources

(Multistate Research Project)

Status: Active

NE9: Conservation and Utilization of Plant Genetic Resources

Duration: 10/01/2018 to 09/30/2023

Administrative Advisor(s):

NIFA Reps:

Statement of Issues and Justification

The Need: Plants are widely utilized as major sources of food, beverages, animal feed, and plant derived products such as medicines, supplements, cosmetics, rubber, and textiles. Other valuable uses include ornamental and landscaping applications, phytoremediation, and improvement or protection of soils. Agricultural industry and innovation depend on the development of improved plant varieties to address new consumer demands, emerging pests and diseases, and ever-changing environments. Research and development of new cultivars requires diverse gene pools to draw upon. Crop genetic diversity is a natural resource that has evolved over many millennia across the globe, via human selection and natural selection. Much of this diversity is not native to North America or the USA, rather, diverse plant materials have been imported, propagated, and subsequently conserved in germplasm repositories such as the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Plant Germplasm System (NPGS). If lost, these gene pools are oftentimes irreplaceable due to diminished popularity of cultivars or landraces, changes in environmental conditions, degradation of native habitats, or international inaccessibility. Furthermore, an emphasis on crop uniformity for increased efficiency of operations has decreased the amount of genetic diversity utilized in many areas of production in the USA and worldwide.

NPGS serves research, breeding, and higher education as a public source of plant genetic diversity. The NPGS is a cooperative effort by State, Federal, and other organizations to acquire, preserve, evaluate, document, and distribute plant germplasm. As of 2017, more than 15,000 plant species in the form of more than 500,000 accessions were actively held by NPGS. Approximately 250,000 samples per year were distributed during the five year period 2012 – 2016; 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, and the National Germplasm Repository-Geneva for clonal crop collections, as well as the Apple Rootstock Breeding Program. The seed and clonal repositories hold 12,670 and 7,606 active NPGS accessions, respectively. Major collections conserved are tomato, onion, celery, winter squash, Brassica (cole crops and Brassica rapa), radish, apple, cold-hardy grape, and tart cherry, including crop species and their wild relatives. Safeguarding these genetic resources is critical to meet future stakeholder demands, including many states in the Northeast USA, 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 NYSAES. 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 nutritious fruits and vegetables 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.
  2. 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.
  3. 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 fruit and vegetable genetic resources and information management.
  4. Develop novel germplasm that integrates diverse, useful genes from various resources and breed, release, maintain, and evaluate improved germplasm and cultivars. 

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 tomato, onion, Brassica, winter squash, celery, artichoke, and asparagus genetic resources managed by this project represent approximately 36% of the combined dollar value of fresh and processing vegetables in the USA. The fruit crops maintained by PGRU account for about 49% of the value of USA fruit and vine crop production (Appendix A, Table 1). Among all fruit and nut crop production in the USA, the economic value of utilized production for grapes, apples, and tart cherries rank 1st, 4th, and 20th with values of $5.561, $3.394, and $0.087 billion in 2016, respectively (Appendix A, Table 1). Production in millions of metric tons is highly significant globally for PGRU’s major clonal and seed crops (Appendix A, Table 2). 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. For example, germplasm of tomato has been extensively used for development of resistance against pests and diseases; the Malus collection has been used for disease and pest resistance, fruit and storage quality, and drought tolerance; and the Vitis collection has been used for cold-hardiness, powdery mildew resistance, and phylloxera resistance.

During the past five years, PGRU maintained more than 12,600 accessions of tomato, onion, radish, winter squash, cabbage, cauliflower, broccoli, other cole crops, celery, tomatillo, asparagus, other vegetables, and buckwheat, representing 29 genera, 151 species and 200 taxa. Approximately 150 – 200 seed crop accessions were regenerated per year to replenish stocks. In addition, 143 new accessions were acquired of Allium, Apium, Brassica, Cucurbita, Fagopyrum, Physalis, Raphanus, Solanum, and other miscellaneous seed crops. PGRU maintained 5,910 accessions of Malus, 1,392 accessions of Vitis, and 130 accessions of tart cherries. Through introduction, exploration, and exchange, PGRU acquired 162 new clonal accessions and 306 seed accessions of Malus, 14 new clonal accessions and 3 seed accessions of Vitis. In total, 367 wild Malus sieversii and selective seedlings of M. sieversii were added to the permanent collection.

The collections have been extensively used worldwide to develop new cultivars and for research purposes, such as genetic analysis of disease resistance, quality, genetic diversity, and population structure. PGRU scientists characterize germplasm for priority traits to make the material more readily usable. Much of this characterization and evaluation is performed in collaboration with scientists from the NE9 region and also 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. From 2013 – 2017, PGRU distributed 29,092 seed lots (49% domestic and 51% foreign). On average, 5,818 unique accessions were distributed per year, i.e., approximately 46% of the active collections each year. PGRU distributed 36,751 clonal crop samples in 1,613 domestic requests and 121 foreign requests. In the states covered by NE9 there were 3,086 seed samples from 2,997 accessions distributed for the seed crops and 18,940 samples from 3,770 accessions distributed for the clonal crops.

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 fruit and vegetable germplasm while plant breeders and other scientists 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.

The PGRU is primarily supported by appropriated funds authorized by Congress, which provides long term stability for performing basic activities. It is located within a vibrant agricultural region on the Cornell AgriTech at 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 fruit and vegetable germplasm of important crops to the Northeast region. Funding from NE9 provides critical resources for better management of the collection 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.

Impact: Genetic resources in the PGRU repository will continue to prove useful in developing improved cultivars of seed and clonal crops, and stabilize agricultural production. Exotic pests and diseases are of increasing threat with the expansion of imports and exports throughout the world. Intensified efforts to improve the sustainability of national food production while reducing deleterious impacts are essential. For example, genetic resistance to pests and diseases reduces dependency on pesticides and preventative chemical sprays, which 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 fruit and vegetable crops. PGRU collections can also be utilized as consumer preferences change. For example, nutritional quality is of increasing importance to consumers and many of the plant species held at PGRU are being studied for health-promoting phytochemicals which reduce the risks of cancer, cardiovascular disease, diabetes, and numerous other chronic or life-threatening conditions. Finally, maximizing the use of available germplasm at PGRU will help USA producers thrive in a competitive global marketplace. For example, within the current NE9 project, PGRU has provided accessions of radish and cabbage as sources of natural pigments for breeding programs aimed at emerging markets; identified a wild tomato germplasm accession used for late blight resistance in cultivated tomatoes; and identified apple germplasm with multiple disease resistances and improved plant architecture to develop new rootstocks.

Germplasm from PGRU has proven useful in developing improved cultivars of fruits and vegetables 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 that are adapted to environments where vinifera could not previously be grown.
  • PGRU was the only institution that maintained the 100+ founding ancestors of popular apple cultivars.
  • 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. Millions of insect and disease resistant apple trees can be traced back to the PGRU apple collection.

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

  • Wild tomato germplasm is being screened for novel sources of resistance to Fusarium wilt race 3 because currently available sources cause negative pleiotropic effects on cultivars such as weaker vines.
  • Brassica oleracea (including cabbage, cauliflower, broccoli, Brussels sprout, kale) germplasm is being characterized for glucosainolate profiles; these are sulfur-containing compounds with chemopreventive properties.
  • PGRU’s fruit and vegetable germplasm collections are being screened for medicinal and nutraceutical properties for development of cultivars that will improve the health benefits of consumption.
  • Germplasm of apple progenitors from Central Asia and other wild Malus is being screened for important disease resistances such as fire blight and scab and is being incorporated into breeding programs.
  • Grape germplasm will continue to be used in developing new grape cultivars for better resistance to disease and climate change.
  • The apple collection has been used extensively by the hard cider industry in the USA and is assisting in the importation of new cider apple varieties from Spain and England and their subsequent distribution.

Related, Current and Previous Work

The Regional Research Project NE9 is responsible for acquiring, conserving, distributing, and characterizing genetic diversity of an array of fruit and vegetable crop taxa adapted to temperate regions, including crop wild relatives (CWR). This reservoir of genetic diversity contributes to food security and nutritional requirements of humankind. Seed or clonal germplasm, pollen, and DNA of accessions plus associated information are distributed worldwide for purposes of breeding, research, and higher education. Gaps in collections must be filled in order to preserve traits that have evolved naturally or through human selection over thousands of years. Germplasm is systematically regenerated, quality tested, and securely backed-up to ensure long-term availability. Regeneration and cultivation protocols must be assessed and refined to overcome dynamically changing pest, disease, and weather conditions. Descriptions of traits including growth, morphology, phenology, production, disease resistance, and health beneficial components are collected to provide for targeted requests and efficient utilization of accessions. Community-wide expertise in best management practices is leveraged to improve efficiency of operations and to document the skills and knowledge required to effectively execute this complex project. Crop vulnerability statements (CVSs) are consulted and updated in collaboration with Apple, Grape, Prunus, Cucurbit, Leafy Vegetable, Root and Bulb, Crucifer and Tomato CGCs, ensuring long-term protection of major components of the fruit and vegetable industries.


Some of the on-going research cooperation includes:


  • M. Mazourek, Horticulture, Cornell University and Dr. Z. Fei, Boyce Thompson Institute, germplasm diversity in winter squash.
  • J. Glaubitz, Institute of Biotechnology, Cornell University, and Dr. M Havey, USDA-ARS, DNA sequencing and mapping in onion
  • L. Mueller and Dr. S. Stickler, Boyce Thompson Institute, DNA sequencing and population structiure in wild tomato species
  • M. Gore, Plant Breeding and Genetics, Cornell University, genotypic and phenotypic diversity in Brassica
  • A. Breksa, USDA-ARS, physicochemical characterization of tomato fruit
  • S. Brown, Horticulture, Cornell University, (1) apple scion breeding and (2) characterization of fruit quality traits of the Malus collection.
  • B. Reisch, Horticulture, Cornell University, (1) grape scion breeding and (2) VitisGen project.
  • K. Xu, Horticulture, Cornell University, genetic and genomics of fruit quality and tree architecture traits.
  • L. Cheng, Horticulture, Cornell University, evaluation of bitter pit using Malus germplasm.
  • L. Cheng, Horticulture and Dr. Z. Fei, Boyce Thompson Institute, Cornell University, deep sequencing of Malus genomes.
  • G. Peck, Horticulture, Cornell University, (1) importation of new cider apple varieties from England, (2) evaluation of Malus collection for hard cider production potential, and (3) establishing new hard cider varietal trials in NY.
  • A. Khan, Plant Pathology and Plant-Microbe Biology, Cornell University, (1) screening Malus collection for new fire blight and scab resistance, (2) importation of international apple varietal set for apple scab screening and monitoring, (3) genetic mapping of fire blight resistance genes and leaf spot resistance gene, (4) allele mining of disease resistance genes in Malus and Vitis.
  • M. Fuchs, Plant Pathology and Plant-Microbe Biology, Cornell University, study of viruses in Malus and Vitis.
  • A. Angello, Entomology, Cornell University, trapping and monitoring of black stem borer of apple.
  • J. Goffreda, Plant Biology and Pathology, Rutgers University, evaluation and selection of wild M. sieversii seedlings.
  • Apple and Grape Vulnerability Statements with members from Apple and Grape CGCs, including many scientists from Cornell University. 


Collecting and conserving geographic and ecological diversity of CWRs in situ and ex situ is of high priority, as many wild populations face extinction due to various factors such as pests and diseases, competition with invasive species, and permanent alteration or loss of habitats. With respect to acquiring novel germplasm, obtaining precise estimates of gaps in cultivars, breeding material, and landrace or weedy material presents challenges because of the predominant influence of human activities. Germplasm acquired to fill gaps in PGRU collections is based on enhancing diversity of collections in order to reduce risks to agriculture.  

Significant accomplishments in the period 2013-2017 include:

  • 143 new accessions were acquired of onion, celery, Brassica, winter squash, buckwheat, tomatillo, radish, tomato, and miscellaneous taxa.
  • Three visits were made by PGRU scientists to the Chinese Academy of Agricultural Sciences, Institute of Vegetables and Flowers in Beijing. Germplasm exchange for vegetable crops and buckwheat was initiated and will be ongoing.
  • 162 Malus and 14 Vitis clones, and 306 Malus and 3 Vitis seed accessions were added to the collections through exchange and exploration within the USA and importation from foreign countries. Malus seed accessions included rare germplasm from Albania, Georgia, Japan, and Turkey, and domestic explorations; North American species Malus angustifolia, Malus coronaria, and Malus ioensis were collected in Alabama, Arkansas, Indiana, Iowa, Louisiana, Michigan, Mississippi, and Missouri in 2015, 2016, and 2017.
  • Cooperation with Crop Trust and Kew Gardens was established in 2017 for future preservation and characterization of seed accessions of wild Malus species from seven countries (Armenia, Azerbaijan, Georgia, Italy, Nepal, Pakistan, and Vietnam; 

Maintenance and regeneration: 

For the PGRU seed repository, accessions are routinely generated as seed stocks are depleted through distribution and viability is reduced during storage. Regeneration and maintenance procedures must minimize genetic changes within accessions. Loss of genetic diversity through genetic drift and through unintentional selection is avoided to the extent possible by managing the optimal health and size of regeneration populations. Long term safety of collections is ensured by back-ups of 2,000 seed with a minimum of 85% viability per accession at Plant and Animal Genetic Resources Preservation (PAGRP), Ft. Collins, CO. For clonal crops, cryopreservation at PAGRP serves as backup storage for Malus and tart cherry accessions. Wild Malus and Vitis seed accessions are maintained in cold storage by the PGRU and PAGRP. A research strategy for long term storage of Vitis is being investigated by Plant Germplasm Preservation Research (PGPR) with cooperation from the National Clonal Germplasm Repository, Davis, CA and PGRU. 

Significant accomplishments in the period 2013-2017 include:

  • Regenerations were completed for 824 seed crop accessions in Geneva, NY and 27 accessions of short day onions were regenerated at New Mexico State University through a Cooperative Agreement.
  • 175 backup samples for seed crops were added or replaced at the PAGRP.
  • A Cooperative Agreement with University of California, Davis was used each year to support the CM Rick Tomato Genetics Resources Center (TGRC) of unique wild and genetic stock tomato accessions.
  • 190 Malus and 28 Prunus accessions to PAGRP for cryopreservation between 2013 and 2017. The status of the cryo-preserved dormant buds of Malus was reviewed and a priority list developed for new accessions and accessions with low cryo-viability (Volk et al., 2017).
  • The Apple CVS was updated in 2015 (Volk et al. 2015), and PGRU had significant input into its content. The Apple CVS is being used as a template for updating other CVSs. Updates of the Grape, Prunus, Cucurbit, Leafy Vegetable, Root and Bulb, Crucifer, and Tomato vulnerability statements are in progress.
  • An international survey of apple germplasm collection carried out by Crop Trust and PAGRP showed that the PGRU apple collection is the largest and most diverse in terms of species representation (Bramel and Volk, personal communication). 


Grant proposals funded by USDA upon recommendation from CGCs serve as a unique and valuable resource with which to study high priority traits in NPGS germplasm collections. NPGS germplasm and associated information are provided to the investigative team and resultant data are deposited into GRIN-Global and/or other public data bases. As ex-officio members of any CGC that includes PGRU crops conserved, the PGRU curators have firsthand knowledge of proposals submitted for screening NPGS germplasm and whether or not they are funded. Criteria for funding include a current Crop Vulnerability Statement, scientific merit, the national need for evaluation data, the likelihood of success, and the likelihood that the evaluation data will be entered into GRIN-Global. 

Significant accomplishments in the period 2013-2017 include: 

  • 52 commercially important tomato accessions were compared for physicochemical and morphological variation in fruits
  • 173 tomato accessions from the core set were analyzed for flavor and flavor-contributing components
  • Genotype x environment interactions were studied for fruit quality traits in 44 vintage tomato varieties.
  • 367 accessions of sieversii were selected for permanent maintenance including seedling evaluations by PGRU and cooperators at the University of Minnesota, Ohio State University, and University of Arkansas.
  • Vitis accessions were selected for permanent maintenance based on seedling evaluations of genetic diversity (GBS), powdery mildew resistance, flower sex, and overall vine health.
  • Phenology (budburst, bloom date, and veraison) was evaluated for 1,426 Vitis accessions over three seasons. Bloom date was evaluated for 3022 trees from the Malus collection over three seasons
  • Genotyping and DNA sequencing of numerous fruit and vegetable accessions (see Research below), including a significant portion of Malus, Prunus, and Vitis collections genotyped using GBS, RosBREED 8K, and Vitis 9K SNP arrays. 


CGCs maintain and update descriptor lists for crop traits that are highly heritable and therefore can be evaluated without costly, replicated experimental trials ( There are typically dozens or more traits for a crop which are grouped into the major categories of disease resistance, growth habit, fruit morphology, phenology, and production. We continue to test and implement new methods and technologies for high-throughput data collection from field plots (Rife and Poland 2014). In addition, digital images of plants and their parts (e.g., fruit, flowers, bulbs) are collected and deposited into GRIN-Global. 

Significant accomplishments in the period 2013-2017 include: 

  • Phenotypic data, including digital images, were collected for routine regenerations of tomato, onion, cole crops and winter squash accessions using CGC descriptors for highly heritable traits.
  • Tomato fruit quality traits such as Brix, Vitamin C, and titratable acids were collected for routine regenerations.
  • Protocols for in-house seed viability tests were adopted and implemented in 2016. Several–hundred tests on regeneration samples were successfully completed.
  • PGRU added 800, 272, and 60 digital images of Malus, Prunus and Vitis accessions, respectively, to the GRIN-Global database.
  • PGRU added 137 descriptor observations of Malus to the GRIN-Global database.
  • Catalogs of our apple, grape, and tart cherry inventory were updated annually, and made publically available for stakeholders to request germplasm ( 


New cultivars developed from germplasm contribute to diversity in crops, expand variety in diets, and provide benefits to human health and nutrition. Progress in crop genetics, genomics, genetic improvement, and horticultural production are accelerated by the information and genetic resources supported by NE9. Information associated with collections is distributed through GRIN-Global and other public databases such as National Center for Biotechnology Information (NCBI) or Sol Genomics Network (SGN). 

Significant accomplishments in the period 2013-2017 include: 

  • The GRIN-Global public website interface for ordering accessions and accessing information has been substantially improved to make it more user-friendly and compatible with a wide range of electronic devices.
  • Thousands of DNA sequences and genetic markers for accessions of tomato, tomatillo, and rapa accessions were deposited into public databases.
  • PGRU distributed 33,466 samples (49% domestic and 51% foreign) of 29,092 seed crop accessions. On average, 5,818 unique accessions were distributed per year, i.e., approximately 46% of the active collections each year (Appendix A, Tables 3 and 4).
  • PGRU distributed 31,602 samples of 15,748 clonal accessions (Appendix A, Tables 5 and 6) in the form of scions, seed, fruit, pollen, DNA, leaves, or use of trees for controlled This included an increase in request for “Botany of Desire” seeds (open pollinated seeds of M. sieversii) from the USA and particularly from European countries such as Austria, England, Finland, France, and Germany 


NE9 is a cooperative research project among the State Agricultural Experiment Stations within the Northeast region of the USA. PGRU strives to provide vigorous, pathogen-inspected, and quarantine-acceptable germplasm samples to researchers and breeders. PGRU curators continue to serve as co-PIs or close collaborators on experimental studies, to ensure success of the research and follow-up on depositing data into GRIN-Global or other public databases. Genotypic research focusses on the analyses of diversity within and among accessions and taxa, as well as identifying functional alleles. Phenotypic research prioritizes traits for genetic improvement, such as tolerance of environmental stresses and extremes, nutritional content, flavor, color, horticultural traits, and host-plant resistance to diseases and pests. 

Significant accomplishments in the period 2013-2017 include: 

  • 190 tomato accessions originating from 31 countries were genotyped using genotyping-by-sequencing (GBS). Accessions were identified that produce favorable fruit traits in a genetic background that contains many wild or primitive genes, these accessions are promising sources of novel alleles for continued crop improvement (Labate, 2017).
  • Many thousands of potentially diagnostic SNP markers were identified among wild tomato taxa; these markers will be valuable for delimiting morphologically similar and interfertile species in germplasm management (Labate et al., 2014).
  • 125 tomatillo accessions were genotyped using GBS; 86 pairs of accessions were quantitatively differentiated from each other based on allele frequencies, and homozygosity was confirmed for nine new inbred lines developed at PGRU (Labate and Robertson, 2015).
  • 363 accessions of rapa, including ten various morphotypes, were genotyped using GBS. Morphotypes were found to be genetically distinct but there were also differences within morphotypes related to geographic origins. Understanding of these relationships will inform future breeding and scientific work in B. rapa (Bird et al., 2017).
  • 146 accessions or lines of onion were genotyped using GBS; 701 of the markers were successfully mapped in an F2 population. This indicated that GBS is a promising technology for marker development in onion despite its very large (16GB) genome (Labate et al., 2016).
  • Development of SNP imputation software LinkImpute for heterozygous species (Money et al. 2015).
  • Genome-wide association study using historic apple data from 689 accessions with >8,000 SNP markers identified a quantitative trait loci (QTL) for harvest date and fruit firmness (Migicovsky et al. 2015).
  • Genetic maps using GBS markers were constructed for crosses of ‘Royal Gala’ apple and 7 different sieversii accessions. Norelli et al. (2014, 2017) utilized these resources to identify novel blue mold resistance. They are also being used to study other traits of interest such as disease resistance, growth traits, fruit quality, and phenological traits.
  • An association and domestication study of Vitis vinifera germplasm from the NPGS clonal repositories in Davis, CA and Geneva, NY identified a QTL for berry size, as well as evidence for selection of skin pigmentation, aroma, and hermaphroditic grapevines (Migicovsky et al. 2017).
  • Genetic diversity was estimated for the Malus core collection (Gross et al. 2013) and wild sieversii populations (Volk et al. 2013, 2016).
  • Vitis species and hybrids were subjected to phylogenetic analyses (Miller et al. 2013; Wan et al. 2013) and genome-wide estimation of ancestry (Sawler et al. 2013).
  • Genetic analysis of ancient and modern apple cultivars showed changes in genetic diversity over time (Gross et al. 2014).
  • A major accomplishment included a study of the domestication history for fruit size of apple by re-sequencing 117 accessions from China and PGRU (Duan et al., 2017).
  • Tree and root architecture were analyzed for sieversii (Fazio et al., 2014)
  • Resistance gene analogues in apple were characterized and their evolutionary histories were deduced (Perazzoli et al., 2014).
  • Apples were studied for the transcriptomics of fruit acidity (Bai et al., 2015).
  • Diversity of volatile compounds was profiled for the Malus core collection (Sugimoto et al., 2015).
  • The mechanisms of blue mold resistance mechanisms was investigated in wild Malus (Janisiewicz et al., 2016). Additionally, Sun et al. (2017) identified an association between blue mold resistance and phenolic composition in apple fruit.
  • Fire blight resistance was evaluated for the Malus collection (Khan and Chao, 2017)
  • Antioxidant and antiproliferative activities were measured in the fruit of twenty-four Vitis accessions (Liang et al., 2014).
  • Dihydrochalcones are chemicals unique to apple and its wild relatives. In collaboration with Dr. Susan Brown (Cornell University), 486 accessions from the Malus collection and five F1 populations were studied for dihydrochalcone content variation. Using association mapping and genetic mapping, we identified QTL associated with dihydrochalcone content and developed a model for the inheritance of three dihydrochalcones in apple.


  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.
  2. 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.
  3. 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 fruit and vegetable genetic resources and information management.
  4. Develop novel germplasm that integrates diverse, useful genes from various resources and breed, release, maintain, and evaluate improved germplasm and cultivars.


  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.

NE9 will continue to serve as a conduit for movement and exploration of valuable plant genetic resources from worldwide origins to the northeastern states and beyond (Appendix A, Tables 3-7). The PGRU is well equipped with facilities and equipment for conducting its service, education, and research activities (Appendix D).


PGRU will fill gaps in the seed and clonal collections through germplasm exchange, cooperator donations, expired Plant Variety Protection materials, and exploration. We are assisting with the importation of new cider apple varieties from Spain and England and helping the fast growing hard cider industry in the Northeast regions and continental USA. Many Vitis species are native to China. Though import of Vitis cultivars or wild species as cuttings is restricted in China, we will pursue opportunities to import seeds and pollen. Additionally, we will complete the importation of Vitis accessions from Vineland Research and Innovation Centre in Ontario, Canada once they have cleared through the quarantine process.  Genetic diversity of tomato, B. oleracea, onion, winter squash, radish, and celery collections will be restored and enhanced by identifying gaps and sources of germplasm to fill the gaps. Genesys free online portal ( will be used to explore sources of seed. Genesys is a plant genetic resources accession database that contains 3.6 million accession records from 481 institutes; the three largest being US-NPGS, Consortium of International Agricultural Research Centers (CGIAR), and European Cooperative Programme for Crop Genetic Resources Networks-European Internet Search Catalog (ECPGR-EURISCO). The USA became a Party to the Food and Agricultural Organization of the United Nations (FAO) International Treaty on Plant Genetic Resources for Food and Agriculture in March, 2017. Details of implementation are currently in progress (P. Bretting, pers. comm., 2017).


We will use best management practices (BMP) to preserve and safe guard the vegetable and fruit collections. We will ensure the long term safety of collection by systematically completing backups of accessions at PAGRP, Fort Collins, CO. We will also work with PGPR, Fort Collins, CO to develop long-term backup strategies for grape. Any seed accession that drops below minimum requirements for seed quantity (1,000) or viability (70%) is routinely regenerated. We will also improve the methods for germplasm regenerations of vegetable crops. One priority for regeneration is the production of seed for backup at PAGRP at -20⁰C to ensure that germplasm is available if lost. Current backups for PGRU major crop collections range from 4% (Tartary buckwheat) to 97% (tomato). Data from GRIN-Global will be used to analyze backup status of all accessions. Backup samples will be produced either from currently stored seed, or if this is not available, from regeneration of an accession. We will have initiated the comprehensive review and repackaging of inventory to assemble backup samples, destroy non-viable and large excess quantities of seed, and to physically segregate seed lots used as distribution samples to store at 4⁰C, 20% relative humidity, for their easy access for filling orders.

Management of fire blight is the primary challenge for the apple collection. Beyond standard horticultural practices, rootstock selection has a significant impact on fire blight incidence. We are investigating the performance of ‘Geneva 210’ rootstock with PGRU accessions. ‘Geneva 210’ is not only highly resistant to fire blight, but tolerant to replant disease, crown rot, root rot, and wooly apple aphid, and is also cold hardy. As it was bred for commercial production, its compatibility with diverse Malus species is uncertain. The first set of Malus accessions propagated on ‘Geneva 210’ will be planted in Spring 2018. We will continue to use ‘Geneva 210’ rootstock for future propagation and monitor their field performance during the next project cycle.

Clonal propagation preserves the unique allelic combinations of individual plants, and is the primary means to maintain the genetic resources of historic and modern cultivars of apple, grape, and tart cherry. However, there are inherent risks of losing these accessions when maintained as field collections, as well as limitations in resources required for long term preservation. For CWRs, clonal propagation can be supplemented through seed preservation. While seeds do not maintain allelic combinations, individual alleles are preserved as seed lots for future deployment. Therefore, we seek to actively expand the seed collections of PGRU clonal crops. Many wild Malus and some Vitis accessions collected as seeds are stored at −20°C at PGRU and at PAGRP. For Malus, seeds with 99.6% viability are dried to 5% moisture and stored at −18°C to maintain an estimated 84% viability for 100 to 455 years. An ongoing experiment involving the germination of M. sieversii seeds from controlled crosses made in 2004 and 2005 should provide an estimate on the medium range viability of cold stored Malus seeds. We will continue collecting controlled cross seeds, open pollinated seeds, and/or apomictic seeds of the collections as an alternative backup method for preservation of Malus and Vitis genetic resources. For all Malus and Vitis seeds collected, a plant introduction (PI) number will be assigned and all associated information will be input into GRIN-Global. For apomictic Malus and selfed Vitis seeds, germination tests and genetic analysis will be carried out to determine seed viability and genetic identity.


PGRU distributes germplasm in six different forms: seeds, winter dormant cuttings, leaves, pollen, summer green cuttings, and DNA. Record keeping for order processing is maintained through GRIN-Global. Distribution of vegetable crops is directed towards research and crop improvement needs. The normal amount of seed distributed is 50 seed per accession. Whenever seed is requested for an accession with low seed supply, it is given priorty for regeneration. Most of the requests for fruit crops come through the apple, grape, and tart cherry catalogs ( and GRIN-Global. Research requests for fruit crop germplasm usually come through email inquiries and discussions with the crop curators. PGRU also extensively provides germplasm to researchers and extension personnel in fruit crop related projects including many cooperations within the NE9 region.


  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.

We will cooperate with scientists from ARS, Cornell University, and other public and private sectors to characterize priority traits in fruit and vegetable collections. PGRU will carry out the characterization and evaluation of key morphological, horticultural, genetic, and biochemical attributes of accessions. We will optimize the protocols and develop/adapt new methods for data collection for vegetable and fruit collections. Characterization and evaluation data are distributed via GRIN-Global and other databases.

Seed regenerations are oftentimes challenging for specific accessions. Many accessions are unimproved for disease, pest and abiotic stress resistances or tolerances. To improve field conditions and promote healthy regeneration populations, we will perform soil tests in the spring before planting and in the fall after harvest is completed each year. A local private company will perform the tests, provide detailed reports and recommendations, and provide service for amending soils. Analytical tests include percent organic matter, pH, mineral nutrients P, K, Mg, Ca, S, B, Cu, Fe, Mn, Zn and nutrient ratios. Results are compared to optimal ranges and soils are treated accordingly, approximately one month before planting, to allow time for nutrients to penetrate the soil. We also utilize a pelleted slow-release dry fertilizer, NPK balanced, suitable for seasonal production of vegetables. Heat treatment of seed can effectively control a broad range of seed-borne pathogens (reviewed by Koch and Roberts 2014). We will apply hot water treatment to seed according to protocols recommended by Plant Pathologists at Cornell University (Vegetable MD Online, Heat treatment will be part of an integrated pest control program. Additional measures we will apply are pesticide treatments, adequate ventilation by minimizing weeds and minimizing the period of time within mesh cages to the extent possible, and promoting vigor of plants through nutrient management and weed control. Diseased plant samples will be sent to a plant pathology testing lab to verify identities of pathogens. For late or sparsely flowering vegetable accessions, we will test whether extending the growing season can improve seed production in regeneration plots. Black plastic mulch will be used to increase soil temperature, provide drainage away from the plants on a raised bed, retain soil moisture, and inhibit weed populations. We will also try regeneration from start to finish in the greenhouse. Data for CGC descriptors for tomato, onion, cole crops, and winter squash will be routinely collected from regeneration plots during the growing season. Descriptor data will be collected on scheduled days depending on the crop and trait, and entered into a portable electronic tablet or smartphone (Rife and Poland 2014). Digital images using standard formats for GRIN-Global will be collected using a flat-bed scanner or a camera for healthy material of typical appearance. Tomato fruit quality traits such as Brix, Vitamin C, and titratable acids will be assayed at PGRU using published protocols (Breksa, Robertson et al. 2015). PGRU has adopted PAGRP’s library of optimized protocols and standard operating procedures (SOPs) for seed testing of NPGS crop species (S. Greene, pers. comm, 2017). Germination tests of routine regeneration plots can be completed in approximately 2.5 months each year. Data in the form of percent germination and associated information are uploaded into GRIN-Global.

“Genomic and phenotypic diversity among Brassica oleracea crops” is a current collaborative project with J. Chris Pires (Univ of Missouri, Columbia) and Michael Gore (Cornell Univ). This B. oleracea germplasm evaluation project is expected to be completed by 2019. The major components of the overall project are as follows: i) Phenotypic diversity will be assessed across all NPGS cultivated morphotypes. A set of 144 accessions will be chosen for a replicated experiment (four replicates each) to phenotype in parallel: leaf shape (flatbed scanner), glucosinolates, and ionomics, ii) The 190 NPGS B. oleracea accessions will be genotyped using GBS (Elshire, Glaubitz et al. 2011). By using thousands of SNP markers mapped to the B. oleracea genome (Liu, Liu et al. 2014; Parkin, Koh et al. 2014), diversity will be quantified and diagnostic markers that distinguish morphotypes among the NPGS B. oleracea accessions may be discovered, iii) High-performance liquid chromatography (HPLC) will be used to identify and quantify glucosinolates (GLSs), bitter tasting compounds that are useful for herbivory defense and that have been reported to have anti-carcinogenic properties (Traka, Saha et al. 2013). Correlation of associated GSLs with SNP markers scored from the GBS analysis for each B. oleracea morphotype will allow for further decisions of the best accessions to target for human health and possible anti-cancer properties. Genome wide association studies (GWAS) will link the glucosinolate data with the genetic map of B. oleracea, iv) to test the elemental composition of the NPGS accessions across morphotypes, ionomics will be conducted using Inductively-coupled Plasma Mass Spectrometry (ICP-MS) at the Donald Danforth Plant Science Center in St. Louis, MO (Baxter 2009). Correlating the elemental composition to the SNP markers will provide an excellent resource to future studies wanting to enhance specific elements in different crops.

For the Malus collection, we will collect the standard twenty-eight descriptors related to fruit characteristics ( and digital images at maturity of fifty accessions each year. We will collect the information once in a single year. All descriptors and digital images will be uploaded into the GRIN-Global database. For cider apples, we will measure fruit size, juice volume, tannin, and titratable acidity of 15 accessions per year, and classify the fruit of the accessions into the historical English classification as bittersweet, bittersharp, sweet, or sharp. Similarly, descriptors for newly acquired Vitis accessions will also be collected. Some horticultural traits are difficult to phenotype in clonal collections due to tree/vine sizes, heterogeneity of the material, and the sizes of the collections. Often, it is challenging to phenotype the collection as a whole due to limited time and resources; often data are collected in subsets over multiple seasons, compromising across season comparisons due to seasonal variations. Various high throughput phenotyping methods have been developed and some of them can be leveraged to overcome many of these challenges. Aerial phenotyping with unmanned aerial vehicles (UAVs) can rapidly collect data, with greater reproducibility, and at lower costs than ground based high-throughput phenotyping approaches. UAV phenotyping is particularly useful in collecting multi-observation phenotypes; important traits such as budburst, bloom, disease status, or growth rate, must be recorded multiple times throughout season. UAVs can provide high resolution images which can be rapidly collected and analyzed. To determine the utility of this method in genetic resource characterization, we will use UAV phenotyping to record bloom date in the Malus collection. Images of the Malus core collection (249 accessions) and the seven ‘Royal Gala’ × M. sieversii populations around bloom date (mid/late April through May) will be captured using a Phantom 4 Pro quadcopter (229×356×406 mm) equipped with a 20 MP, 94° field of view RBG sensor (Precision Hawk, Raleigh, NC). Several specifications need to be worked out through pilot studies; for example, ideal altitude and time of day for imaging, speed of UAV, and camera settings (ISO, exposure, and aperture). Precision Mapper software (Precision Hawk, Raleigh, NC) will be used to combine data into a single orthomosaic image and identify trees in bloom. Image analysis functions include plant counting (designed for field crops) and crop load analysis. Using these functions we will need to train the software to identify blossoms and provide an accurate count. If the software cannot detect apple blossoms, visual scoring of images will be required. Bloom date will also be cross validated from field observations to determine accuracy of analysis. To minimize effect of tree age, planting date will be included as a variable for statistical analysis. We have obtained appropriate permits to operate UAV for the stated purpose. The PGRU Vitis collection includes cold-hardy grape cultivars and species, adapted to winter climates similar to the Northeastern USA. In addition to cold-hardiness, the Vitis collection has significant variation for fruit quality traits, such as cluster architecture and flavor. Cluster architecture is associated with yield, pre/postharvest pathology, and consumer acceptance. Berry clusters from a set of 336 hybrid accessions will be evaluated based on a set of standard descriptors. Additionally, fruit chemistry will be analyzed using GC/MS and HPLC to characterize flavor diversity within the collection. The information from both projects will be distributed to stakeholders through GRIN-Global and provide genetic resources to aid in the development of superior cultivars, adapted to cold-climate regions. 


  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 fruit and vegetable genetic resources and information management.

The knowledge, expertise, and experience of CGC members, and staff at other NPGS and international germplasm repositories will be leveraged to strengthen and improve germplasm conservation through best management practices (Rao, Dulloo et al. 2016). Other NPGS sites with shared taxa include NC7 (Brassica, Cucurbita), S9 (Cucurbita), and W6 (Allium, Grape, Prunus). Curators and other scientists meet on a regular basis at scientific conferences, CGC meetings, Regional Technical Advisory Committee meetings, and Plant Germplasm Operations Committee meetings. This provides many opportunities for mutually beneficial consultation, exchange of information, formulation of new ideas, and soliciting recommendations. All components of PGRU operations will be reviewed and documented as SOPs with sufficient detail to reduce risk of any lapse in operations. Thereafter, the finalized PGRU Operations Manual will be reviewed and updated annually. To strengthen and implement the BMP for conservation of the germplasm collections, we will cooperate and consulate with Cucurbit, Crucifer, Leafy Vegetables, Root and Bulb, Tomato, Apple, Grape, and Prunus CGCs and other NPGS genebanks. Additionally, PGRU Clonal will invite an independent horticulturalist to review practices and offer suggestions to update SOPs. We will also collaborate with Cucurbit, Crucifer, Leafy Vegetables, Root and Bulb, Tomato, Apple, Grape, and Prunus CGCs to update the CVS. The CGC chair will organize a committee to draft a CVS and assign sections based on the template CVS ( It is expected that finalized, updated CGC crop vulnerability statements will be completed by 2020.


  1. Develop novel germplasm that integrates diverse, useful genes from various resources and breed, release, maintain, and evaluate improved germplasm and cultivars.

This objective is primarily met through collaborations among members of the SAESs of the Northeast (Appendix E) and the PGRU and other ARS scientists (Appendix F). We are working with breeders in the vegetables through collaborative characterizations/evaluations to provide the germplasm necessary for improvement of disease and insect resistance. Additionally, we provide germplasm to cooperators in order to improve traits such drought and cold tolerance resistance in winter squash, novel resistance for pink root in onion, and improvement of tomato and Brassica nutritional components. Through discussions with researchers, breeders, and CGCs, we continue to update phenotyping and genotyping efforts of the PGRU accessions to provide information useful for crop improvement and cultivar development. In collaboration with the GGRU, Cornell University, Appalachian Fruit Research Station (ARS) in W. Virginia, Washington State University, University of Minnesota, and other institutions in the USA and worldwide, we will continue to identify new sources of disease resistance and other useful traits in Malus accessions. We will make crosses with commercial apple varieties such as 'Honeycrisp' to create new germplasm lines for future improvement of disease resistance and other traits. We will deploy the same approach for Vitis and tart cherry germplasm.

Measurement of Progress and Results


  • Identified priority germplasm to enhance collections and addition of new accessions with targeted characteristics.
  • Improved field conditions for better maintenance and improved regeneration protocols.
  • Germplasm security, viability and availability secured through germination testing and back-ups
  • Collected data for growth, morphology, phenology, and production of priority accessions.
  • Application of new technologies suited for germplasm studies (UAV phenotyping).
  • An expanding GRIN-Global database with passport, characterization, and evaluation data including digital images.
  • Organized germplasm and increased efficiency of filling orders allowing timely distribution of germplasm and associated information.
  • Improved usability of germplasm for genetic research and cultivar development.

Outcomes or Projected Impacts


(2019):The major milestones that occur every year include routine regenerations, storage, and testing of germplasm; acquisition of cultivars, landraces, and wild species; characterization, digital imaging and evaluation of germplasm; and distribution of germplasm. Research in the form of replicated field trials typically requires externally funded competitive grants and collaborations. • Backup seed and clonal accessions and test viability of cryo treated buds if resources are available. • Carry out exploration of wild M. coronaria in Ohio if funded. • Collect descriptor data and digital images of accessions. • Determine specification and evaluate technical feasibility for aerial phenotyping of Malus collection. • Consult with plant pathologists to identify chronic diseases during seed regenerations, identify winter squash accessions with no seed set or production of low viability seed. • Consult with CGC members to prioritize traits for evaluation of collections. • Draft outline for PGRU Operations Manual. Participate in CGC meetings and consult with members on status and plans for CVS.

(2020):• Backup seed and clonal accessions and test viability of cryopreserved buds if resources are available. • Carry out exploration of wild M. angustifolia in Southern USA if funded. • Collect descriptor data and digital images of accessions. • Collect bloom date information from field observations using aerial phenotyping, and determine the correlation between ground observations and UAV. • Apply treatments to reduce chronic diseases during seed regenerations, consult with experts for recommendations on regenerating winter squash accessions with no seed set or production of low viability seed. • Compile and edit content of Operations Manual and contribute to updated CVS.

(2021):• Backup seed and clonal accessions and test viability of cryopreserved buds if resources are available. • Carry out exploration of wild M. coronaria in West Virginia if funded. • Collect descriptor data and digital images of accessions. • Collect second year bloom date information from field observations using UAV. • Improve soil and assess onion bulb production. • Compile and edit content of Operations Manual, check for deficiencies in information and finalize content.

(2022):• Backup seed and clonal accessions and test viability of cryopreserved buds if resources are available. • Carry out exploration of wild Vitis species in eastern USA if funded. • Collect descriptor data and digital images of accessions. • Collect bloom date data with UAV for final season. • Continue to refine regeneration protocols of seed crops.

(2023):• Backup seed and clonal accessions and test viability of cryopreserved buds if resources are available. • Collect descriptor data and digital images of accessions. • Summarize and distribute the results of aerial phenotyping and upload the information to GRIN-Global. • Update the CVS. • Continue to refine regeneration protocols of seed crops.

Projected Participation

View Appendix E: Participation

Outreach Plan

Outcomes or Projected Impacts

Consumers in the US and abroad will benefit from stable production of improved, expanded and nutritionally enhanced vegetable crops with reduced risk of susceptibility to pests, diseases, and changing environments. The international horticultural community, including farmers; government and academic scientists including plant pathologists, physiologists, food scientists, entomologists; and scientists at private companies are major users of the products from this project. We host many public tours, including an annual open house of our collections, and engage in science-learning events for underserved populations. Additionally, we are often highlighted through tours of the Cornell AgriTech at NYSAES campus. These opportunities serve to educate the general public of our value to agriculture and biological conservation. Customers looking for sources of rare or exotic fruit or vegetable varieties, for example, small growers serving local niche markets, are also frequent requestors and recipients of our germplasm. This project provides a well-organized and secured supply of germplasm, thereby ensuring the availability of genetic diversity required by US fruit and vegetable producers to remain successful and competitive in global markets. Outcomes include:

  • Gaps in PGRU collections filled
  • Optimized regeneration protocols and cultivation conditions
  • Healthy germplasm with genetic integrity
  • Optimized characterization and documentation methods
  • Publically available data and images for accessions
  • Updated PGRU Operations Manual and updated Crop Vulnerability Statements
  • Improved germplasm and cultivars

Data are submitted to PGRU’s germplasm curator and information management staff for formatting and uploading into GRIN-Global, or uploaded directly by the research team into public databases such as National Center for Biotechnology Information or Sol Genomics Network. This includes: phenotyping, i.e., characterizing NPGS accessions during routine regenerations in the field for highly heritable horticultural traits (“descriptors”), or through funding for evaluation of high priority traits, and genotyping high priority NPGS accessions. Crop-specific standard descriptors and research community standard sets of genetic markers will be used. 

The public is informed of PGRU through open house events and visits to the collections; we lead educational tours and discussions with primary, secondary, college and graduate students, growers, commodity groups, researchers, and individuals from botanical gardens, arboreta, and garden clubs. Stakeholders are also aware of our activities through our website (, GRIN-Global, local and national news, and media productions featuring our collections. PGRU continues to extend the outreach component of the USDA Organic Research and Extension Initiative funded project “Northern Organic Vegetable Improvement Collaborative (NOVIC)” by distributing germplasm, providing information on performance of varieties under organic conditions, and technology transfer for best management practices in producing quality vegetable seed.



Regional Research Project NE9 can be effective only through federal, state, and private cooperation. The federal agency ARS, through acquisition, maintenance, characterization, documentation, and distribution activities, will make plant genetic resources available for evaluation and utilization research. ARS will provide support, staff, facilities, equipment, and specialized technical assistance at both the regional and national levels. The SAESs provide facilities, additional support staff, equipment, utilities, and local assistance. The NE9 Regional Technical Advisory Committee (RTAC) will provide technical guidance in this effort. This committee is composed of an Administrative Advisor, Regional Coordinator, plus technical representatives invited to participate from each of the Northeastern SAESs plus the District of Columbia. ARS representatives from the National Program Staff, the National

Germplasm Resources Laboratory, and the PAGRP are also included on the committee as ex officio members. The names, affiliations, and areas of specialization of these individuals are presented in Appendices E and F. This committee has annual meetings with the PGRU staff at locations throughout the NE9 region which provides yearly review of genetic resources research in the region and provides technical advice to PGRU scientists.

Other committees contribute to the planning and management and are active participants in the NPGS. These include:

  1. The ARS Plant Germplasm Operations Committee (PGOC) evaluates and recommends foreign/domestic exploration proposals, and assists the NPGS, ARS National Program Staff and other officials with plans needed to manage the NPGS.
  2. CGCs have been established for 42 crops (or crop groups) to help advise the NPGS with regard to genetic vulnerability, gaps in current collections, operational procedures, evaluation needs, and current enhancement and utilization research associated with their specific commodity. 

Project scientists have monthly meetings to discuss progress in meeting milestones and to modify activities in order to obtain goals. Scientists have regular meetings with support staff to ensure all activities are coordinated and directed towards project milestones. Scientists within the USDA-ARS Geneva, NY Location meet on a regular basis to discuss new technologies and methodologies and their potential application to project research. An annual Plant Germplasm Operations Committee (PGOC) meeting provides a forum for NPGS scientists to discuss germplasm issues with each other and National Program leaders. Shared network folders are used for storage and use of common files, both documents and data. A SharePoint communication portal offered by the USDA-ARS OCIIO Web Branch as part of its ARSNet is used to facilitate communication. Our major source of stakeholder feedback is from the Crop Germplasm Committee (CGCs) members who meet annually to discuss germplasm user needs and concerns pertaining to the various crop collections. We also regularly discuss with our collaborators the research and regeneration activities through emails, conference calls, discussions at scientific meetings, and site visits. Progress towards meeting project milestones is reported annually in the project annual report (AD 421). Any changes in activities necessitated by unforeseen circumstances that will affect progress towards meeting project milestones are also documented in the project annual report.

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Volk, G.M., A.D. Henk, A. Baldo, G. Fazio, C.T. Chao, and C.M. Richards. 2015. Chloroplast heterogeneity and historical admixture within the genus Malus. Amer. J. Botany 102(7):1-11.

Volk, G.M., A.D. Henk, P.L. Forsline, A.K. Szewc-McFadden, G. Fazio, H. Aldwinckle, and C.M. Richards. 2016. Seeds capture the diversity of genetic resource collections of Malus sieversii maintained in an orchard. Genet. Resour. Crop Evol. doi:10.1007/s10722-016-0450-8

Volk, G.M., M.M. Jenderek, and C.T. Chao. 2017. Prioritization of Malus accessions for collection cryopreservation at the USDA-ARS national Center for Genetic Resources Preservation. Acta Hort. 1172:267-272.

Wan, Y., H.R. Schwaninger, A. M Baldo, J.A. Labate, G.Y. Zhong and C.J. Simon. 2013. A phylogenetic analysis of the grape genus (Vitis) reveals broad reticulation and concurrent diversification during Neogene and Quaternary climate change. BMC Evolutionary Biology 13:141.

Wang, A., H. Aldwinckle, P. Forsline, D. Main, G. Fazio, S. Brown, and K. Xu. 2012. EST congig-based SSR linkage maps for Malus x domestica cv ’Royal Gala’ and an apple scab resistant accessions of M. Sieversii, the progenitor species of domesticated apple. Mol. Breeding 29:379-397.


Land Grant Participating States/Institutions


Non Land Grant Participating States/Institutions

USDA ARS, USDA-ARS/Plant Genetic Resources Unit
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