Brief Summary of Minutes of Annual Meeting

The 2006 annual meeting was held Tuesday June 6, 2006 from 1:00 p.m. to 5:00 p.m. on the campus of Iowa State University. It was held in conjunction with the joint RTACs, CGC Chairs and PGOC. Dr. Tom Burr introduced himself as the Administrative Advisor of the NE-09 and Director of the NYSAES. Donglin Zhang was Chairman of the committee in the absence of Robert Bernatsky whose flight was cancelled. The comprehensive Research Leaders report was distributed to the committee and this was highlighted by short oral reports on PGRU activities by Phil Forsline, Larry Robertson and Chuck Simon. Tom Burr and Tom Fretz, NERA Director led a long discussion about how funding to support NE-09 could be increased. There is presently a new model for Federal Formula Funds. This may allow for a new way to determine off-the-top funding. Tom Fretz discussed the activities of the National Plant Germplasm Committee (NPGCC) which is made up of 9 members: (3 each from ARS, CSREES, and SAES). In order to increase funding to NE-09, it was recommended that a fact sheet be developed to present to the Directors of the NE region when NERA meets in Geneva on July 10. It will be important that all Directors know how germplasm from the entire NPGS (not just PGRU) is being used in each Northeastern state. A study of distribution of germplasm to the NE was completed. Over the last 10 years, nearly 30,000 samples from NPGS have been distributed to NE states and all states have been recipients. Funding levels for NE-09 have not increased over the last 10 years ($145,000 has been the annual contribution). This is impacting operations at PGRU in that this allocation no longer supports the salary levels of three critical positions at PGRU that are Cornell hires. These three are all farm managers that maintain, characterize and distribute germplasm. As a comparison, S9, NC-7 and W6 have seen annual increases that support germplasm programs in those regions. We also discussed how we might increase the involvement of all NE states in NE-09 activities including attendance of representatives at the annual meetings. The meeting continued with state reports by Phil Griffiths of NY, Brent Loy of NH, and Donglin Zhang of ME. We also received reports from Peter Bretting of USDA-ARS National Program staff for Germplasm, Dave Ellis of USDA-ARS NCGRP in Fort Collins, CO and Jimmie Mowder of USDA-ARS DBMU in Beltsville, MD. The meeting adjourned at 5:00 p.m. and the events continued into the evening with a dinner where all RTAC, CGC Chairs and PGOC members participated. The visit by NERA (National Economic Research Associates) to Geneva hosted by Tom Burr commenced on July 9-10 and a Fact Sheet was provided to the members at that time. PGRU hosted the group with a very informative tour of the field plantings of both the fruit and vegetable crops being maintained. The fact sheet that was presented can be found under the heading Impacts and Appendix 1 (member list) that includes a list of: 1) the active NE-09 members; 2) Inactive members; and 3) States that have vacancies on the NE-09 committee The next meeting will be hosted by Donglin Zhang in Maine sometime in spring/summer 2007.

During FY2006 approximately 460 accessions were regenerated; additionally 157 biennial crop accessions were grown to produce plants for use in seed production in 2007; and 6414 seed lots of 4868 accessions were distributed in 280 orders (225 domestic and 55 foreign). A total of approximately 11,812 accessions of seed-propagated crops were successfully maintained during the past year. The future availability of this germplasm is therefore assured. Approximately 546 digital images were recorded from 191 accessions of tomato, onion and winter squash. These are being processed and will be loaded onto GRIN. Characterization data was recorded on 191 accessions of onions and tomato for minimal descriptor lists for loading on GRIN. Short-day onion accessions cannot be regenerated in Geneva, NY. An SCA with New Mexico State University was extended for regeneration of these accessions. In FY2006 this resulted in regeneration of 65 short-day onions that were in danger of being lost (30 for seed and 35 for bulb production for seed production in 2007). The accessions are being made available for distribution to short-day onion breeders. We evaluated approximately 100 new accessions of tomatillo (Physalis philadelphica) from a recent collection in Mexico for 35 descriptors and took digital images of fruit and plants. One of the most important traits we evaluated for was self-fertility, which is needed by breeders to increase efficiency of operations. We found six accessions with a high level of self-fertility. We obtained accurate estimates of DNA sequence variation within a diversity panel of domesticated tomato (L. esculentum) by analyzing 48 gene fragments (22.3 kb) per plant in 31 plants. The majority of loci (81%) were polymorphic, the minor allele was at a frequency of less than 10% for a large fraction (95 of 150) of single-nucleotide polymorphisms (SNPs), and the average number of SNPs between pairs of sequences was about one per kb. For 40 of the 48 fragments we also sequenced one plant from wild tomato L. peruvianum. This data allowed us to test and reject at a high level of significance (P < 0.00001) a neutral equilibrium model of molecular evolution in Lycopersicon. This test provides candidate loci for exploring microevolutionary processes such as selection, bottlenecks, and introgression in tomato. In collaboration with Dr. T. Bjorkman (Cornell University) we published a manuscript (Labate, J.A., Robertson, L.D., Baldo, A.M., and Bjorkman, T. 2006. Inflorescence identity gene alleles are poor predictors of inflorescence type in broccoli and cauliflower. JASHS, accepted with revisions) that reports on three heading-phenotype candidate loci in a genetically diverse sample of 40 broccoli and cauliflower accessions from the PGRU and the Genetic Resources Unit of HRI Warwick (HRI). Simple genetic models assuming dominance or codominance of alleles were analyzed. Goodness-of-fit tests rejected the null model that the mutant genotype was associated with a cauliflower phenotype. A correlation analysis showed that BoAP1-a and BoCAL-a alleles or loci were significantly correlated with phenotype but the fraction of variation explained was low, 4.4% to 6.3%. Adding BoGSL-ELONG to the analysis improved predictive power using the linear regression procedure max r2. In the best 3-variable model, only 24.8% of observed phenotypic variation was explained. Because tested genetic models did not hold robustly for the surveyed accessions, it is likely that there are multiple genetic mechanisms that influence whether the phenotype is broccoli or cauliflower. Our results in commercial varieties indicated that other genetic mechanisms are more important in determining the horticultural type than are BoAP1-a and BoCAL-a. This work will help redirect attention to additional genes, epistatic interactions, and environmental factors that do have major influence on the horticultural type. There is need for heirloom and new publicly bred germplasm for use by organic farmers. A Reimbursable Cooperative Agreement with Cornell University provides support to PGRU for training of organic farmers and small seed producers in small-scale seed production of heirloom and new publicly improved vegetable varieties, whose production has been limited because of lack of seed. In FY2006 demonstrations, training workshops, and community seed days were conducted for over 800 participants. This has increased the availability of heirloom and new publicly bred germplasm for use by small and organic farmers. Workshops, demonstrations and community seed days were held at the Black Kettle Farm in Essex, NY on October 5, 2005; at the Valley Laboratory of the Connecticut Agricultural Experimental Station in Windsor, CT on October 20, 2005; at the On-Farm Seed Production Workshop at the NOFA-NY Annual Winter Conference in Syracuse, NY on January 27, 2006; at the NOFA-MA Summer Conference in Amherst, MA on August 11 and 12, 2006; at Rehoboth Homestead Farm in Peru, NY on August 30, 2006; at the Norwich Meadows Farm Community in Norwich, NY on September 5, 2006; at the Peacework Organic Farm in Newark, NY on September 16, 2006; and at the Common Ground Country Fair in Unity, ME on September 22 and 23, 2006. These workshops provided essential training in small-scale seed production to growers and organic-farmers interested in incorporating seed production into their existing farm systems. During the community seed day workshops held in Essex, Peru, Norwich and Newark, NY; and Windsor, CT organic farmers and small-scale seed producers were trained and given the opportunity to clean their seed using the equipment provided in the mobile seed processing unit. These activities were supported by the RCA with Cornell University where the PGRU has the lead role in this project in the extension of small-scale seed production of heirloom vegetable germplasm and new public open-pollinated varieties by organic farmers and small-scale seed producers. In FY2006, The PSI (Public Seed Initiative) website continues to be a major source of information for organic farmers with over 7,000 hits since its creation. This website supplies detailed information on pepper genomics, seed production, participatory breeding, on-farm commercial variety trial results, and other related projects which occurred during the life of the PSI project: www.plbr.cornell.edu/psi. The OSP (Organic Seed Partnership) website contains information about the new goals and direction of the new OSP project. This website contains all the detail that the PSI website has plus information about nationwide cooperators, updated organically centered news and events around the country, and streaming video detailing on-farm vegetable breeding and seed production. The OSP website also includes a section for organic resources, a detailed calendar of events and links to related projects worldwide: www.organicseedpartnership.org. To complete the PSI project, which ended at the beginning of FY2006, a final PSI CD was that combines all annual reports for participatory breeding, on-farm commercial variety trialing and seed production. The CD shows detailed instruction for seed production and breeding of several common vegetable crops, including a 20-minute video detailing plant breeding techniques for many standard crops, a 5-minute video describing and demonstrating dry seed processing of Brassica seed and a 9-minute video describing and demonstrating wet seed processing of tomato and tomatillo. This CD is made available at all community seed days, demonstrations and presentations by the PGRU staff working within this RCA. PGRU has 2370 Malus accessions maintained as clones in the collection. Fifteen new apple landraces from France were obtained. In addition, we maintain 1565 seed-lot accessions with 310 of these having variable size seedling populations under evaluation presently. These plantings include 2900 individual seedlings that have been added to the GRIN record. Nine accessions of M. orientalis seed was recently obtained from Georgia (former USSR). Thirty four additional grape accessions were received in 2005 and 2006 from the Elmer Swenson breeding program at the University of Minnesota. This brings the grape collection to 1204 accessions. Distributions in FY 2006 included 292 orders for 6144 accessions. With these distributions, we require the user community to respond with data on the performance of the accessions in their locality giving us useful information to document on GRIN. Presently, the PGRU tart cherry collection consists of 105 accessions. This includes Prunus cerasus (72 accessions), Prunus fruticosa (13 accessions) and other Prunus species and hybrids (20 accessions). Three new accessions were added under provisional release permit. In addition 14 Prunus cerasus cultivars were added from the program at Cornell University that is phasing out its breeding program for sour cherries. The entire core collection and 80 % of the main collection have been characterized for priority descriptors with the data loaded to GRIN. We have completed digital imaging of 1140 (50 %) of the clones The original core collection of 190 accessions established at five sites in 1992 has been expanded with the addition of 57 accessions representing individuals of 12 species collected from the wild. As of fall 2005, 746 of the 1591 Central Asian seedlings of M. sieversii fruited and have been characterized for horticultural traits with 530 having digital images of fruits completed. The sour cherry collection had adequate fruit in 2003 and 2005 to begin characterizing minimal descriptors for those accessions not yet characterized. We completed characterization and digital images of 50 accessions using 8 descriptors along with digital images of the fruit. We hope to characterize and digitally image about 25 more accessions in summer 2006. In Grapes, a complete data set for 17 descriptors on nearly 900 of the clonal accessions can be found at: http://www.ars-grin.gov/npgs/descriptors/grape. Digital images of ripe fruiting clusters, intact on the vine have been completed on 414 accessions. These images are being assessed for quality and will be loaded to GRIN. We are now planning to take digital images of clusters and berries on a background grid for better perspective. The grid method has been used for 1600 apple and 50 cherry accessions. We are also collaborating with the USDA-ARS National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, Co on a project to determine strategies to preserve alleles (in the form of seeds) from wild accessions of Malus collections. Using SSR markers, we have determined strategies for preserving for the long term, seeds of wild germplasm to supplement seed and clones from original collections. In spring 2004 and 2005, we completed the two phases of the seed increase of M. sieversii using fruiting seedlings from two specific sites in Kazakhstan which produced 35,000 seeds. Some of the core members that were used paternally and maternally were replaced with new accessions in 2006. Additional pollinations were made in May 2006 to complete this phase of the project. Starting in 2007, we will be doing the seed increases on trees from five other Kazakhstan sites. SSR fingerprint database development has been initiated for the Geneva grape and apple collections. Initial commitments were made to produce fingerprints for all accessions for each collection with eight SSR loci. DNA is being extracted for both collections and markers are being identified and developed. For apple, marker selection is being coordinated with the Ft. Collins fingerprinting effort in the wild apple species. Further coordination will occur with other apple collections in France and Italy et al. For grape, marker selection is being coordinated with Davis and with the French germplasm collection in Montpellier. After the initial eight loci are completed for each collection we will consider extending the effort to more markers. We are collaborating on a functional allele marker development project with three Cornell faculty members on an NRI funded grant to study tritrophic relationships between pestiferous and predatory mites on a grape mapping population segregating for leaf trichome anatomy. The population pedigree includes at least five grape species, and our role is to develop QTL markers that may be potentially used for marker assisted selection. The population also segregates for many other traits, and other marker associations will be identified. We anticipate that SNPs will be increasingly applied to crop germplasm conservation and management. This information is being used to develop new genetic markers for characterization of PGRU germplasm. An in-house software method was developed for EST-based SNP discovery. This tool has been used to identify polymorphism among apple, tomato and grape EST sequences. A related package was developed to design Polymerase Chain Reaction (PCR) primers bracketing the polymorphisms. These primers have been used to amplify and sequence genomic fragments of genes in all three crops for identification of distinguishing molecular features. In the past year we wrapped up the lab work for a diversity study in the grape genus that involves 310 accessions representing 44 grape species plus a number of outgroups. From this data we anticipate developing a SNP assay system for the grape genus. The project also includes analysis of eight SSR markers as a baseline comparison of techniques. In addition PGRU scientists annually host graduate and undergraduate students from Cornell and other Northeast Universities conducting tours and lectures related to germplasm management. Serving as Adjunct appointments at the NYSAES, Cornell University, Geneva, NY, PGRU scientists participate in faculty meetings and present and organize seminars

Baldo, A.M., Robertson, L., Sheffer, S.M., and J.A. Labate. 2006. Polymorphism among EST-based markers in Tomato. Tomato Breeders Roundtable, Tampa, FL. Baldo, A.M., L.D. Robertson, S.M. Sheffer, W.F. Lamboy, and J.A. Labate. 2006. Evaluation of SNP markers across tomato landraces. Plant and Animal Genome XIV, San Diego, CA. Chetelat, R. T. 2005. Revised list of monogenic stocks. TGC 55:48-69. Baldo, A.M., L.D. Robertson, and J.A. Labate. 2005. Discovery of highly polymorphic genes in tomato cultivars. In Conference Program, Intelligent Systems for Molecular Biology 2005, Detroit, MI. Jones, C. M. 2005. The extreme search for tomato genetics: hunting wild tomato in the Andes. In Good Tilth 16 (4): 10-11. Labate, J.A., L.D. Robertson, S.M. Sheffer, F.Wu, S.D. Tanksley and A.M. Baldo. DNA polymorphism estimates within domesticated tomato. Sol2006. Madison, WI. Robertson, L.D. 2006. Apium Collection of the PGRU at Geneva, New York: July 2006. Report to the Leafy Vegetable Crop Germplasm Committee. New Orleans, Louisiana. July 2006. Oral Presentation and Written Report. Robertson, L.D. 2006. Allium Collection of the PGRU at Geneva, New York: July 2006. Report to the Root and Bulb Crop Germplasm Committee. New Orleans, Louisiana. July 2006. Oral Presentation and Written Report. Robertson, L.D. 2006. Tomato Collection of the PGRU at Geneva, New York: May 2006. Report to the Root and Bulb Crop Germplasm Committee. Tampa, Florida May 2006. Oral Presentation and Written Report. Robertson, L.D. 2006. Evaluation of Tomatillo Varieties: Report for Northeast Organic Farming Association of New Yorks Winter Conference. Syracuse, New York. January, 2006. Oral Presentation. Robertson, L.D. and T.L. Ferrin. The National Plant Germplasm System and You. Report for the Northeast Farming Association of New Yorks Winter Conference. Syracuse, New York. January, 2006. Oral Presentation. Final Public Seed Initiative Compact Disc Public Seed Initiative Website: www.plbr.cornell.edu/psi. Organic Seed Partnership Website: www.organicseedpartnership.org. Myers, C.T. and P.L. Forsline. 2005. Research on potential host resistance to apple pests. 2005 ESA Annual Meeting, December 15-18, 2005, Fort Lauderdale, Florida Stushnoff, C., T. Einhorn, A.E. McSay, P.L. Forsline, S. Cox, J.R.L. Ehrenkranz and L. Sandoval. 2005. Biodiversity of the Flavonoid Phlorizin in a Subset of the USDA Apple Germplasm Core Collection. HortScience 40:1067 Volk G.M., C.M. Richards and P.L. Forsline. 2005. Genetic Diversity of Wild Apple Accessions in the National Plant Germplasm System: USDA NRI Award #2005-00751. HortScience 40:973 Forsline, P.L. 2005. Plant exploration supported by the National Plant Germplasm System. Workshop Plant exploration for new fruits: past, present and future. HortScience 40:975 Aradhya, M., E. Stover, C. Weeks, and P. Forsline. 2006. Prunus Genetic Resources and Research at the Davis California National Clonal Germplasm Repository. 3rd International Rosaceae Genomics Conference. Pg 91 Forsline, P.L., P.S. Cousins, C.J. Simon, A. Baldo, H.R. Schwaninger, and E. Stover. 2006. Status of USDA Vitis germplasm collection in Geneva, New York with accessions primarily of North American origin. 9th International Conference on Grape Genetics and Breeding. Forsline, P.L., Gennaro Fazio, Herb Aldwinckle, Amy F. Iezzoni, and Gayle M. Volk. 2006. Diversity and characterization in USDA Malus and tetraploid cherry germplasm in Geneva, NY. 3rd International Rosaceae Genomics Conference. Pg 74. Volk, Gayle M., Christopher M. Richards, and Philip L. Forsline. 2006. Characterization of wild Malus populations using genotypic and phenotypic traits. 3rd International Rosaceae Genomics Conference. Pg. 34 Luby, James, Karen Hokanson, Phil Forsline, Herb Aldwinckle, Sue Gardiner, and Vincent Bus. 2006. Evaluation of horticulturally elite Malus sieversii germplasm for apple scab resistance genes using phenotypic and marker-based screenings. 3rd International Rosaceae Genomics Conference. Pg 75 Simon, C.J. 2006. Molecular Characterization of the US Apple Germplasm Collection. 3rd International Rosaceae Genomics Conference. Pg. 112 Forsline, P.L. and K.E. Hummer. 2006. Fruit Exploration Supported by the National Plant Germplasm System 1980 to 2004. HortScience  accepted Postman, J., K. Hummer, E. Stover, P. Forsline, L.J. Grauke, F. Zee, T. Ayala-Silva, R. Krueger, B. Irish, P. Bretting. 2006. Fruit and Nut Genebanks in the USDA National Plant Germplasm System. HortScience - accepted Baldo, A., Suren Samuelian, and Courtney A. Weber. 2006. Computational Analysis of Putative Resistance Gene Analogs in Raspberry. 3rd International Rosaceae Genomics Conference. Pg. 65. Aradhya, M.K., B.H. Prins, G.S. Dangl, C.J. Simon, and E. Stover 2005. Genetic diversity and phylogeographic structure of the genus Vitis: implications for conservation. First International Conference on Crop Wild Relative Conservation and Use, Sicily, Italy. Aradhya, M.K., G.S. Dangl, B.H. Prins, and C.J. Simon 2004. Molecular characterization of genetic variability and differentiation among European and Asian grape cultivars. Plant and Animal Genome XII, San Diego, CA. Final Abstract Guide p. Forsline. P.L. 2005. Vitis Collection of the PGRU at Geneva, New York: September 2005. Report to the Grape Crop Germplasm Committee, University of Minnesota, September 2005. Oral Presentation and Written Report. Forsline. P.L. 2006. Malus Collection of the PGRU at Geneva, New York: February 2006. Report to the Apple Crop Germplasm Committee, Geneva, NY February, 2006. Oral Presentation and Written Report. Forsline, P.L. 2006. Forum - Travels To Gather, Improve Apples Start To Bear Fruit. Agricultural Research 54:2. Forsline, P.L. 2006. Pons, L. 2006. Remarkable Kazak Apples. Agricultural Research 54:4-6. Forsline, P.L. January 25, 2006. Invited presentation to the Cornell University Horticulture Department seminar series. "Exploration for Fruit Germplasm: From Ancient History Up to the Present Day". Forsline, P.L. January 13, 2006. THE NORTHWEST AG INFORMATION NETWORK. http://www.aginfo.net/. Back to the future of apples, Pt. 1 Forsline, P.L. January 16, 2006. THE NORTHWEST AG INFORMATION NETWORK. http://www.aginfo.net/. Back to the future of apples, Pt. 2 Forsline, P.L. April 5, 2006. Invited presentation to Syracuse University Department of Forest Genetics. Apple Kith and Kin: From Johnny Appleseed and Kazakhstan to Geneva, New York. Forsline, P.L. September 8, 2006. Invited presentation to Annual meeting of California Rare Fruit Growers  Festival of Fruit at California Polytechnic State University, San Luis Obispo, CA. Genetic Treasures from Apples Ancestral Home