Duration: 10/01/2013 to 09/30/2018

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

The Need: America's abundant and inexpensive supply of food and fiber is based on a productive and progressive agricultural system. The foundation for this productivity has been based on scientific knowledge and exploitation of useful genetic diversity for developing new, higher quality cultivars that can resist pests, diseases, and environmental stresses. However, genetic diversity for various crops is diminishing, in a large part due to the extensive use of modern cultivars with genetic uniformity but a noteworthy lack of genetic diversity for developing new traits and combating against new biotic and abiotic stresses.


The genes that are needed to provide a continued source of new varieties that produce higher yields with better quality and nutritional value, and better withstand pests, diseases, and abiotic stresses can only come from diverse plant germplasm. Most of the food crops important in the American diet have their origins in other parts of the world. Genetic diversity of plant species has evolved in centers of origin wherever this has occurred in the world. This source of different genes continues to be essential for plant breeders and other scientists to breed new varieties that are important to American consumers today. To meet this need and sustain the future success of American agriculture, the United States Department of Agriculture, Agricultural Research Service (USDA, ARS) has established a National Plant Germplasm System (NPGS) in which hundreds of thousands of plant germplasm collections are preserved. USDA-ARS Plant Genetic Resources Unit (PGRU) at Geneva, New York is a vital part of this system and preserves the germplasm of apple, grape, tart cherry, Cruciferous vegetables, onion, tomato and many others.


Continuing safeguarding these germplasm is critical to meeting future production challenges of these crops in the United States, including many U.S. northeastern states where these crops are a key source of income for farmers. Many northeastern State Agricultural Experiment Stations (SAESs) have research and extension responsibilities for these valuable commodities and access to critical germplasm resources is essential for progress in research and crop improvement of these crops. While preserving this germplasm is critical, evaluation and characterization of this germplasm and making it more accessible to breeders and researchers are also important.


There are ongoing efforts nationwide to promote increased consumption of fruits and vegetables because of their nutritional and therapeutic value to the human diet. PGRU will contribute to these efforts because many fruit and vegetables we preserve, such as apples, grapes, broccoli, onion and tomato, contain certain compounds, such as polyphenolics or glucosinolates, that have been linked to reduced risk of various chronic conditions or life-threatening diseases. PGRU can further enhance the success of these efforts by evaluating, characterizing and identifying various plant trait attributes with health benefits in these germplasm. This NE-9 Project has been an important source of funding for sustaining the PGRU germplasm activities in the past and it will become even more important in the future.


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 Northeastern United States and worldwide:

1. Strategically expand the genetic diversity and improve associated information for the fruit and vegetable genebank collections held at the PGRU in Geneva, NY for use in the Northeast, the United States and the World.

2. Conserve and regenerate the accessions in the genebank to ensure long-term availability of this germplasm to distribute for research and crop improvement to meet the evolving needs of the United States and the World. This is especially important in the face of climate change and increasingly limited water resources for increased production of nutritious food products. This requires ensuring proper regeneration to maintain disease free, high viability seed and clonal propagules while maintaining trueness to type of the 20,671 lines maintained at Geneva, NY.

3. Develop better collection and conservation strategies for this germplasm on the basis of their genetic diversity patterns, geographic distribution and phylogenetic and taxonomic relationships with closely related species.

4. Increase the utilization efficiency of the germplasm collections through phenotypic and genotypic characterization and evaluation of the germplasm held in the collections for high-priority traits, especially resistances to biotic and abiotic stresses and nutritional traits.

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


Note: Objectives 3-5 require the cooperation of collaborators. Forging the links between PGRU and reliable and productive cooperators should be viewed as part of these objectives.


Importance of the Work: The fruit crops maintained in the PGRU account for about 49% of the value of U.S. fruit and vine crop production and the vegetable crops account for 44% of the value of production of vegetables(Appendix A, Tables 1-2). The fruit and vegetable crops conserved at the PGRU are also highly valuable world wide (Appendix A, Tables 3-4).

Previous and current versions of this project (NE009) have made considerable contributions to the vegetable and fruit industry through provision of the basic genetic material for developing improved varieties with higher and more stable yield, disease and insect resistance, and improved quality. For example, germplasm of tomato has been used extensively for resistance to pests and diseases and genes from the apple collection have been used for resistance to apple scab, fire blight, blue mold, bitter rot, superficial scald, wooly apple aphids and drought.

In the past five years, this project has acquired 925 new accessions of rare or endangered samples of germplasm for incorporation into the NE-9 collections. Many of these accessions are native to parts of the world where natural habitats are being destroyed as populations increase and move into underdeveloped lands. The NE-9 project currently maintains 9,571 accessions of rare and valuable fruit crops such as apple (7,811), grape (1,485), and tart cherries (121). The clonally-propagated apple and tetraploid tart cherry accessions are backed up in cryogenic storage based on the protocols developed with the USDA, ARS, National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, CO. Also maintained are 12,589 accessions of vegetable crops such as tomato, onion, cabbage and other cole crops, and a number of smaller collections including asparagus, celery, buckwheat, etc. Without the acquisition and maintenance of these materials, erosion of habitats in centers of origin of these and other important crops would surely result in extinction of much or most of this important genetically diverse material that has evolved over millions of years.


While maintaining the germplasm, scientists working on this project also characterize it for useful traits to make the material more readily usable by plant breeders and others who request accessions from the collections. Much of this characterization and evaluation is performed in collaboration with scientists from the NE-9 region and also other regions in the United States and even with scientists from other countries. Research into quality and health-beneficial traits was initiated at the request of partners in the crop CGCs and other users and information has started to be compiled for the core collections of the tomato, apple, and grape germplasm.


During the last five years of the NE-9 project, 29,515 seed samples were distributed for the vegetable crops and 39,347 samples of budwood, cuttings, pollen, DNA as well as seed of wild species for the fruit crops. These samples have been sent from 9,959 accessions of vegetable crops and 4,078 accessions of fruit crops. In the states covered by NE-9 there were 3,441 seed samples from 2,671 accessions distributed for the vegetable crops and 18,940 samples from 3,770 accessions distributed for the fruit crops.


Technical Feasibility and Value of a Multi-state Project: Acquisition, conservation, and characterization of germplasm collections are activities that by their nature are best done at a central location rather than being done by individual states, which would result in inefficient duplication of efforts. An integrated team approach involving state partners and the PGRU allows for an efficient conservation of fruit and vegetable germplasm while plant breeders and other scientists from individual states take the lead in characterization and evaluation, especially for high-priority quality traits and selection for biotic and abiotic resistance/tolerance. Utilization of germplasm for crop improvement by geneticists at individual state experiment stations capitalizes on the genetic resources conserved and the characterization/evaluation information maintained by the PGRU.


The PGRU is supported by the USDA-ARS and is best positioned to take maximum advantage of additional multi-state funds from the NE-9 project for conservation and characterization/evaluation of fruit and vegetable germplasm of important crops to the Northeastern region. Additional funds from NE-9 provide the critical resources for better management of the collection and quality service of germplasm distribution. It also supports the major efforts in screening 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 SAES within this region.


Impact: Genes acquired from the NE-9 collection will continue to prove useful in breeding disease-resistant cultivars of fruit and vegetable crops, thereby stabilizing production and reducing dependency on agricultural pesticides. This will become increasingly important with the rapid emergence of exotic diseases and the growing emphasis on sustainability of fruit and vegetable production while reducing deleterious environmental effects. The collections at Geneva, NY will be used as sources of resistance to environmental stresses, such as high temperatures that reduce fruit set, and also as sources to increase the range of adaptation of the fruit and vegetable crops. This will prove useful to meet the changes in environmental conditions that the world now faces. With the growing public acceptance of the relationship between diet and health, many of the plant species in the NE-9 collection are increasingly being studied for the health-promoting phytochemicals they contain that are important in the human diet to reduce the risk of cancer, cardiovascular disease, and other chronic or life-threatening conditions. Finally, maximizing the use of available germplasm at the PGRU will help to keep U.S. producers competitive in a world marketplace where there is now 'One World' competitiveness within agriculture. Examples of use of the germplasm collections at PGRU during the current NE9 project include identification of accessions of radish and cabbage as sources of natural pigments for breeding programs aimed at emerging markets, identification and use of a wild tomato germplasm accession to provide late blight resistance in cultivated tomatoes, and the use of apple germplasm characterization to identify multiple disease resistances and improved plant architecture being used in new rootstocks.


Germplasm from the NE-9 collection held at PGRU has proven useful in developing improved cultivars of fruits and vegetables in the Northeast, the United State and the World:

• Phylloxera resistant grape rootstocks and hybrids derived from North American wild germplasm were instrumental in rescuing the European wine industry.
  
• The recent spread of grape cultivation throughout the U.S., 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 V. vinifera could not previously be grown.
  
• The PGRU was the only institution that maintained the 100+ founding ancestors of popular apple cultivars.
  
• Genes 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 trace their genes to the PGRU apple collection.
  
• 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 Geneva tomato collection for bacterial speck, spotted wilt virus, tobacco mosaic virus, leaf mold, fusarium wilt, verticillium wilt, light blight, and nematode resistance have been bred into modern varieties.
  

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

• Biochemical characterization of tomato germplasm at Geneva will be exploited by breeders for enhancement of fruit quality for flavor, texture, and health beneficial components such as vitamins, minerals, and cancer-preventing compounds.
  
• Onion germplasm from Geneva is being used to develop Iris Yellow Spot Virus resistance, considered the number one imminent threat to onion production.
  
• Germplasm of apple progenitors from Central Asia is being screened for important disease resistances such as fire blight and scab and is being incorporated into breeding programs.
  
• Grape germplasm from Geneva will continue to be used in developing new grape cultivars for better resistance to biotic and abiotic stress.
  
• The fruit and vegetable germplasm collection in Geneva is being screened for medicinal and nutraceutical properties for development of cultivars that will improve the health benefits of consumption.

Related, Current and Previous Work

The Regional Research Project NE-9 partially supports and complements service and research activities encompassed within the scope of the responsibilities of the USDA, ARS, PGRU at Geneva, NY. Despite similarity among missions at various ARS locations, unique regional interests as well as crop responsibilities determine the specific efforts of a location. The major crops supported by the Regional Research Project NE-9 are onion, vegetable Crucifers (cabbage, broccoli, cauliflower, kale, etc.), winter squash, tomato, apple, tart cherry, and cold-hardy grape. Responsibility for U.S. national germplasm collections of these crops lies solely with the PGRU.


Most crops of commercial significance in the northeastern U.S. are of exotic origin. NE-9 support has enabled the ARS and other federal agencies, the SAESs of the 12 northeastern states, and other cooperators, to engage in a coordinated effort to conserve, characterize, and utilize plant genetic resources. The continued demand for plant genetic resources underscores the importance of maintaining collections which preserve the vast reservoirs of genes needed to fulfill the plant breeding and research activities so critical to the economic well-being of the Northeast and other U.S. regions. Also, increasing restrictions on access to germplasm in other countries makes preservation of the existing germplasm collections in the U.S. imperative. The central issue is how well each collection represents the diversity of each genus in nature and how it succeeds in meeting the needs of the user community. Therefore, qualitative factors supersede the need for sheer quantity of accessions. In this plan, those qualitative factors are addressed that maximize: 1) the ability to define and fill gaps in the collection; 2) development of characterization and evaluation data sets on each accession that are readily accessible, and the use of new research tools to refine the collection not only by adding to the collection, but also by eliminating redundancy; and 3) collaboration with the user community to enhance utilization of the collection. With the actual or potential loss of some of our most effective herbicides, fungicides, and insecticides, the need for novel sources of resistance or tolerance genes will increase. Also, the development of new biotic stresses such as Iris Yellow Spot Virus (IYSV) in onions and the recurrence of late blight epidemics in tomato require a diverse source of germplasm for development of genetic resistance (Schultz et al., 2010; Diaz-Montano et al., 2010). Furthermore, changing landscapes, urbanization, irrigation, and other habitat changes increase the need for plants having tolerances to more stressful environments.


Acquisition:


In a survey by the General Accounting Office (1997), all 40 Crop Germplasm Committees (CGCs) stated that acquisition of additional germplasm is a moderately to extremely important activity and about one-half of the CGCs reported that wild and weedy relatives are under-represented in germplasm collections. We agree that targeted additions to all of the PGRU's collections are needed. Because of changes in the international political climate as well as ramifications of the Convention on Biological Diversity, continued plant exploration and exchange is needed. The PGRU in cooperation with Animal and Plant Health Inspection Service (APHIS) also needs to take an active role in developing improved quarantine procedures for both import and export of germplasm. This was an area that the General Accounting Office (1997) survey also highlighted as needing additional attention.


Significant accomplishments in the period 2007-2012 include:


-We have added 97 accessions annually on average (Appendix A, Table 5.


-In 2012, we acquired approximately 900 lines of radish from Monsanto that are currently being processed before being added to the collection. These include some unique characteristics such as interior red hypocotyl.


-55 new Malus accessions were added to the collection including 29 foreign introductions.


-140 Malus sieversii seedlings from Kazakhstan and 27 M. orientalis seedlings were added to the permanent collection.


-39 new accessions were added to the grape collection from Cornell University and other sources within the U.S.


-16 accessions were added to the tart cherry.


Maintenance and regeneration:


For seed accessions, both secure backup and distribution are dependent upon regeneration activities. Plans for regeneration and NCGRP backup of the major seed collections are in place, as are plans for further evaluation studies of clonal crops. More attention has been paid to the PGRU's minor seed crops, such as buckwheat (an important crop in Japan and a crop for which we have a breeder/researcher at Geneva, Thomas Bjorkman, Cornell University), artichoke, and radish. Regeneration plans to make the buckwheat and radish completely available are nearly complete. Core subsets need to be established for some of the major seed crops, such as winter squash, vegetable Crucifers and onion. For clonal crops, we use cryopreservation as backup storage of Malus and tart cherry at NCGRP. We store wild Malus and Vitis seed accessions in cold storage at the PGRU and NCGRP. Research on strategy for long term backup storage of Vitis is being investigated by NCGRP.


Significant accomplishments in the period 2007-2012 include:


-Maintained a routine system for monitoring seed viability for the vegetable crops to ensure that high quality seed is always available.


-Added and replaced over 2,000 backups at the NCGRP for the tomato germplasm collection, which is now currently 99% backed up at the NCGRP.


-Regeneration resulted in 1,234 accessions of all crops becoming available for distribution and provided seed for samples to be prepared to allow back up of all these accessions at the NCGRP, assuring their long term availability.


-Used a Specific Cooperative Agreement (SCA) with Las Cruces of New Mexico State University for regeneration of short-day onions.


-Extended a Trust Fund Agreement with University of California, Davis for an additional two years to support the CM Rick Tomato Genetics Resource Center (TGRC) of unique wild and genetic stock tomato accessions.


-1,939 seedlings of 10 wild Malus species from collections in Armenia, China, Former Soviet Union, Georgia, Kazakhstan, and Turkey were planted from 2000-2005 at the PGRU. 27 M. orientalis seedlings were selected for permanent collection to represent the genetic diversity of the populations in the collections.


-We have added 67 individuals representing 12 wild Malus species to the original Malus core of 190 accessions established in 1992.

-2,336 Malus accessions out of 2,365 accessions in permanent collections are in cryo-backup at the NCGRP (99%). 75 tart cherry accessions out of 121 (62%) are backed up at the NCGRP.


Characterization:


Accessions having little or no characterization, evaluation, or passport data tend not to be ordered for use by cooperators. Regenerations are used to characterize vegetable collections as much as possible for descriptor lists developed by the relevant CGCs. A core subset have been established for the tomato collection and needs to be established for some of the other major seed crops, winter squash, vegetable Crucifers and onion. For clonal crops, we have established core collection subsets for both apples and grapes. We will continue to focus on the core collection for trait characterization. Both descriptors and traits of horticultural significance will continue to receive top prioritization for trait characterization.


Significant accomplishments in the period 2007-2012 include:


-Completed characterization through 2011 of 268 tomato, 306 onion, and 244 squash accessions, including adding 1971 digital images of fruit and foliage during regeneration of 1,433 accessions of all seed propagated crops.


-In addition to minimal descriptors as defined by the tomato CGC, characterization of tomato (Solanum lycopersicum) regenerations now includes a pipeline to measure fruit size, shape and color through digital imaging (Gonzalo et al., 2009), followed by assays for vitamin C, titratable acids, brix and lycopene.


-General, geographical, and diversity core collections of tomato were established based on Villand et al. (1998). These core collections have been established using strategies as discussed by Brown (1989) and Kresovich et al. (1995). These have been expanded into a larger PGRU core collection of tomato consisting of 185 accessions assembled and genotyped with a minimum of 17 SNPs.


-All 185 accessions of the tomato core set have been phenotyped in replicated trials. Minimal descriptors as defined by the CGC were collected. Tomato Analyzer (Gonzalo et al., 2009) software was used to estimate size, shape, and flesh color (Figure 1). Homogenized fruit color was measured using a tristimulus colorimeter, vitamin C content using a commercial kit (SHIMA Laboratories Co., Japan), brix using a refractometer, and titratable acids with a NaOH assay (Figure 2).


-Wild tomato Lycopersicon peruvianum has been reclassified into four new Solanum spp. taxa as per Peralta et al. (2005, 2008).


-Genetic diversity was evaluated and core collections were established for Solanum section Juglandifolium, through a SCA with R. Chetelat at the TGRC.


-We evaluated wild Lycopersicon species for resistance to bacterial speck race 1 resistance with Gene Miyao, University of California, Davis but found no sources of resistance.


-Phyto-nutrient content of Allium fistulosum was evaluated with C. Sams and D. Kopsell at the University of Tennessee, Knoxville to characterize carotenoids found in scallion tissues


-We are evaluating onion accessions for IYSV and onion thrips resistance/tolerance through a CGC grant with C. Cramer at New Mexico State University and H. Schwartz at Colorado State University and have found three accessions with fewer thrips and two that showed less IYSV damage than other accessions in the trial.


-We screened tomato germplasm for resistance to target spot caused by Corynespora cassiicola through a CGC grant with G. Vallad at the University of Florida.


-ECOTILLING was used for tomato single nucleotide polymoprhism (SNP) marker development in a CGC grant with J. Edwards, University of Florida. He published 119 polymorphisms, 39 of which were between cultivated tomato lines.


-We added a new ploidy level descriptor to the Malus GRIN database in 2012.


-We recorded approximately 2,500 bud break date, bloom date and veraison date of all Vitis accessions at the PGRU in 2011. This information is useful to grape breeders in North America due to the impact of global warming and reduction in winter chilling accumulation (White et al., 2006).


-In collaboration with M. Fuchs, Plant Virologist, Cornell University, we indexed all of the PGRU Vitis accessions using enzyme-linked immunosorbent assay (ELISA) for 10 major grape viruses and 7 strains.


Documentation:


The Genetic Resources Information Network (GRIN) National Database is the focal point for PGRU germplasm information documentation. Accessions, inventory, order, and characterization data are continually updated to provide the most current PGRU information possible. A major effort was initiated to produce digital images of all crops at various stages of development to show their characteristics which are then uploaded to the GRIN National Database where they may be accessed via the Internet. A new version of GRIN, named GRIN-Global, has been under development for the past several years. It consists of two applications: a revamping of the Public Interface which is to include an improved ordering process, and the Curator Tool for the maintenance of the GRIN database.


Significant accomplishments in the period 2007-2012 include:


-956 tomato accessions and 533 onion accessions have been characterized and 2,000 images from tomato, onion, and squash were taken.


-221 of 257 Malus core accessions have fruit digital images (86%). 1,760 accessions out of 2,356 Malus accessions in the permanent collections have fruit digital images (75%). 620 Vitis accessions have fruit digital images with a grid background and 467 have images from the field. 891 Vitis accessions have flower digital images from the field with or without grid background. We collected 2,032 digital images of the top and bottom of the leaves for Vitis accessions.


-An additional file and print server with Windows Server 2008 has been added to the network. The current Windows Server 2003 will be phased out in 2012.


-The PGRU staff also updates web pages for the Northern Organic Vegetable Collaborative grant project.


Distribution:


Distribution of germplasm is primarily through requests that are received through web access to GRIN. The PGRU distributes germplasm in four different forms: seeds, dormant cuttings, pollen, and green cuttings. More rapid movement of germplasm through the quarantine system needs to be encouraged by the PGRU, for both seed and clonal crops. The PGRU, in collaboration with the Plant Exchange Office, must be prepared with a reasoned response to actual or potential restrictions to germplasm importation and exportation that may result from the Convention on Biological Diversity and the International Treaty on Plant Genetic Resources for Food and Agriculture of 2004.


Significant accomplishments in the period 2007-2011 include:


-Automated order processing has been improved and updated to a shopping cart system


-The PGRU distributed 21,498 seed accessions (Appendix A, Table 6) with 29,515 samples (Appendix A, Table 7) in the form of seeds.


-The PGRU distributed 12,148 clonal accessions (Appendix A, Table 8) with 39,347 samples (Appendix A, Table 9) in the form of scions, seed, fruit, pollen, DNA, leaves for DNA extraction, or use of trees for crossing.


-The PGRU distributed 648 orders in the Northeast, representing7,898 accessions (Appendix A, Table 10) with 13,629 samples (Appendix A, Table 11) in the form of scions, seed, fruit, pollen, DNA, leaves for DNA extraction, or use of trees for crossing in the Northeast region.


-Tracking of seed orders has been accomplished using SharePoint as a central repository of all information and documents pertaining to NE-9 orders.


Research:


To complement current conservation efforts, problem-oriented research has been conducted for facilitating improvements in germplasm acquisition, maintenance, and characterization. Research focusing to increase the effectiveness and efficiency of the management of the PGRU's germplasm is an essential component in achieving the unit's service goals (References cited in Appendix B). The primary goal of the research has been to describe intra- and interspecific genomic variation and to define genetic relationships among individuals, populations, and species. Gene bank curators have used the results to establish and maintain useful and representative crop collections and core subsets based on the integrated information representing DNA sequences, genes, genotypes, and phenotypes. Such information has also been used to determine collection strategies for wild foreign germplasm in the field, and in designating domestic populations of wild species for in situ preservation.

The personnel associated with the Regional Research Project NE-9 cooperate and participate in activities associated with 11 relevant Crop Germplasm Committees (CGCs) of the NPGS. These activities include planning and participating in plant germplasm exploration/exchange proposals and conducting germplasm evaluation studies. In addition, research carried out by current and former members of the Regional Technical Advisory Committee for NE-9 has interfaced productively with the goals of the NE-9 project at the PGRU (see Appendix C for a list of relevant publications).


Significant accomplishments in the period 2007-2012 include:


-We demonstrated that tomato SNP markers were unbiased (Labate et al. 2009b). Therefore, the hundreds of polymorphisms that we previously identified can be applied to mapping, fingerprinting and diversity studies.


-We found that genetic diversity of tomato is similar to other self-fertilizing crops (1-2 SNPs per kb) and 5-10% of genes showed evidence of introgression from wild tomato species (Labate et al. 2009a; Labate et al. 2009b). We also found that geographic centers of origin showed slightly higher diversity and lower coefficients of inbreeding, but most diversity (91%) was not restricted within particular geographic regions and diversity increased over time due to introgression breeding (Labate et al. 2011).


-The tomato core set is comprised of 50 PGRU geodiversity/landrace accessions, 47 fruit shape diversity lines, 36 vintage and 52 obsolete varieties. Geodiversity and landraces were represented by Mexico and Central America, Asia, Europe, U.S. and Canada, and S. America, and included pre-introgression (1930s), post-introgression (late 1940s to 1960s), and modern (1980s to present) samples. SNP genotyping revealed the obsolete varieties to be relatively the most genetically diverse (unpublished results). These accessions represent germplasm from the 1950s through 1990s for which the associated Plant Variety Protection (PVP) had expired within one of the five decades. The core set serves as a representative sample of broad phenotypic and genotypic diversity available in PGRU tomato germplasm.


-We completed sequencing 47 loci within five wild tomato species and compared alleles to cultivated tomato to look for evidence of linkage drag. Of the 47 markers surveyed, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers originated from natural hybridization with S. pimpinellifolium (manuscript in review). The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm.


-Broccoli and cauliflower are ancient polyploids. When applying molecular markers, allelism can be difficult to distinguish from paralogous copies. We resequenced 48 gene fragments in inbred parent lines and one progeny line of the N x B mapping population (Labate et al. 2008). The tested markers included candidate genes for agronomic traits and ecological adaptation. The polymorphisms can be used to verify allelism and will also be valuable for marker-assisted breeding.


-We successfully fingerprinted a diversity panel of squash accessions using SBAP (Sequence Based Amplified Polymorphism) markers (Robertson et al. 2004). We have archived several-thousand leaf tissue samples stored at -800C for genotyping.


-We published a software tool AlleleCoder and a method that analyzes DNA sequences collected from plant samples and performs Principal Components Analysis (PCA) to create a 3-D, color-coded graph (Baldo et al. 2011). Distances between the points, which represent individual plants, characterize the genetic relationships among the samples. This tool will aid in the conservation and exploitation of new alleles for breeding and improvement.


-SSR fingerprints of 8 loci for 1,274 apple were uploaded into GRIN in 2009. 19 SSR markers and chloroplast loci were used to study 264 wild Malus accessions in collaboration with NCGRP. The SSR marker data were used to determine the genetic diversity of wild Malus species, identify accessions that represent the genetic diversity of the wild populations and select them for the permanent collection and possibly the Malus core, identify duplicated accessions, provide new sources of traits of interest such as disease resistance (Forsline et al., 2008), study the evolution and domestication processes of modern apples, and identify parents for future breeding efforts (Richards et al., 2009a; 2009b; Volk et al., 2008; Volk et al., 2009a; 2009b; Wang et al., 2012)


-Seven M. sieversii seedlings with high disease resistance identified at the PGRU were used as male parents in crosses with Royal Gala as the female parent to produce seven F1 mapping populations. These seven populations with size ranging from 101 to 222 individuals growing at the PGRU since 2004 are being used in genetic mapping of different traits such as resistance to fire blight, apple scab (Wang et al., 2012), blue mold (Janisiewicz et al., 2008), bitter rot (Jurick et al., 2011), superficial scald (a physiological disorder, drought tolerance (Bassett et al., 2011), morphological traits and growth characters (Bai et al., 2012), phenological traits and fruit quality traits (Xu et al., 2011). Many of the disease resistance genes identified from M. sieversii are new sources of resistance that could be used in future apple breeding efforts.


-We have studied the natural variation of 36 phenolic compounds in ripe berry of 344 Vitis vinifera accessions at the National Clonal Germplasm Repository (NCGR) at Davis, CA and the PGRU (Liang et al., 2011). We also compared 48 phenolic compounds in ripe berry of 147 accessions from 16 wild Vitis species (Liang et al., 2012a). 28 phenoloic compounds in the seeds of 102 accessions from 17 Vitis species were also studied (Liang et al., 2012b). This effort will contribute to the development of a database of health and nutrition related metabolites in the USDA Vitis germplasm.


-We investigated the causal relationships among total phenolics, total flavonoids, total antioxidant activity and antiproliferative activity of 24 representative V. vinifera accessions.


-Powdery mildew and downy mildew resistance of the entire Vitis collection at the PGRU were analyzed by L. Cadle-Davison, Grape Genetic Research Unit (Cadle-Davison et al., 2011; Cadle-Davison, 2008). Resistance was race-specific. There was also variation in resistance within individual Vitis species.


-SSR fingerprints at 8 loci of 955 Vitis accessions were uploaded into the GRIN database in 2008. Fingerprints of first and second vines were compared to identify discrepancies between the two vines of the same accession as well as redundant accessions in the collections.


-In collaboration with researchers in China, we studied the genetic structure, relationships and evolutionary history of Vitis using sequences of 27 gene fragments from 43 Vitis species. We found that grapes formed a well-connected gene pool until it fragmented due to climatic and tectonic changes millions of years ago. We identified candidate markers for species identification and corrected the names of misidentified accessions in the germplasm repositories at the NCGR and the PGRU (Simon et al., 2008).


-We initiated a genotyping by sequencing (GBS) marker study of Malus accessions at the PGRU in 2012 with collaboration from NCGRP, Cornell University and Nova Scotia Agricultural College. Over 1,500 Malus accessions including M. domestica, all possible progenitor wild species of modern apples and other wild Malus species are included in the study. The GBS technique involves high throughput sequencing of short fragments in multiplexed format, and has been used successfully for genotyping species that lack a published reference genome (Cronn et al. 2012; Davey et al. 2011; Gao et al. 2012).


-In collaboration with K. Xu, Cornell University, we are characterizing the alleles of the MdACS3 gene in the Malus core collections. MdACS3 is a gene crucial for regulating the apple fruit shelf life (Wang et al., 2009). The goals of this research are to develop MdACS3 gene specific PCR based markers for future detection and identification of accessions with homozygous null alleles that could be used in breeding prolonged shelf life in apple.

Objectives

1. Strategically expand the genetic diversity and improve associated information for the fruit and vegetable genebank collections held at the PGRU in Geneva, NY for use in the Northeast, the U.S. and the World.
   
2. Conserve and regenerate the accessions in the genebank to ensure long-term availability of this germplasm to distribute for research and crop improvement to meet the evolving needs of the U.S. and the World. This is especially important in the face of climate change and increasingly limited water resources for increased production of nutritious food products. This requires ensuring proper regeneration to maintain disease free, high viability seed and clonal propagules while maintaining trueness to type of the 20,671 lines maintained at the PGRU.
   
3. Develop better collection and conservation strategies for this germplasm on the basis of their genetic diversity patterns, geographic distribution and phylogenetic and taxonomic relationships with closely related species.
   
4. Increase the utilization efficiency of the germplasm collections through phenotypic and genotypic characterization and evaluation of the germplasm held in the collections for high-priority traits, especially resistances to biotic and abiotic stresses and nutritional traits.
   
5. Develop novel germplasm that integrates diverse useful genes from various resources and breed, release, maintain, and evaluate improved germplasm and cultivars.
   

Methods

NE-9 will continue to serve as a conduit for movement of valuable plant genetic resources from worldwide origins to the northeastern states as well as the entire U.S. (see Appendix A, Tables 6-11). The objectives and the procedures of the project are organized as a continuum. Objectives 1 and 2 will be performed primarily by personnel of the PGRU, whereas latter objectives (3-5) will be in collaboration with cooperators associated with NE-9 activities. The PGRU is relatively well equipped with facilities and equipment for conducting its service and research activities (Appendix D). 1. Strategically expand the genetic diversity and improve associated information for the fruit and vegetable genebank collections held at the PGRU in Geneva, NY for use in the Northeast, the U.S. and the World. Acquisition To ensure the acquisition of broad genetic diversity, the curators work closely with relevant CGCs to determine germplasm needs for these crops. Mapping the locations of existing accessions identifies geographic gaps. Genetic and phenotypic gaps are determined by characterization data. We will complete the passport database in GRIN through acquisition reports, Plant Introduction literature (books now digitized) and trip reports. Germplasm will be collected using optimum sampling strategies (Allard, 1970; Hawkes, 1975; Marshall and Brown, 1975; Sykes, 1975; Zagaja, 1970). Because of the increasing importance of heirlooms for crop improvement for breeding for organic production, we will add improved varieties for organic production. Activities will be intensified to obtain wild and weedy relatives from other genebanks. Interactions with organic and small farms will be used to identify important heirloom germplasm to add to the collections. Material transfer agreements (MTA) will be used where necessary to obtain new cultivars and introgressed populations. Breeders will be contacted to obtain introgression populations for maintenance and distribution that will be maintained by a modified single seed technique (Brim, 1966) to maximize available genetic variability. Heirloom apple cultivars from American collectors and wild Malus species from arboreta in the U.S. will be surveyed along with collections of elite and heirloom cultivars in European genebanks. Cider apples that represent a unique gene pool acquired from Spain will be added to the collection. We will target four wild Malus species in North American for collection with cooperation from the NCGRP. We will also seek collection opportunities for landrace apple varieties in Turkey and wild Malus species and modern Chinese Malus varieties in China. We have minimal representation of 12 North American Vitis species. A 2012 Midwest and southeast U.S. collection trip by scientists from the Grape Genetics Research Unit at Geneva, NY and the Julius Kühn-Institut, Federal Institute for Grapevine Breeding, Germany significantly increased the seed collections of V. labrusca and V. aestivalis. Seedlings from the two species are being evaluated for traits such as cold dormancy. Individuals representing the genetic diversity of the populations and with unique traits will be included in the permanent collections at the PGRU. Collection trips for other native North American Vitis species are planned . We will also seek opportunities to collect Vitis materials in Mediterranean regions and wild Vitis species in China. For fruit and vegetable crops, duplicates and gaps in the collections will be assessed by GBS and other genotyping methodologies. For tomato, a minimum of two plants per accession will be genotyped for multiple accessions that were inferred to be duplicates based on passport information. Statistical methods will be used to estimate how genetic diversity is partitioned within and among plants, accessions, and groups (cultivars). Documentation The GRIN National Database has been established as the sole and central source of germplasm information. A major effort is also underway at the PGRU to produce digital images of all crops at various stages of development to show their characteristics. They are uploaded to the GRIN National Database where they may be accessed via the Internet. A new version of GRIN, named GRIN-Global includes a revamping of the public interface including an improved ordering process and easier access to passport and evaluation data is expected the end of 2012. We will suggest to the staff of the GRIN development team the development of a system of automatatic notifications of important users of the collections whenever there is a new upload of characterization data. Site data and evaluation for morphological traits is done while on collection expeditions for new wild germplasm. Similarly, evaluation for morphological traits has been done for the main field collection of clones and the seedling grow outs by observation and analysis of living plants growing in orchards and vineyards. Digital imaging completed on vegetative and reproductive organs is made available through GRIN. The relevant CGCs have defined priority descriptors for apple, grape, tart cherry, tomato, onion and cabbage. A large list of descriptors has been uploaded into GRIN and CGCs have defined many of these to be priority descriptors. Phenotypic data have been uploaded into GRIN. Evaluation data from collaborators is checked for accuracy and proper linkage to accessions and uploaded into GRIN. Evaluations for traits such as disease resistance (including development of molecular markers for specific disease-resistant genes), pest susceptibility, nutrient content, and stress tolerance are carried out by cooperators. Areas of evaluation emphasis in recent years include screening for disease resistances, cold hardiness, leaf hairiness, and anti-oxidant concentrations. Many of these evaluations are funded through the CGCs using crop evaluation proposals funded by the NPGS. Molecular genotype data will be uploaded into GRIN according to recent protocols adopted for this procedure (C. Richards and G. Volk, unpublished), but implemented in GRIN. In addition, relevant data will be uploaded to GenBank, and/or organism-specific databases such as the Genome Database for Rosaceae (GDR), and cross-linked between respective databases wherever possible. 2. Conserve and regenerate the accessions in the genebank to ensure long-term availability of this germplasm to distribute for research and crop improvement to meet the evolving needs of the U.S. and the World. This is especially important in the face of climate change and increasingly limited water resources for increased production of superior food products. This requires ensuring proper regeneration to maintain disease free, high viability seed and clonal propagules while maintaining trueness to type of the 20,671 lines maintained at the PGRU. Conserve and Regenerate In the case of vegetable seed crops, when seed supply is reduced below 1,500 and/or germination below 60% the accession will be marked for regeneration. Routine monitoring of germination of accessions will be conducted (every 15 to 25 years, based on species) and any accession where the germination falls below 60% will be regenerated. Priorities for regeneration are for Crucifers (especially biennials) and Cucurbits because these collections have the most need for regeneration due to low viabilities. Seed regenerations are conducted using the appropriate pollination techniques and pollinators. During the next five years, the PGRU plans to regenerate an average of 50 tomato, 50 Brassica, 50 onion, 40 Cucurbits, and 25 other genera annually. Duplicate seed of most accessions are backed up in cold storage or cryopreservation at the NCGRP. An SCA will be used to regenerate short-day onions at New Mexico State University. Continued funding to support regenerations of tomatoes at the Rick Tomato Genetic Resources Center at Davis, California is dependent on developments with the ARS budget. Collection health is assured using Integrated Pest Management and conventional practices. In apple, to better reduce fire blight incidence most of our apple plantings are grown exclusively on EMLA 7 rootstocks. Also, prohexadione calcium (Apogee) that reduces shoot growth is applied annually to all apple plantings to minimize fire blight incidence (Forsline and Aldwinckle, 2002). About 193 seedlings of M. sieversii from Kazakhstan will be added to the collection. Grape accessions, each with 2 vines, are grown on their own roots. Most of these are cold-hardy and in good conditions in the repository. Virus infection is a significant problem we will need to resolve for providing clean grape accessions free from virus to germplasm users. We will continue collaborating with M. Fuchs of Cornell University for Vitis virus indexing (Al Rwahnih et al., 2009; Giampetruzzi et al., 2012). The tart cherry collection is preserved in duplicates in a field planting. The rootstock of choice is the commercially-acceptable MxM2. Control of cherry leafspot is our greatest challenge to prevent mid-summer defoliation. Apple and tart cherry are backed up with cryogenically stored dormant buds at the NCGRP. As needed, backups will be replenished. We will continue cooperation with NCGRP to conduct research on shoot tip cryopreservation or other approaches for Vitis accession backup. Distribution: The PGRU distributes germplasm in six different forms: seeds, dormant cuttings, leaves, pollen, green cuttings, and DNA. No special handling is necessary for seeds (coin envelopes), pollen (microfuge tubes or vials), or DNA (microfuge tubes). Record keeping for order processing is automated. We expect orders for distribution of DNA will increase over the next five years. 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 this is placed at the top of the queue for regenerations. For wild Malus seed accessions collected from other countries, we can not regenerate them. We could preserve the genetic alleles if we have seedlings from the wild seed, then collect seeds from the seedlings for distribution. 3. Develop better collection and conservation strategies for this germplasm on the basis of their genetic diversity patterns, geographic distribution and phylogenetic and taxonomic relationships with closely related species. The most genetically diverse wild tomato taxon Lycopersicum peruvianum was recently reclassified into four separate Solanum species (Peralta et al., 2005; 2008). We will apply GBS to 12 accessions from each of the four taxa to confirm that the species based on morphotypes are genetically distinct and to develop species-specific diagnostic PCR markers. Tomatillo has been rising in consumption in the U.S. with increased influence of Mexican and Latin American cuisines. Very few molecular genetic or genomic resources have been developed for this crop (Vision et al., 2006). We greatly expanded the tomatillo collection with a expedition to Mexico. Our goal is to optimize GBS for tomatillo using a set of five inbred lines, then apply the method to the entire collection to estimate genetic diversity and relationships among 128 accessions. U.S. per-capita consumption of winter squash has nearly doubled between 1980 and 2012 (USDA Economic Research Service, 2012). Current objectives of winter squash breeding include improved fruit color and morphology, yield, and biotic stress resistance or tolerance (Ferriol and Pico, 2008). The PGRU's collection of 824 accessions represents a wide range of morphological diversity including butternut, acorn, spaghetti, and Hubbard horticultural types. We will optimize GBS by sampling a few accessions of each type, and then apply the technique to a larger panel to discover whether SNP markers can diagnose horticultural type. Significant progress in characterizing genetic diversity patterns and phylogeny studies of grapes has been made in last few years by using molecular markers (Myles et al., 2011). We will apply the research results and genetic markers to our Vitis collection and identify gaps for collection, and re-define our core collection for capturing the maxiumum diversity as well as rare alleles and genotypes. We are currently involved in a collaborative diversity study of apple collections using the GBS techniques. We expect that the study will provide a comprehensive characterization of the genomic variation patterns in our apple collections. In parallel, we will continue investigating the variation patterns of morphological traits, such as leaf shape, fruit size, flowering time, in Malus and Vitis. The morphological data will be used in combination with genetic markers to study the phylogeny, evolution, domestication processes, and classification of Malus and Vitis species. 4. Increase the utilization efficiency of the germplasm collections through phenotypic and genotypic characterization and evaluation of the germplasm held in the collections for high-priority traits, especially resistances to biotic and abiotic stresses and nutritional traits. GBS (Elshire et al., 2011) is a genotyping technique recently developed for generating hundreds of thousands of SNP markers at a very low cost. It applies a high-throughput DNA sequencing platform to the terminal ends of restriction fragments, and scores SNPs in genomic DNA samples. Briefly, genomic complexity is reduced by restriction enzyme (RE) digest. Each DNA digest sample is ligated to one of 96 unique barcoded adapters that include primer binding sites. This allows multiplexing of 96 samples for subsequent PCR amplification and high-throughput sequencing on an Illumina NGS platform. Tags are analyzed through a bioinformatics pipeline consisting of modules that are implemented through perl scripts and applied based on the scientific hypothesis (Glaubitz et al., 2012). Sequence tags are aligned against each other and a reference genome if available. In species without a published genome sequence, a reference catalog of alleles can be developed around restriction sites from the genotyped samples. Applications of GBS to the PGRU fruit and vegetable collections will include disambiguation of accessions with duplicate names, identification of wild species introgressions in cultivars, genetic diversity, fingerprinting for identification, and developing genetic markers for diagnosing crop morphotypes. Cost is currently $25/sample for 96-plex reactions. Currently we can afford 3  4 experiments (one experiment = one 96-well plate) per fiscal year using base funds. In addition, external funding has been secured for apple GBS. GBS for the vegetables will be prioritized based on crop economic importance. Strategies for GBS optimization are crop specific. For example, if a draft genome sequence is unavailable then we will optimize using a RE that cuts less frequently so as to reduce genome representation, increase the number of sequence reads per SNP and improve data quality. GBS of tomato will be performed on the 52 'obsoletes' subset of the core collection and done in comparison to at least six wild tomato species that are known sources of the two dozen most common introgressions found in released cultivars. The aim is to estimate whether genome-wide diversity has increased in cultivated tomato from 1940s through 1990s, and to estimate what fraction of the genome contains introgression from breeding and linkage drag. Onion genome marker development presents an enormous challenge due to a predominance of middle-repetitive DNA, large size (1C = 16.4 billion bp), low GC content (32%) and coding regions sparsely interspersed within retroelements and transposons (Havey et al., 2008; Havey and Bohanec, 2010). These challenges combined with a draft whole genome sequence in progress (Havey and Bohanec, 2010) make GBS a highly promising tool with which to develop SNP based markers in a collaborative effort with M. Havey (USDA, ARS). DNA will be sampled from parents and progeny of a Red DH x Yellow OH-1 F1 mapping population, and the optimized GBS will then be applied to a core set from the PGRUs collection to verify robustness of markers and association with flavonoids (see below). To characterize the genetic diversity among the apples, grapes and tart cherry collections, we will use a variety of molecular markers including GBS-generated SNPs. These markers will be applied to collection analysis issues of diversity, phylogeny, allelic diversity, and collection quality control measures.These include existing markers such as SSR and SNP that have been used to map very wide populations unique to the PGRU that segregate for many horticultural, viticultural, pomological, pathological and entomological traits. Research with Malus GBS has been ongoing since 2012. The effort includes over 1,500 accessions of M. domestica, the progenitor wild Malus species of modern apple, some wild Malus species with unique traits, and 128 apple varieties used by the RosBREED genome mapping project, a SCRI funded research effort (http://www.rosbreed.org/). High-pressure liquid chromatography (HPLC) will be used to identify and quantify chemical components of the PGRU fruit and vegetable crops. Evaluating collections for human health beneficial compounds and other quality traits through replicated field experiments will serve as the main focus. Long-term goals are to associate genetic polymorphisms with trait variation through linkage and association analyses (Schneeberger and Weigel, 2011). We will complete the evaluation of nitrogen-containing bioactive components in the tomato core collection (133 accessions) by providing cryogenically prepared samples to our collaborator A. Breksa (USDA, ARS) for HPLC. These components contribute to fruit ripening, quality and utilization, and include essential nutrients, phytochemicals and toxins. Among vegetable crops, onion has relatively high levels of flavonoid compounds such as quercitin. These compounds are of interest for their potential inhibitory effects on inflammation, allergies, microbes and certain cancers (Prasad et al., 2010). We will collaborate with A. Breksa (USDA, ARS) and P. Dubois (Nunhems) to assay bioflavonoids in the core set of onion accessions that will be genotyped by GBS. We will continue characterizing the composition and content of both primary and secondary metabolites for the Malus core collections. The primary metabolites include sugar, acids, and amino acids. The secondary metabolites include various polyphenols such as anthocyanins and flavonoids, and Vitamin C. As resources permit, we will also characterize the metabolites of the tart cherry collections at the PGRU. We will continue leveraging our current various collaborations for evaluation of traits resistant to biotic and abiotic stresses. Germplasm of onion is actively being used to screen for resistance to Iris Yellow Spot Virus and tomato germplasm, especially wild species are being used to provide resistance to late blight in tomato. M. sieversii germplasm is being used for screening and breeding of resistance to fire blight, apple scab, blue mold, bitter rot, superficial scald, and drought. Wild Vitis accessions provide new sources of powdery mildew and downy mildew resistance and cold hardness. There is an ongoing effort to determine the identities of SI alleles in our collections. Dr. G. Fazio (apple rootstock breeder) and Gayle Volk (NCGRP Fort Collins) are testing >1,500 Geneva accessions for their SI alleles diversity. Hopefully we could add this information to GRIN within next five years. We expect that at the end of the project we will have a better understanding of the genetic and phenotypic diversities preserved in the PGRU germplasm collections, particularly for those traits of significant value to yield, fruit quality and health benefits. 5. 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 have been collaborating in other characterizations to provide germplasm being used to produce novel varieties that have traits such as high sugar, various color grape tomatoes, deep red hypocotyl radish varieties, and improvement of tomato flavor 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 U.S. 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

Outputs

• More complete representation of fruit and vegetable germplasm diversity with wild and weedy relatives, introgression populations, modern cultivars, landraces, and heirlooms of fruits and vegetables.
• Secured genetic resources . Cryopreserved apple and tart cherry accessions and storage and backup of high-quality vegetable seed at NCGRP. Well-managed ongoing repropagation of clonal germplasm and regeneration of vegetable germplasm. Explored new protocols or methodologies for backup of Vitis germplasm in collaboration with the NCGRP.
• An expanding database of passport, characterization and evaluation data made available through an improved and user-friendly GRIN Global. Increased coverage of digital images and characterization data of apple, grape, tart cherry, tomato, onion, squash, and cabbage available on GRIN. This will improve efficiency of use of germplasm.
• Development of new core subsets and refinement of existing core subsets for major crops.
• Molecular markers (SNPs) and bioinformatics pipelines for processing genotypic data for accession identification and fingerprinting, phylogenetics, population genetics, genetic mapping and marker-assisted selection of apple, grape, tomato, onion, winter squash and tomatillo.
• Evaluations and genetic studies of quality traits. These include nutritional components such as antioxidants in apples, carotenoids and Vitamin C in tomato and anthocyanins in grapes; disease resistance to apple fire blight, apple scab, and grape nematodes; cold tolerance in grapes and dwarfing in apples.
• Datasets for the PGRU fruit and vegetable germplasm collections for quality traits including health beneficial compounds.

Outcomes or Projected Impacts

• Valuable germplasm will be readily available at the PGRU and back-ups will be secured at the NCGRP.
• The genetic base of crops will be broadened to reduce the dangers of genetic vulnerability through the increased representation of wild species, landraces, and introgression lines, which are prime sources of favorable new alleles and are in increasingly high-demand for crop improvement and research.
• Critical tools are developed for germplasm conservation, characterization and improvement, in the form of publicly available molecular markers and genotypic data for high-priority species and traits.
• Molecular genotyping will improve existing core subsets resulting in more efficient characterization and management of our collections.
• Results from biochemical characterization of the PGRU fruit and vegetable germplasm will be exploited by breeders for enhancement of quality for flavor, texture, and health beneficial components such as vitamins, minerals, and cancer-preventing compounds.
• Discovery of genes for increased disease and pest resistance will decrease reliance on pesticides and reduce growers' costs and negative environmental impacts.
• Germplasm of apple progenitors from Central Asia will be used to improve resistances to diseases such as fire blight and scab.
• Grape germplasm from the PGRU will continue to be used in developing new grape cultivars for better resistance to biotic and abiotic stress.
• Onion germplasm from the PGRU will be used to develop IYSV resistance, considered the number one imminent threat to onion production.
• Wild tomato germplasm will be used to develop late blight resistance cultivars in tomato.
• More importantly, productivity, profitability and viability of agriculture in the northeast will be ensured as a result of the secured and well-characterized germplasm preserved at PGRU.

Milestones

(2014): Ongoing regeneration, storage and backup of germplasm; ongoing acquisition of modern vegetable cultivars, landraces, and wild species; ongoing characterization, digital imaging and evaluation of vegetable and clonal germplasm; and ongoing distribution of germplasm. Primary and secondary metabolites of 200 apple accessions will be characterized. If budget allows, 100 tart cherry accessions will also be characterized. Propagate well-characterized wild Malus accessions of unique traits for addition to the permanent collections. Optimize GBS for cultivated and wild tomato, and tomatillo. GBS of tomatillo, tomato duplicates, obsoletes and wild tomato species used for introgression breeding. Development of bioinformatics pipelines to analyze GBS. Begin data analyses of Malus GBS data.

(2015): Ongoing regeneration, storage and backup of germplasm; increase backup cryopreservation storage of tart cherry accessions; ongoing acquisition of modern vegetable cultivars, landraces, and wild species; ongoing characterization, digital imaging and evaluation of vegetable and clonal germplasm; ongoing distribution of germplasm. Begin removal of M. sieversii seedling block after 2014 season. Primary and secondary metabolites of 200 additional apple accessions will be characterized. If budget allows, 100 additional tart cherry accessions will also be characterized. Analyze introgression in tomato and partitioning of genetic variation in tomatillo. Use GBS in four wild tomato species to verify revised taxonomy. Use HPLC in tomato to measure health-beneficial compounds. Complete laboratory phase of GBS fingerprinting of Malus accessions.

(2016): Ongoing regeneration, storage and backup of germplasm; ongoing acquisition of modern vegetable cultivars, landraces, and wild species; ongoing characterization, digital imaging and evaluation of vegetable and clonal germplasm; ongoing distribution of germplasm. Collect 2nd year data for metabolites for clonal accessions characterized in Year 1. Select additional well-characterized wild Malus for unique traits for addition to the main collection, complete genetic and trait evaluation of V. labrusca and V. aestivalis seedling families for possible addition to permanent collections. Analyze four wild tomato species GBS data, optimization of GBS for onion mapping population and squash morphological diversity panel. Apply HPLC for assays of health-beneficial compounds in tomato and Malus.

(2017): Ongoing regeneration, storage and backup of germplasm; cryopreserve additional apple accessions that were added to the main collection recently; continue research collaboration on Vitis back up storage; ongoing acquisition of modern vegetable cultivars, landraces, and wild species; ongoing characterization, digital imaging and evaluation of vegetable and clonal germplasm; ongoing distribution of germplasm. Collect 2nd year data for metabolites for clonal accessions characterized in Year 2. Seed increase and clone selection of M. sieversii; collect wild Vitis accessions in North America. Develop diagnostic SNP markers for four wild tomato species. GBS analysis of onion and squash collections (minimum of 96 accessions each). HPLC screening of onion for health-beneficial compounds. Fingerprint grape and apple germplasm.

(2018): Ongoing regeneration, storage and backup of germplasm; ongoing acquisition of modern vegetable cultivars, landraces, and wild species; ongoing characterization, digital imaging and evaluation of vegetable and clonal germplasm; ongoing distribution of germplasm. Collect data from selected clonal accessions for metabolites to confirm the results of Year 1-Year 4 and summarize the data for the project. Develop diagnostic SNP markers for squash morphotypes. Analyze partitioning of variation in onion and association between SNP markers and health-beneficial compounds.

Projected Participation

View Appendix E: Participation

Outreach Plan

The primary mechanism for dissemination of products of the PGRU service activities is the distribution of germplasm. This is accomplished through providing passport and characterization information about the germplasm maintained at the PGRU through GRIN where the PGRU has a strong presence. As mentioned previously, a new user friendly version of GRIN, GRIN-Global will be available for users by the end of 2012, which will increase ease of use and efficiency of use of the germplasm collections. Additionally, information concerning germplasm maintenance, characterization, collection, and genetic diversity research is maintained on the PGRU website. PGRU scientists serve as ex-officio members of CGCs which provide strong linkages to crop improvement and research programs for the crops maintained at the PGRU. This provides a mechanism to ensure that service and research activities of the PGRU are relevant to the needs of our stakeholders. PGRU scientists work collaboratively with other ARS and university scientists on research grant projects.


Scientists are responsive to requests for information, advice, or assistance from colleagues in ARS, SAES, industry and foreign groups. Scientists initiate and/or participates in program-related activities which support ARS operations and goals, and which contribute meaningfully to the accomplishment of the ARS mission, strategic objectives, and National Programs of which the Management Unit is a part. Included in this are: 1) Scientific publications reporting the genetic diversity in the PGRU collections; 2) Lectures and demonstrations to visitors at the PGRU; 3) Education modules for study by elementary, secondary and college students; and 4) Participation in press releases for the popular media including radio, television, and other avenues. Recent outreach activities have included: Science Exploration Days at St. John Fisher College, Science Night at North St. Elementary School, Rochester Institute of Technology Public Service Career Fair, Empire Farm Days, and Wayne-Fingerlakes schools A Diversified Enrichment Program for the Talented (ADEPT). One or two undergraduate summer students or interns are trained in PGRU lab each year.

The PGRU has been a partner with three special projects dealing with Organic Agriculture: (a) The Public Seed Initiative, (b) the Organic Seed Partnership, and (c) the Northern Organic Vegetable Improvement Collaborative, which is currently in progress. The role of the PGRU in these projects has been to provide training, workshops, and demonstrations of small-scale seed production to support the release and use of vegetable varieties bred specifically for organic farming environments and to provide germplasm for use in breeding vegetable varieties for organic agriculture. We have also taken a lead role in providing outreach events and documents for these three projects.

Organization/Governance

The NE-9 project does not have a defined end point since there is a continual and ever-increasing need for plant genetic resources. It also follows that the organization and technical aspects of the project outlines will change only in points of emphasis from year to year.

Regional Research Project NE-9 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 NE-9 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 NCGRP 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 NE-9 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.

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DE, NH, NJ, NY, PA

Non Land Grant Participating States/Institutions

USDA ARS, USDA-ARS, USDA-ARS/Plant Genetic Resources Unit, USDA, ARS, USDA/ARS-National Seed Storage Laboratory