Annual/Termination Reports:

[07/25/2005] [08/11/2006] [08/20/2008]

Report Information

Participants

Attendees:

Bernatsky, Robert - rb@pssci.umass.edu , University of Massachusetts

Goffreda, Joseph - goffreda@aesop.rutgers.edu , Rutgers University

Jahn, Molly - mmk9@cornell.edu, Cornell University

Griffiths, Phillip - pdg8@cornell.edu, Cornell University

Burr, Thomas - tjb1@cornell.edu, Cornell University

Other Attendees:

Forsline, Philip - plf1@cornell.edu, USDA, ARS

Robertson, Larry - lrobertson@pgru.ars.usda.gov, USDA, ARS

Bretting, Peter - pbretting@ars.usda.gov, USDA, ARS, National Program Staff

Martinez, Wilda - wmartinez@naa.ars.usda.gov, USDA, ARS, NAA Director

Brief Summary of Minutes

The meeting was called to order by Robert Bernatsky, current Chair of the RTAC. Dr. Tom Burr introduced himself as the new Administrative Advisor, having started as the Director of the NYSAES in January.

Cucurbita has been obtained from Rutgers. Already had maxima and mushchaga and separated it to send to Ames, IA location. Accessions have been cataloged and the database and books will go along with it. Pedigrees still have to be traced. 3,800 samples distributed this past year. In terms of Cryogenic storage we have been looking at the viability. Some of it is not as cold hardy. We are looking for 40% viability to be able to consider it successful. Material that was less than 40% has been re-processed to get the viability numbers higher. Forty accessions of grape from a project in Minnesota (Mr. Albert Swenson deceased) was acquired.

There was some really interesting material to add to the collection. Joe Postman & Rich Hannan have collected some Malus orientalis recently and added that to our collection. One of the more visible SCA's is the one with Herb Aldwinckle with fire blight resistance. There is a project with Minnesota and New Zealand and scab resistance is going well with a possibility that we will have a useful batch of germplasm. There is potential value in this material for apple rootstocks. New project with Kearneysville in the NAA that will hopefully expand. The PGRU also had a very successful public open house in September, with the possibility of a repeat in 2007 to coincide with the NYSAES 125th Anniversary open house.

Tom Burr attended meetings in January that we had sent the budget request prior. They allocated $145K for 2005 and would like to request more for 2006 at the meeting in July. Do the NE directors still supply money to NE9 from their funds? Have heard two years ago that there was discussions that they would not want to give monies to NE-09. The vote was done the previous summer and they are not reducing the budget amount.

What about Bush's Hatch proposals? 2005 is already done, 2006 was approved in the house and increased slightly. It will be on the cut list in 2007. Formula fundings are important. If the formula funding disappear, the breeding programs will disappear. The outcry was tremendous when this was initially put in the Presidents budget. Many Universities have 100's of faculty on the formula funding. This will still be a year to year situation. There is an image in OMB that the only properly funded research is competitive. They dictate where monies go and good research is overlooked in favor of grant placements. We have been going through this for 5 years. Any congressional add on's that have been terminated have to be restored before they can add any more. The whole grape program is a congressional add-on and it is a third of our federal budget. We need to have our act together on the State & Federal level and say what a budget cut will mean for public, state, economy, jobs, etc. We need to have workshops and prepare something. We need documentation.

When the NE9 directors got together the focus was 100% intent on restoring federal formula funding. They could not think of anything else. Need to talk about impact of the research rather than just saying you need this because salaries are going up. We have some very long term Cornell employees that support our farm activities. If we didn't get the NE-09 money, we may have to move some researchers out of here to maintain these people. We will have a one page write-up of impact for the 2006-2007 budget request. Maybe increase the request to match the percentage that the Hatch was increased. Ask for $145k and the 5% increase Hatch got.

News from NPGS: There have been some substantial site increases at Geneva and Pullman, WA. For each year that there is no increase, the discretionary funds are decreased 5% per annum. In 2005 all ARS budgets received .8% rescission. ARS budget is part of the discretionary budget, not part of mandatory budget, so we are particularly susceptible to being squeezed.

National Programs: Our research is now organized into National Programs. The research here is part of 301. That includes Gene bank, genetic mapping, genetic enhancement. We are just starting the second cycle, moving into the first retrospective review. There will be a customer stakeholder workshop this fall. There will also be a non-financial audit that has to do with how we do plants and physical security at our sites. The audits are almost done and OIG seems pleased.

NP disease recovery system: Presidential directive last year that says it is suppose to plan to recover as soon as possible after a natural or human mediated crop destruction event. Asked all CGC's to include crop vulnerability reports and most reports were handed over to steering committees. Experiment stations should take advantage of this initiative, can be a source for Plant Disease Recovery System. In process of priority setting for which diseases have the highest priorities. Geneva was put on the list.

Some sites are higher on the list, like Ft. Collins and already received some funds. Somewhere down the line there will be resources above and beyond your budget for security. I believe you are all on second tier because you are a Plant Introduction station. Do you know what some of the issues came out of this audit were? What specifically? The audit that made OIG interested in it was one read about the starling project 'an un-approved event' transgenic material was mixed in corn flower and got into Tostitos, etc. Someone asked about our genebank materials. They asked how we manage them. Said they were managed according to our federal regulations. Not sent to requestors without APHIS permit numbers, etc. Lead to discussions because the Clinton admin and Bush admin said approved transgenic materials should not be labeled. Policy that we are implementing now. It says that because of rapidly changing nature of plant breeding and genetics, when material comes in we have to ask when it was bred and how it was maintained. In terms of feasibility, if one of our partners like the plant protection sends stuff to Ft. Collins, they send a questionnaire asking if the material is transgenic or non-transgenic, but now it says that we cannot ask that question. We try to collect as much info as possible to help our users decide if they want the material and how to use it if they do. The policy is being incorporated into all our genebank manuals and will be posted then. Policy determined above ARS level.

In the area of transgenics, Kearneysville developed plum pox agent that is transgenic and APHIS is saying it will be allowed for release. It seems like it is going to float. Being recognized as something that should be released. Not sure it can be patented because of the amount of people involved. Can it be used in breeding purposes? Plant patent law is ambiguous in that regard. It really says it cannot be used in the US, which means you can take it to Canada and do it. We don't as a rule go for utility patents in varieties. Is it USDA's position that patented varieties should be allowed to be used for breeding purposes? USDA material, yes, but not sure about others. Who should we transmit information to?, whether plum variety will be patented and second what is the progress? This dates back to last summer. One of the participants asked about plant patent and indicated that it needs to be tested.

It is a very trying budget cycle for the State. SUNY funds are being cut even though tuition is increasing. This year it was 85 M SUNY cut, which doesn't help Geneva at all. We have very little tuition here. Dean Henry and others saw this coming and did a lot of lobbying in Albany and had Senator Nozzolio here. The idea was to give Nozzolio some ammunition to go to Albany and talk about applied research, the other reason was the Cornell Ag & Food Tech Park. Some of our local Senators have a lot of policital capitol invested here. Show types of work that Cornell Scientists do to support food technologies, wine industry, food safety, etc.

The NYSAES has initiated 160 small food companies in New York. Also helped that our President from Cornell called the Governor and explained what the cut would mean to the Land Grant Commission of Cornell and how it would affect the stake-holders. We ended up with no cuts. We were looking at 10% cut and all Hatch . We came through this year OK, but we still have our other challenges like salaries going up and other increases. The other that came out is that our college will be looking at developing one pagers we can use in Washington. Saw what happened to the state, moving forward with ARS building here, which is extremely important event for us in Geneva. Very positive about future of Station, have some excellent scientists with the Grape Genomicist crew NE9 has. Geneva will be leading force in grape enology and viticulture in New York state.

Bill Nelson was talking about National Clean Plant Network FY05 proposed and has been done to decrease funding through 2008. Very important program with an emphasis on virus breeding material. Suggestions for PGRU: One suggestion is the PGRU should hold more developed germplasm. It is often hard to get a hold of materials. Recently, want to get beans that hold yellow virus resistance, can't find them. This problem was discussed at the last CGC. The policy in ARS is that if it is protected or registered in Crop Science it goes to Ft. Collins. We are talking about varieties from breeding program that no longer exist. Preference is given to wild species when some of the developed materials should be given the priorities. A lot of breeding programs disappear and no one saves them. The CGC's do a good job of monitoring everything that is going on, but you pointed out one spot that is a problem. Periodically one or several scientist that is a member of the committee would go through an old list and check it against GRIN to see if it is there, if not they'll put out an email looking for that particular accession.

The CGC's are very good about monitoring collections that are in danger due to breeders that retire. Dick Robinson was pouring his stuff in a bin. PGRU took what we could from his field. The best person to help you is the breeder. If you go with the Breeder, they will tell you what is wrong with their varieties. The hardest is when the retirement has occurred and the collection has to be culled through. Jerry Marx was dying and had scientists go through his collection and helped expedite culling through it. Recently, we sent a van down to pick up a collection from a family member. A list of the collection was sent to Cris Cramer to go through. CGC for tomato, Al Stoner identified a tomato collection , there were 15-20 that weren't in there and we went and got them. It is a continual process. Developed traits in breeder lines get lost. The CGC should request them as they relate to different curators. 95 % are deposited in Ft. Collins. Quite often, whoever is hired after the person has left they have no interest in maintaining the cultures. Would love to have the early varieties, but the wild material is richer in diversity. NAFEX. Seed Savers Associations, etc. there are places out there that do that. We have given a priority to genetic diversity and not heirloom diversity. The Johnny Appleseed gene pool is very narrow.

Plan for next year : Ames, IA along with other groups. RTAC and CGC chairs as well as PGOC . 3rd-4th week in July. Donglin Zhang will be new Chair next year. After IA, he invited us to Maine the next year.

Accomplishments

Approximately 11,700 accessions of seed propagated crops (tomato, onion, squash, radish, cabbage, cauliflower, broccoli, other cole crops, celery, ground cherry, asparagus, and buckwheat) were maintained. There were 300 accessions regenerated; 230 biennial crop accessions were grown to produce plants for use in seed production in 2005. In 2004 there were 3873 seed lots distributed in 270 orders (1657 seed samples for 103 seed orders were distributed to users in the states that are part of NE-9). In 2005, up through April 1, there were 1149 seed lots distributed in 95 seed orders (238 samples for 21 orders were distributed to users in the states that are part of NE-9).<br /> <br /> <br /> Approximately 5200 accessions of vegetatively-propagated crops (apple, grape and sour cherry) were maintained In 2004 there were 7202 accessions distributed in 238 orders (5146 accessions for 78 orders were distributed to users in the states that are part of NE-9). In 2005, up through April 1, there were 1769 accessions distributed in 83 orders (941 accessions for 21 orders were distributed to users in the states that are part of NE-9). Most of the samples of the clonal collection were for DNA and leaf samples for DNA extraction, but multiple samples of cuttings, pollen and seeds of wild species were sent as well. <br /> <br /> <br /> The future availability of vegetable crop germplasm has been assured through several new initiatives. The tomatillo collection was increased in size by a factor of 3.5 with the incorporation of 100 accessions recently collected in Mexico. The Cucurbita collections of Ovid Shifriss (Rutgers University) were acquired and are now being evaluated for incorporation in the Cucurbita collections of Geneva, Ames, IA, and Griffin, Georgia. Because short-day onions cannot be regenerated at Geneva, an ongoing SCA was continued with New Mexico State University for regeneration of short-day onions. <br /> <br /> <br /> Approximately 243 digital images were recorded from 143 accessions of tomato, onion and winter squash. These are being processed and will be loaded onto GRIN. Characterization data was recorded on 118 accessions of onions and tomato for minimal descriptor lists for loading on GRIN to enable stakeholders to better search for their requirements. In apple, 171 additional accessions were characterized with 25 descriptors. Morphological characterization with priority descriptors in grape is continuing with nearly 95% of the collection completed. Digital images were taken on 130 additional apple accessions bringing the total to 900. Additional disease resistance screening of seedlings from the collection of wild apple from Armenia as well as grafted seedlings from Kazakhstan inoculated with fire blight was completed in 2004 as a result of the SCA with H. Aldwinckle. Preliminary results indicate that both fire blight and apple scab resistance is present in the genotypes tested. If durable, they could be important new sources of disease resistance genes for use in apple breeding programs. As of fall 2004, 600 of the 1200 Central Asian seedlings of M. sieversii fruited and have been characterized for horticultural traits. In addition, we completed digital imaging on fruits of 465 of those seedlings. In 2005 we expect to complete 200 additional seedlings that will fruit for the first time. <br /> <br /> <br /> Cryopreservation in apple is nearly complete with 37 more samples preserved in 2005. In 2004 we processed 120 new accessions with the recovery tests completed in March 2005. We found that 50% of those had low viability which was expected because this group included a large number of accessions representing Malus species that originated in mild climates. This group provides our collaborators at NCGRP a group of accessions to investigate alternative methods of cryogenic storage. In 2004 and 2005.we reprocessed 123 apple accessions that had confirmed low viability (<30% viable) after the first processing run. As we calculated based on previous investigations, a significant number of these would have improved viability. For the 103 processed in 2004, graft recovery tests in April 2005 showed that 72 of these accessions had viability >40%. The 31 that remained < 30% will be part of further investigations. Therefore, overall, >2300 accessions or 95% of the collection are backed up. We completed graft recovery assays on apple buds stored for 15 years and found no decline in viability as compared to the same accessions tested at eight years in storage. Nearly 50% of the tart cherry security backup via cryopreservation is completed. <br /> <br /> <br /> We are also collaborating with NCGRP on a newly-initiated project to determine strategies to preserve alleles (in the form of seeds) from wild accessions of Vitis and Malus collections. Using SSR markers, we determined strategies for preserving for the long term, seeds and pollen of wild germplasm to supplement seed and clones from original collections.<br /> <br />

Publications

Baldo, A.M., L.D. Robertson, and J.A. Labate. 2005. Highly polymorphic genes in cultivated tomato. HortScience (in press).<br /> <br /> <br>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.<br /> <br /> <br>Baldo, A.M., D. Huntley, L.D. Robertson, and J.A. Labate. 2005. High-throughput SNP prediction in tomatoes based on ESTs. p. 7 In Final Abstracts Guide, Plant and Animal Genome XIII, San Diego, CA.<br /> <br /> <br>Baldo, A.M., D. Huntley, L.D. Robertson, and J.A. Labate. 2004. High-throughput SNP prediction in tomatoes based on ESTs. p. 14 In Program Abstracts, Tomato Breeders Roundtable, Annapolis, MD.<br /> <br /> <br>Baldo, A.M., J. Labate., and L.D. Robertson. 2004. Prediction of single nucleotide polymorphisms in domestic tomato: How useful is EST sequence diversity? In Conference Program, Intelligent Systems for Molecular Biology 2004, Glasgow, Scotland.<br /> <br /> <br>Baldo, A.M., D. Huntley, L.D. Robertson, and J.A. Labate. 2005. High-throughput SNP prediction in tomatoes based on ESTs. P. 7 In Final Abstracts Guide, Plant and Animal Genome XIII, San Diego, CA.<br /> <br /> <br>Cramer, C. and L.D. Robertson. 2004. Seed Regeneration of Short-Day Onion Accessions in the U. S. collection. Poster presented at the National Allium Research Conference. 9-10 December 2004, Grand Junction, CO.<br /> <br /> <br>Fazio, G., A.M. Baldo. 2005. Placement of apple rootstock cultivars within the Malus germplasm. P. 196 In Final Abstracts Guide, Plant and Animal Genome XIII, San Diego, CA.<br /> <br /> <br>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:--<br /> <br /> <br>Labate, J.A., and A.M. Baldo. 2005. Discovery of highly polymorphic genes in tomato cultivars. (manuscript under review by Mol Breeding).<br /> <br /> <br>Volk G.M., Ann A. Reilley, Adam D. Henk, Christopher M. Richards, P.L. Forsline, and H.S. Aldwinckle. 2005. Ex situ conservation of vegetatively propagated species: Development of a seed-based core collection or Malus sieversii. J. Amer. Soc. Hort. Sci. 130: 203-210.<br /> <br /> <br>Baldo A.M., J. Labate, and L.D. Robertson. 2004. A search for molecular diversity in tomato. P. 147 In Final Abstracts Guide, Plant and Animal Genome XII, San Diego, CA. <br /> <br /> <br>Forsline, P.L. H.S. Aldwinckle, E.E. Dickson, J. J. Luby, and S.C. Hokanson. 2004. Collection, Maintenance, Characterization and Utilization of Wild Apples of Central Asia, p. 1-61. In: J. Janick, P. Forsline, E. Dickson, R. Way and M. Thompson (eds.). Horticultural Reviews, vol. 29. Wild apple and fruit trees of Central Asia. Wiley, New York. <br /> <br /> <br>Forsline, P.L. and H. S. Aldwinckle. 2004. Seven expeditions to collect wild apple germplasm in Central Asia, China, Russia and Turkey. HortScience. 39:743 (abs).<br /> <br /> <br>Forsline, P.L. and Aldwinckle, H.S. 2004. Evaluation of Malus sieversii seedling populations for disease resistance and horticultural traits. Acta Hort. 663:529-534.<br /> <br /> <br>Labate, J.A, L.D. Robertson, and T. Bjorkman. 2004. Utility of BoCAL-a and BoAP1-a genotypes in identifying broccoli and cauliflower accessions. HortScience 39:773.<br /> <br /> <br>Luby, J.J., Bedford, D.S. and Forsline, P.L. 2004. Winter hardiness in the U.S. Department of Agriculture Malus Core Collection. Acta Hort. 663:605-608.<br /> <br /> <br>Owens, C. A.M. Baldo. 2004. Mining the EST database and genomic sequences for SNP discovery in Vitis. P. 148 In Final Abstracts Guide, Plant and Animal Genome XII, San Diego, CA. <br /> <br /> <br>Robertson, L.D., A.M. Baldo, S.M. Sheffer, and J.A. Labate. 2004. Sequence-based amplified polymorphisms (SBAPS) are useful for studying genetic diversity of winter squash. P. 153 In Final Abstracts Guide, Plant and Animal Genome XII, San Diego, CA.<br /> <br /> <br>Stushnoff, C., A.E. McSay, J.J. Luby, and P.L. Forsline. 2004. Diversity of phenolic antioxidant content and radical scavenging capacity in the apple germplasm collection. XXV1 International Horticultural Congress. Symposium 21 (Plant Genetic Resources: The Fabric of Horticultures Future). Acta Horticulturae 623: 305-312.<br /> <br /> <br>Towill, L.E., P.L. Forsline, C. Walters, J. Waddell and J. Laufman. 2004. Cryopreservation of Malus germplasm using a winter vegetative bud method: Results from 1915 accessions. Cryoletters 25:323-334.<br />

Impact Statements

1. Germplasm is maintained and distributed in accordance with standards for viability, genetic integrity, and accurate identity. Increased characterization of germplasm and the addition of digital images have increased the efficiency of use of the germplasm collections. Fingerprinting B. oleracea accessions may lead to diagnostic molecular tools to distinguish broccoli versus cauliflower seeds. Discovered genetic variation in tomato that will enable breeders to target existing genetic variation.

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Report Information

Participants

Burr, Thomas  tjb1@cornell.edu, Cornell University;
Griffiths, Phillip - pdg8@cornell.edu, Cornell University;
Loy, Brent  jbloy@cisunix.unh.edu, University of New Hampshire;
Zhang, Donglin  donglin@umit.maine.edu;
Other Attendees:
Bretting, Peter - pbretting@ars.usda.gov, USDA, ARS, National Program Staff;
Ellis, Dave  david.ellis@ars.usda.gov, NCGRP;
Fretz, Tom  NERA Director  tfretz@umd.edu;
Forsline, Philip - Philip.Forsline@ars.usda.gov, USDA, ARS;
Mowder, Jimmie  jmowder@ars.usda.gov, USDA, ARS, NGR;
Robertson, Larry - lrobertson@pgru.ars.usda.gov, USDA, ARS;
Simon, Charles  csimon@ars-grin.gov;
Francis, David  francis.77@osu.edu

Brief Summary of Minutes

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.

Accomplishments

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. <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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. <br /> 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.<br /> <br /> <br /> 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. <br /> <br /> <br /> 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. <br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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<br />

Publications

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.<br /> <br /> <br /> 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.<br /> <br /> <br /> Chetelat, R. T. 2005. Revised list of monogenic stocks. TGC 55:48-69. <br /> <br /> <br /> 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.<br /> <br /> <br /> Jones, C. M. 2005. The extreme search for tomato genetics: hunting wild tomato in the Andes. In Good Tilth 16 (4): 10-11.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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. <br /> <br /> <br /> Final Public Seed Initiative Compact Disc<br /> <br /> <br /> Public Seed Initiative Website: www.plbr.cornell.edu/psi.<br /> <br /> <br /> Organic Seed Partnership Website: www.organicseedpartnership.org.<br /> <br /> <br /> 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<br /> <br /> <br /> 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<br /> <br /> <br /> 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<br /> <br /> <br /> 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 <br /> <br /> <br /> 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<br /> <br /> <br /> 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. <br /> <br /> <br /> 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.<br /> 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<br /> <br /> <br /> 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<br /> <br /> <br /> Simon, C.J. 2006. Molecular Characterization of the US Apple Germplasm Collection. 3rd International Rosaceae Genomics Conference. Pg. 112<br /> <br /> <br /> Forsline, P.L. and K.E. Hummer. 2006. Fruit Exploration Supported by the National Plant Germplasm System 1980 to 2004. HortScience  accepted<br /> <br /> <br /> 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<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> 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.<br /> <br /> <br /> Forsline, P.L. 2006. Forum - Travels To Gather, Improve Apples Start To Bear Fruit. Agricultural Research 54:2.<br /> <br /> <br /> Forsline, P.L. 2006. Pons, L. 2006. Remarkable Kazak Apples. Agricultural Research 54:4-6.<br /> <br /> <br /> 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".<br /> <br /> <br /> Forsline, P.L. January 13, 2006. THE NORTHWEST AG INFORMATION NETWORK. http://www.aginfo.net/. Back to the future of apples, Pt. 1<br /> <br /> <br /> Forsline, P.L. January 16, 2006. THE NORTHWEST AG INFORMATION NETWORK. http://www.aginfo.net/. Back to the future of apples, Pt. 2<br /> <br /> <br /> 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.<br /> <br /> <br /> 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<br />

Impact Statements

1. 1. Both the seed and clonal crops for which Geneva has responsibility are important components of agriculture in the Northeast. Many Northeastern State Agricultural Experiment Stations (SAESs) have research and extension responsibilities for these valuable commodities. The vegetable crops maintained at Geneva account for about 45% of the value of U.S. production and the fruit crops account for 53% of the value of production of fruit trees and vines.
2. 2. Germplasm is maintained and distributed in accordance with standards for viability, genetic integrity, and accurate identity. Increased characterization of germplasm and the addition of digital images have increased the efficiency of use of the germplasm collections. Fingerprinting B. oleracea accessions may lead to diagnostic molecular tools to distinguish broccoli versus cauliflower seeds. Discovered genetic variation in tomato will enable breeders to target existing genetic variation.
3. 3. Combining genes from diverse sources into germplasm is more useful to plant breeders to produce improved germplasm and cultivars.
4. 4. As biotechnology programs in the Northeastern U.S. have grown, plant genetic resource conservation has become more critical. Molecular biologists and genome researchers must have this reservoir of diversity available if they are to identify plants with useful genes that breeders can then exploit. Continuing progress in improving the performance of crop plants while simultaneously improving our understanding of plant biology will be accomplished by the integration of new technologies with the broadest possible array of genetic resources.

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Report Information

Participants

Burr, Thomas - tjb1@cornell.edu, Cornell University;
Griffiths, Phillip - pdg8@cornell.edu, Cornell University;
Merwin, Ian - im13@cornell.edu;
Stoner, Kimberly - kimberly.stoner@po.state.ct.us;
Bretting, Peter - pbretting@ars.usda.gov, USDA, ARS, National Program Staff;
Forsline, Philip - Philip.Forsline@ars.usda.gov, USDA, ARS;
Robertson, Larry - larry.robertson@ars.usda.gov, USDA, ARS;
Labate, Joanne - joanne.labate@ars.usda.gov, USDA, ARS;
Simon, Charles - charles.simon@ars.usda.gov, USDA, ARS;
Baldo, Angela - angela.baldo@ars.usda.gov, USDA, ARS (Conference Call);

Brief Summary of Minutes

The 2008 annual meeting was held Tuesday June 8, 2008 from 8:30 AM to 12:00 PM on the campus of Cornell University. Dr. Tom Burr introduced himself as the Administrative Advisor of the NE-09 and Director of the NYSAES. Dr. Ian Merwin was Chairman of the committee and made arrangements for the meeting and the afternoon visits to Freeville and Lansing farms. Phil Forsline, Larry Robertson, Charles Simon, Joanne Labate, and Angela Baldo made brief presentations about the activities and research for the past year and referred to the RL report for NE9 for further details. Kim Stoner presented the work with entomology at the Connecticut Agricultural Experiment Station. Phillip Griffiths briefly discussed his use of bean germplasm and his evaluation of the radish collection and the collection of digital images of foliage and hypocotyls for upload to GRIN. Reports from Brent Loy at New Hampshire and Joseph Goffreda from Rutgers were passed out to the group. Peter Bretting discussed the status of ARS budgets and then discussed the Plant Germplasm Operations Committee meeting held in Ft. Collins, Colorado in June of this year. An impact statement comparing the budgets of NE9 with W6, S9, and NC7 was passed out showing the significantly less support for NE9 versus the other regional germplasm projects. The RL report provided a proposed five year budget to bring the budget of NE9 closer to that for the other germplasm projects. The meeting adjourned for lunch at 12 PM. After lunch the group visited the Freeville farm to observe work with organic agriculture with Michael Gloss and then proceeded to Lansing farm where Ian Merwin presented current research at Cornell with fruit crops.

Accomplishments

During the period of October 1, 2003 through September 30, 2008 seed regenerations of vegetable Brassicas, tomatoes, tomatillos, celery, artichokes, celery, buckwheat, and Cucurbits were completed for 1508 accessions. Approximately two thirds of these accessions were grown over two years (seasons) because of their biennial nature. A total of 12,641 accessions of seed-propagated crops were successfully maintained during the past year. The future availability of this germplasm is therefore assured.<br /> <br /> Approximately 1525 digital images were recorded in during the period of this project from 800 accessions of tomato, onion and winter squash. These are being processed and will be uploaded to GRIN. Characterization data was recorded on 792 accessions of onion and tomato for minimal descriptor list for loading on GRIN to enable stakeholders to better search for their requirements.<br /> <br /> During the period of this project (from October 1, 2008 through August 14, 2008) a total of 1,322 orders for 22,884 seed germplasm samples and 1,476 orders for 41,726 samples of apple, grape and cherry germplasm were filled for clients and stakeholders. A large number of these samples were distributed in the northeast; 273 seed and 4,616 clonal samples for 487 seed and 24,498 clonal orders were distributed to users in the states that are part of NE-9. Most of the samples of the clonal collection were for DNA and leaf samples for DNA extraction, but multiple samples of cuttings, pollen and seeds of wild species as well as were sent. Delivery of germplasm to clients and stakeholders is the primary way in which the results of this Unit's activities are distributed to the public. <br /> <br /> 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. All characters are scored according to OIV recommendations. 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. A project was initiated in Spring 2008 to phenotype the grape collection based on a proposal submitted to the Grape CGC. A student was hired in May 2008 supported by the CGC grant and she has collected bloom data on the entire grape collection. This data will be compared with data collected in 3 previous years. Bloom will then be assessed for each of these years using the Growing Degree Day criteria. This data will be published and loaded to GRIN. In addition, the student is taking digital images of leaves on the entire grape collection and later on of clusters and berries on a background grid for better perspective. The grid method has been used for 1600 apple and 50 cherry accessions. <br /> <br /> During 2008 we completed data analysis and manuscript submission of a multilocus SNP (single nucleotide polymorphism) diversity study using a panel of 30 diverse L. esculentum accessions, one breeding line, and one L. peruvianum accession. The first manuscript focused on comparing three sequence-based marker types. The results showed that there was no apparent bias in diversity estimates among marker types developed by various bioinformatics methods (JA Labate, LD Robertson, F Wu, SD Tanksley, and AM Baldo. 2008. EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato (Solanum lycopersicum L.), submitted to Heredity). The second manuscript focused on variation among accessions. Three populations - primary centers of diversity, contiguous countries, and secondary centers, shared 0.97 of their variation (FST = 0.03). Mean diversity decreased (He = 0.254, 0.152, 0.092, respectively) while the mean coefficient of inbreeding increased (FIS = 0.793, 0.947, 1.000, respectively), in the populations. Linkage disequilibrium (LD) was high within but not between loci. Interspecific introgression was observed for at least seven tomato lines and five loci. Complex demographic processes (e.g. bottlenecks, global exchange of germplasm, and introgression from multiple wild species), as are clearly evident in tomato, must be incorporated into inferences regarding the molecular basis of domestication and crop improvement. (Labate, JA, LD Robertson, and AM Baldo. 2008. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.), submitted to Heredity).<br /> <br /> Broccoli (Brassica oleracea var. italica Plenck.) and cauliflower (Brassica oleracea var. botrytis L.) are ancient polyploids. When applying molecular markers, allelism can be difficult to distinguish from paralogous copies. We have resequenced 48 gene fragments in both inbred parent lines and one progeny line of the N x B mapping population. Polymorphisms are currently being assessed for good reproducibility and diploidy. SNPs that show favorable properties can be further tested for robustness on a large sample of diverse accessions. The tested markers include candidate genes for agronomic traits and ecological adaptation. These markers will later be used to estimate population structure in B. oleracea to see if broccoli accessions are genetically distinguishable from cauliflower accessions. The polymorphisms will also be valuable for marker-assisted breeding. (Labate, JA, SM Sheffer, LD Robertson, and AM Baldo. 2008. SNP marker development in broccoli and cauliflower (Brassica oleracea). Plants and Soils: Montreal '08 Conference).<br /> <br /> Cryopreservation in apple is nearly complete with 2275 of the 2508 clones on inventory completed (91% of the collection backed up). These were processed over time from 1993 to 2007 (Towill, L.E., P.L. Forsline, C. Walters, J. Waddell and J. Laufman. 2004. Cryopreservation of Malus germplasm using a winter vegetative bud method: Results from 1915 accessions. Cryoletters 25:323-334). In 2008, we completed graft recovery assays on apple buds stored for 16-19 years (those processed in 1989, 1990, and 1991, 1992 which were part of the original 'Pilot Project'): (Forsline, P.L., C. Stushnoff, L.E. Towill, J.W. Waddell, W.F. Lamboy and J. R. McFerson. 1998. Recovery and longevity of cryopreserved apple buds. J. Amer. Soc. Hort. Sci. 123:365-370). This grafting was done to make a final determination of viability over the long term. We previously tested viability for the accessions processed only in the year of anniversary for: 1 month; 1 year; 2 years; 4 years; 8 years; and 15 years of storage. This year we determined it was important to remove the rootstock variability and we grafted all 80 accessions across the processing years. That left the only variable as 'years in storage' from 16 to 19 years. Early analysis shows that there has been no decline in viability for most of the accessions when comparing baseline viability with LN storage from 16-19 years. This data is being analyzed by collaborators at NCGRP and a manuscript will be drafted as the sequel to J. Amer. Soc. Hort. Sci. 123:365-370 which included up to 4 years in storage. <br /> <br /> Cryogenic storage in Malus is very effective in managing our collection because we know that we can recover accessions if they are lost due to an environmental influence in our field plantings. Previously 80 accessions had been rescued mostly due to severe fire blight infestation. In June 2008, we rescued 40 additional accessions by grafting these on EMLA 7 directly in the field nursery. We have been able to better manage the field collections of apple by repropagating on EMLA 7, a semi-dwarf rootstock that limits the vigorous growth that induces 'shoot blight'. The six-year, phased repropagation project was completed with last planting made in spring 2007. In addition, a plant growth regulator (prohexadione calcium, 'Apogee') is being applied routinely to minimize fire blight on shoots.<br /> <br /> We processed for cryogenic storage in February 2008 at NCGRP 30 more tetraploid cherry accessions. This brings our total to 78 of our 125 accessions now backed up in cryogenic storage. We will test the baseline viability of those 30 in 2009 along with the 10 yr viability of the other 48. This will be done using the graft recovery process where 10 buds/accession are grafted.<br /> <br /> We collaborated with 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. We produced 60,000 seeds on trees of Malus sieversii that represent two diverse sites in Kazakhstan. These were from controlled crosses of selected sub sets and the pollinations and harvests were made in 2004-2006. Final seeds were harvested in fall 2006 and seeds were placed in long term storage. Sub sets of these seeds were germinated in fall 2007 to confirm allele recovery. Over 800 seedlings in 2008 were screened for apple scab resistance in an SCA project and leaves were collected to extract DNA to validate the genetic diversity from these crosses. This project is important since it supplements original seed collected from the wild in Kazakhstan in 1995.<br /> <br /> A Reimbursable Cooperative Agreement (RCA), the Organic Seed Partnership, was initiated with Cornell University and was supported by the Organic Agriculture Research and Extension Initiative (OREI). The Organic Seed Partnership is a continuation of efforts for another current RCA project, the Public Seed Initiative and built on the success of this project. The Organic Seed Partnership provided training and facilities for organic farmers producing organic seed of heirloom and new publicly developed vegetable varieties. It also provided germplasm resources for organic farmer participatory vegetable breeding projects. The project supported efforts with organic farmers, small farmers, and small seed producers in training and demonstrating small-scale seed production of heirlooms and improved public varieties of vegetables. A web site was developed that provided easy access to details about scheduled events, information about seed production and processing, results of on farm trials, and variety descriptions. This website is still maintained to provide useful information to organic farmers. During the period 2003-2008 these projects provided demonstrations, training workshops, and community seed days. More than 10,000 people observed demonstrations at the Common Ground Fair in Unity, Maine, the NOFA summer conference at Amherst, Massachusetts, and the Empire Farm days at Seneca Falls, NY. Workshops and community seed days were conducted for over 700 participants. This has increased the availability of heirloom and new publicly bred germplasm for use by small and organic farmers.<br /> <br /> Abscission or retention of ripening fruit is a major component of seed dispersal strategies and also has important implications for horticultural production. Abscission-related traits have generally not been targeted in breeding efforts and their genetic bases remain mostly unknown. Collaborating with Horticulturists from Michigan State University, 144 Malus accessions representing wild species, domestic cultivars, and hybrids for abscission-related traits were evaluated. We found that seasonal timing of fruit abscission in wild species and hybrids showed a broad distribution similar to that seen for domestic cultivars, and that internal ethylene concentration at the time of abscission varied by over three orders of magnitude. Wild species, domestic cultivars, and hybrids all included representatives that showed abscission of fruit prior to substantial production of ethylene, as well as accessions that retained fruit for a significant period of time following ethylene production. For all accessions that retained fruit, fruit removal resulted in abscission of the pedicel, and exogenous ethylene promoted abscission, suggesting that the abscission zone was functional. Our results suggest important roles for mechanisms independent of fruit ethylene production in abscission.<br /> <br /> The future availability of vegetable crop germplasm has been assured through continuation of two SCAs for regeneration. Because short-day onions cannot be regenerated at Geneva, an ongoing SCA was continued with New Mexico State University for regeneration of short-day onions as well as an ongoing SCA with University of California for regeneration of wild tomato germplasm.<br /> <br /> The cultivated tomato germplasm collection at PGRU underwent several major changes in 2006/2007. First approximately 750 unique accessions maintained at the National Center for Genetic Resources Preservation (NCGRP) was incorporated into the collection maintained at Geneva and marked as backups at the NCGRP. All duplicate accessions of tomato from the PGRU and NCGRP were inactivated, though seed is being maintained for possible future genetic studies. The accessions with local numbers ('G') that were left after the inactivation were assigned 'PI' accession numbers, with only a few local numbers maintained for material that is being used in genetic studies and that will not be incorporated into the germplasm collection at this time. Approximately 2,000 samples for backup at NCGRP were sent to replace older, smaller, and poor quality previous backups. This leaves us now with a cultivated tomato germplasm collection of 5,869 accessions.<br /> <br /> We sequenced 48 loci (22.5 kb) for a panel of 30 diverse L. esculentum accessions, one breeding line, and one L. peruvianum accession. These data will give us precise estimates of single nucleotide polymorphism (SNP) diversity within domesticated tomato and divergence with a wild relative. The data will be used to test hypotheses regarding selection, drift, and introgression in the tomato gene pool (Labate, J.A., L.D. Robertson, S.M. Sheffer, F.Wu, S.D. Tanksley and A.M. Baldo. 2006. DNA polymorphism estimates within domesticated tomato. Sol2006. Madison, WI). The data will also be used to estimate bias in SNP marker types developed by various bioinformatics methods (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).<br /> <br /> Limited genetic variation within the cultivated tomato Solanum lycopersicum has restricted the use of molecular markers as tools for crop improvement. During the past year we have completed the lab work for surveying a set of 51 gene fragments in a tomato geographic diversity panel to analyze Solanum lycopersicum intraspecific variation. This will give us an increased understanding of the nature of variation in our collection. The newly discovered polymorphisms can be used in intraspecific populations for marker-assisted breeding.<br /> <br /> We continue to lay the groundwork for molecular diversity studies of broccoli (Brassica oleracea var. italica) and cauliflower (Brassica oleracea var. botrytis), two closely related botanical varieties. We are resequencing 48 gene fragments using inbred parent line BI87053 (homozygous recurrent inbred Calabrese broccoli) of the N x B mapping population. Primers were chosen based on literature searches and include many candidate genes for agronomic traits and ecological adaptation such as flowering time, secondary metabolism, fatty acid synthesis, disease and pest resistance, phytochromes, floral meristem identity, and ethylene transduction. These markers will later be used to estimate population structure in B. oleracea to see if broccoli accessions are genetically distinct from cauliflower accessions. The polymorphisms will also be valuable for marker-assisted breeding.<br /> <br /> The majority of the tomatillo collection was characterized in 2005 with data taken for 35 descriptors and with digital imaging of all accessions at several stages of plant phenology. The most import character measured was self-fertility, which was estimated by taking measurements to compare seed production with and without pollinators to determine self-fertility. Several accessions were found that had high levels of self-fertility, a limiting factor in developing breeding programs for this potential new crop in the U.S. Twelve organic farmers in New York evaluated these accessions in 2006 for their potential for production under organic production systems through the Organic Seed Partnership (of which PGRU was a part of) which was funded by the OREI.

Publications

Aradhaya, M.K., C.F. Weeks, and C.J. Simon 2004. Molecular characterization of variability and relationships among seven cultivated and selected wild species of Prunus L. using amplified fragment length polymorphism. Scientia Horticulturae. 103:131-144<br /> <br /> Aradhya M.K., G.S. Dangl, B.H. Prins, J.M. Boursiquot, M.A. Walker, C.P. <br /> Meredith, C.J. Simon 2003. Genetic structure and differentiation in cultivated grape, Vitis vinifera L., Genetical Research 81:179-192<br /> <br /> Aradhya, M.K., C.J. Simon, and D. Potter 2006. Origin, evolution, and biogeography of Juglans L: A phylogenetic perspective. Acta Horticulture 705:85-94<br /> <br /> Aradhya, M.K., D. Potter, and C.J. Simon 2005. Cladistic biogeography of Juglans (Juglandaceae) based on chloroplast DNA intergenic spacer sequences. In: Darwin's Harvest: New approaches to the Origins, Evolution, and Conservation of Crop Plants. Motley, T.J., Zerega, N., and Cross, H. (eds.), Columbia University Press, New York. 143-170<br /> <br /> Baldo, A.M., D. Huntley, L.D. Robertson, and J.A. Labate. 2004. High-throughput SNP prediction in tomatoes based on ESTs. p. 14 In Program Abstracts, Tomato Breeders Roundtable, Annapolis, MD.<br /> <br /> Baldo, A.M., D. Huntley, L.D. Robertson, and J.A. Labate. 2005. High-throughput SNP prediction in tomatoes based on ESTs. p. 7 In Final Abstracts Guide, Plant and Animal Genome XIII, San Diego, CA..<br /> <br /> Baldo, A.M. and J. Labate. 2003. Polymorphism prediction. p. 126 In Conference Program, ISMB 2003, Brisbane, Australia.<br /> <br /> Baldo, A.M., J. Labate, and L.D. Robertson. 2004a. A search for molecular diversity in tomato. p. 147 In Final Abstracts Guide, Plant and Animal Genome XII, San Diego, CA.<br /> <br /> Baldo, A.M., J. Labate., and L.D. Robertson. 2004b. Prediction of single nucleotide polymorphisms in domestic tomato: How useful is EST sequence diversity? In Conference Program, Intelligent Systems for Molecular Biology 2004, Glasgow, Scotland.<br /> <br /> Baldo, A.M., W.F. Lamboy , L.D. Robertson, S.M. Sheffer, and J.A. Labate. 2007. Genetic variation among tomato landraces. p. 33 In Final Program, 2007 Tomato Breeders Roundtable, State College, PA<br /> <br /> Baldo, A.M., W.F. Lamboy, C.J. Simon, J.A. Labate, Y. Wan, and S.M. Sheffer. 2007. SNP validation and genetic diversity in cultivated tomatoes and grape. p. 144 In Final Abstracts Guide, Plant and Animal Genome XV, San Diego, CA.<br /> <br /> Baldo, A.M, Malnoy, M., Aldwinckle, H.S. 2008. A Search For Novel Apple Resistance Genes Among Wild And Rootstock Accessions. p. 233. In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA.<br /> <br /> Baldo, A.M., L.D. Robertson, and J.A. Labate. 2005a. Discovery of highly polymorphic genes in tomato cultivars. In Conference Program, Intelligent Systems for Molecular Biology 2005, Detroit, MI.<br /> <br /> Baldo, A.M., L.D. Robertson, and J.A. Labate. 2005b. Highly polymorphic genes in cultivated tomato. HortScience 40:999.<br /> <br /> Baldo, A.M., L. Robertson, S.M. Sheffer, and J.A. Labate. 2006. Polymorphism among EST-based markers in tomato. p. 20 In Final Abstracts Guide, 2006 Tomato Breeders Round Table & Tomato Quality Workshop, Tampa, FL.<br /> <br /> Baldo, A.M., L.D. Robertson, S.M. Sheffer, W.F. Lamboy, and J.A. Labate. 2006. Evaluation of SNP markers across tomato landraces. p. 146 In Final Abstracts Guide, Plant and Animal Genome XIV, San Diego, CA.<br /> <br /> Baldo, A.M., L.D. Robertson, S.M. Sheffer, W.F. Lamboy, and J.A. Labate. 2008. Genetic diversity in tomato: SNPs from various sources show similar amounts of polymorphism and bottlenecking due to domestication. p. 6. In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA.<br /> <br /> Baldo, A.M, Volk, G.M., Olmstead, J., Iezzoni, A. 2008. Resistance Gene Analogs In Cherries (Prunus spp.). p. 236. In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA.<br /> <br /> Bassett, C.L., Wisniewski, M.E., Baldo, A.M., Artlip, T.S., Farrell, R.E. 2008. Differential Expression Of Genes In Apple During Gradual Water Deficit Conditions. p. 136. In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA.<br /> <br /> Berger, J.D., L.D. Robertson, and P.S. Cocks. 2003. Agricultural potential of Mediterranean grain and forage legumes 2) Anti-nutritional factor concentrations in the genus Vicia. Genetic Resources and Crop Evolution 50: 201-212.<br /> <br /> Borejsza-Wysocka, E.E., Norelli, J.L., Baldo, A.M., Farrell, R.E., Bassett, C.L., Aldwinckle, H.S. 2008. High-Efficiency Generation Of RNAi Mutants Of Apple By Use Of Multi-Vector Transformation. p. 232. In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA.<br /> <br /> Cramer, C.S. and L. D. Robertson. 2005. Seed increase of short-day onion accessions. Allium Improv. Newsl. 14:18-20.<br /> <br /> Cramer, C.S. and L. D. Robertson. 2005. Seed regeneration of short-day onion accessions in the U.S. collection. HortScience. 40:998. (Abstr.)<br /> <br /> Dangl, G.S., K. Woeste, M.K. Aradhya, A. Koehmstedt, C. Simon, D. Potter, C.A Leslie, and G. McGranahan 2005. Characterization of 14 microsatellite markers for genetic diversity analysis and cultivar identification of walnut. Journal of the American Society for Horticultural Science. 130(3):348-354<br /> <br /> Fazio, G., H.S. Aldwinckle, G.M. Volk, C.M. Richards, W. J. Janisiewicz, and P.L. Forsline. 2008. Progress in evaluating Malus sieversii for disease resistance and horticultural traits. Acta Horticulturae (accepted).<br /> <br /> Fazio, G., P.L. Forsline, H. Aldwinckle, and L. Pons. 2008. The Apple Collection in Geneva, NY: A Resource for The Apple Industry Today and for Generations to Come. New York Fruit Quarterly 3:3-6. 16: 5-8.<br /> <br /> Forsline, P.L. and H. S. Aldwinckle. 2004. Evaluation of Malus sieversii seedling populations for disease resistance and horticultural traits. EUCARPIA Symposium on Fruit Breeding and Genetics; 1st to 5th September 2003, Angers, France. Acta Horticulturae 663: 529-534.<br /> <br /> Forsline, P.L. and K.E. Hummer. 2006. Fruit exploration supported by the National Plant Germplasm System 1980 to 2004. HortScience 42:200-202.<br /> <br /> Forsline, P.L. H.S. Aldwinckle, E.E. Dickson, J. J. Luby, and S.C. Hokanson. 2003. Collection, Maintenance, Characterization and Utilization of Wild Apples of Central Asia, p. 1-61. In: J. Janick, P. Forsline, E. Dickson, R. Way and <br /> M. Thompson (eds.). Horticultural Reviews, vol. 29. Wild apple and fruit trees of Central Asia. Wiley, New York. <br /> <br /> Forsline, P.L., J. Luby, and H.S. Aldwinckle. 2008. Fire blight incidence on Malus sieversii grown in New York and Minnesota. 11th International International Workshop on Fire Blight Conference. Acta Horticulturae (accepted).<br /> <br /> Huntley, D, Baldo, A.M., Johri, S, and Sergot, M. SEAN: SNP prediction and display program utilizing EST sequence clusters. 2006. Bioinformatics 22(4):495-496<br /> <br /> Janisiewicz, W., Robert Saftner , William Conway and Philip Forsline. 2008. Preliminary Evaluation of Apple Germplasm from Kazakhstan for Resistance to Blue Mold Decay Caused by Penicillium expansum After Harvest. HortScience 43:420-426.<br /> <br /> Labate, J.A. 2008. Ch. 2 Molecular markers in germplasm conservation. p. 45-74. In C. Kole and A. Abbott, (ed.) Principles and practices of plant genomics vol 2. Science Publishers, Inc., Enfield, New Hampshire, USA; Plymouth, UK (in press).<br /> <br /> Labate, J.A. and Baldo, A.M. 2005. Tomato leaf tissue Lycopersicon esculentum STS genomic, sequence tagged site. Accessions BV448051 to BV448073.<br /> Labate, J.A. and Baldo, A.M. 2007. Anonymous genomic sequence of tomato. Accessions EU365695 to EU365773.<br /> <br /> Labate, J.A. and Baldo, A.M. Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion polymorphisms (Indels) in four cultivated tomato lines. Submitted to dbSNP. NCBI ss# 76883011 to 76883086, 77106585 to 77106606.<br /> <br /> Labate, J.A. and Baldo, A.M. Tomato SNP discovery by EST mining and resequencing. 2005. Molecular Breeding 16(4):343-349<br /> <br /> Labate, J.A., and A.M. Baldo. 2005. Tomato SNP discovery by EST mining and resequencing. Mol. Breeding 16:343-349.<br /> <br /> Labate, J.A., S. Grandillo, T. Fulton, S. Muños, A.L. Caicedo, I. Peralta, Y. Ji, R.T. Chetelat, et al. (39 total authors). 2007. Ch. 1 Tomato. p. 1-125. In C. Kole, (ed.) Genome mapping and molecular breeding in plants: Volume 5 Vegetables. Springer Publishing Co., NY.<br /> <br /> Labate, J.A., L.D. Robertson, A.M. Baldo, and T.N. Björkman. 2006. Inflorescence identity gene alleles are poor predictors of inflorescence type in broccoli and cauliflower. J. Amer. Soc. Hort. Sci. 131:667-673.<br /> <br /> Labate, J., L. Robertson, and T. Bjorkman. 2003. Genotypes at the BoCAL-a locus in B. oleracea do not predict broccoli, cauliflower, and purple cauliflower phenotype. HortScience 38:736.<br /> <br /> Labate, J.A, L.D. Robertson, and T. Bjorkman. 2004. Utility of BoCAL-a and BoAP1-a genotypes in identifying broccoli and cauliflower accessions. HortScience 39:773.<br /> <br /> Labate, J.A., L.D. Robertson, S.M. Sheffer, W.F. Lamboy, and A.M. Baldo. 2007. DNA sequence analyses of tomato germplasm conserved at the Plant Genetic Resources Unit (PGRU). p. 51 In The 4th Solanaceae Genome Workshop 2007, Jeju Island, Korea<br /> <br /> Labate, J.A., L.D. Robertson, S.M. Sheffer, F.Wu, S.D. Tanksley and A.M. Baldo. 2006. DNA polymorphism estimates within domesticated tomato. PAA/Solanaceae Abstract 366. Madison, WI.<br /> <br /> Labate, J.A., L.D. Robertson, S.M. Sheffer, W.F. Lamboy, F. Wu, S.D. Tanksley, and A.M. Baldo. 2007. EST, COSII, and arbitrary markers give similar estimates of nucleotide diversity in cultivated tomato (S. lycopersicum). p. 15 In Final Program, 2007 Tomato Breeders Roundtable, State College, PA<br /> <br /> Labate, J.A., S.M. Sheffer, W.F. Lamboy, and A.M. Baldo. 2008. Genomic sequences of tomato (Solanum lycopersicum) for comparison of three marker types. Direct submission to GenBank. Accessions EU797528 to EU797577.<br /> <br /> Labate, J.A. and Baldo, A.M. Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion polymorphisms (Indels) in four cultivated tomato lines. 2008. Submitted to dbSNP. NCBI ss# 76883011 to 76883086, 77106585 to 77106606.<br /> <br /> Labate, J.A. and Baldo, A.M. 2008. Anonymous genomic sequence of tomato. NCBI accessions EU365695 to EU365773.<br /> <br /> Labate, J.A., Robertson, L.D., Baldo, A.M. and Bjorkman, T. Inflorescence identity gene alleles are poor predictors of inflorescence type in broccoli and cauliflower. 2006. JASHS 131(5):667-673<br /> <br /> Labate, J.A., Robertson, L.D., Baldo, A.M., Sheffer, S.M. and Bjorkman, T. 2006. Brassica oleracea var. italica, GSL-ELONG, partial cds. Accessions DQ445730, DQ445731.<br /> <br /> Labate, J.A., S. Grandillo, T. Fulton, S. Muños, A.L. Caicedo, I. Peralta, Y. Ji, R.T. Chetelat, et al. (39 authors in total). 2007. Tomato. p. 1-125. In C. Kole (ed.) Genome mapping and molecular breeding in plants: Volume 5 Vegetables. Springer Publishing Co., NY.<br /> <br /> Luby, J.J., D. S. Bedford and P.L Forsline. 2004. Winter hardiness in the U.S. Department of Agriculture Malus core collection. EUCARPIA Symposium on Fruit Breeding and Genetics; 1st to 5th September 2003, Angers, France. Acta Horticulturae 663: 605-608.<br /> <br /> Malnoy, M., Baldo, A.M., Carlisle, C.M., Bowatte, D., Borejsza-Wysocka, E.E., Norelli, J.L., Farrell, R.E., Bassett, C.L., Gardiner, S.E., Aldwinckle, H.S. 2008. Identification And Mapping Of Genes Differentially Expressed During Interaction Of Resistant And Susceptible Apple Cultivars (Malus Xdomestica) With Erwinia amylovora. p. 232. In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA. <br /> <br /> Myers, C. T., and P. L. Forsline. 2008. Pest resistance status of hybrid releases housed in USDA's "core" Malus germplasm collection. Entomological Society of America, Eastern Branch. Annual Meeting, 9-11 March, 2008, Syracuse, NY.<br /> <br /> Myers, C.T., T.C. Leskey and P.L. Forsline. 2007. Susceptibility of fruit from diverse apple and crabapple germplasm to attack from plum curculio, Conotrachelus nenuphar (Herbst) (Coleoptera: Curculionidae). J. Econ. Entomol. 100(5): 1663-1671.<br /> <br /> Myers, C.T., W.H. Reissig, and P.L. Forsline. 2008. Susceptibility of fruit from diverse apple and crabapple germplasm to attack from apple maggot, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae). Journal of Economic Entomology. J. Econ. Entomol. 101(1): 206-215.<br /> <br /> Norelli, J.L., Gardiner, S.E., Malnoy, M., Aldwinckle, H.S., Baldo, A.M., Borejsza-Wysocka, E.E., Farrell, R.E., Lalli, D.A., Celton, J.M., Bassett, C.L., Korban, S.S., Wisniewski, M.E. 2008. Using Functional Genomics To Develop Tools To Breed Fire Blight Resistant Apples. p. 232. In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA. <br /> <br /> Postman, J., K. Hummer, E. Stover, P. Forsline, L.J. Grauke, F. Zee, T. Ayala-Silva, R. Krueger, and B. Irish. 2006. Fruit and Nut Genebanks in the U.S. National Plant Germplasm System. HortScience 41:1188-1194.<br /> <br /> Richards, C.M., Gayle M. Volk, Ann A. Reilley, Adam D. Henk, Dale Lockwood, Patrick A. Reeves, and Philip L. Forsline. 2008. Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Journal. (submitted to Tree Genetics and Genomics).<br /> <br /> Robertson, L.D., A.M. Baldo, S.M. Sheffer, and J.A. Labate. 2004. Use of Sequence-based polymorphisms for studying genetic diversity of winter squash. Eighth Eastern Great Lakes Molecular Evolution Meeting. Ithaca, NY<br /> <br /> Robertson, L.D., A.M. Baldo, S.M. Sheffer, and J.A. Labate. 2004. Sequence-based amplified polymorphisms (SBAPs) are useful for studying genetic diversity of winter squash. p. 153 In Final Abstracts Guide, Plant and Animal Genome XII, San Diego, CA.<br /> <br /> Robertson, L.D., and J.A. Labate. 2007. Genetic resources of tomato (Lycopersicon esculentum var. esculentum) and wild relatives. p. 25-75. In <br /> M.K. Razdan and A.K. Mattoo (eds.) Genetic improvement of Solanaceous crops vol. I: Tomato, Science Publishers Inc., New Hampshire, USA; Plymouth, UK. <br /> <br /> Rupasinghe, H.P.V, G.M. Huber, C. Embree, and P.L. Forsline. 2008. Red-fleshed apples as a source for functional beverages. Canadian Institute of Food Science and Technology Conference. May 25-27, 2008.<br /> <br /> Samuelian, S.K., Baldo, A.M., Pattison, J.A., and Weber, C.A. 2008. Isolation and linkage mapping of NBS-LRR resistance gene analogs in red raspberry ( Rubus idaeus L.) and classification among 270 Rosaceae NBS-LRR genes. Tree Genetics & Genomes. Electronic Online First article http://www.springerlink.com/content/n423jnx741586448<br /> <br /> Saleh Al-Turki, Mohamed A. Shahba, Philip L. Forsline and Cecil Stushnoff. 2008. Biodiversity of total phenolics, antioxidant capacity and juice quality in apple cider taxa. Koean Journal (pending).<br /> <br /> Sheffer, S.M., J.A. Labate, T.N. Bjorkman, L.D. Robertson and A.M. Baldo. 2004. BoGSL-ELONG as a candidate diagnostic marker in phenotypically diverse brassica populations. Eighth Eastern Great Lakes Molecular Evolution Meeting. Ithaca, NY<br /> <br /> Simon, C.J. 2004. Genetic conservation of nonseed materials. In: Encyclopedia of Plant and Crop Science1:1. Robert G. Goodman (ed), Marcel Dekker Inc. pp.1-3<br /> <br /> Simon, C.J., Y. Wan, H. Schwaninger, G.-Y. Zhong, J.A. Labate, and A.M. Baldo. 2008. Nucleotide polymorphism analysis in Vitis: A broad survey across the grape genus. p. 240 In Final Abstracts Guide, Plant and Animal Genome XVI, San Diego, CA.<br /> <br /> Stushnoff, C., A.E. McSay, J.J. Luby, and P.L. Forsline. 2003. Diversity of phenolic antioxidant content and radical scavenging capacity in the apple germplasm collection. XXV1 International Horticultural Congress. Symposium 21 (Plant Genetic Resources: The Fabric of Horticulture's Future). Acta Horticulturae 623: 305-312.<br /> <br /> Sun, Lingxia, . Steve van Nocker, and Philip L. Forsline. 2008. Natural Variation for Fruit Abscission in Apple (Malus). HortScience 43: 1271.<br /> Sun, Lingxia, Steve van Nocker, and Philip. L. Forsline. 2008. Natural Variation in Fruit Abscission-Related Traits in Apple (Malus). Euphytica. (accepted).<br /> <br /> Towill, L.E., P.L. Forsline, C. Walters, J. Waddell and J. Laufman. 2004. Cryopreservation of Malus germplasm using a winter vegetative bud method: Results from 1915 accessions. Cryoletters 25:323-334.<br /> <br /> Vision T, Chacon M, Tsompana M, Robertson L, Pena Lomeli A, Ponce O (2006). Microsatellite variation and population structure in tomatillo (Physalis philadelphica Lam.). PAA/Solanaceae Abstract 408, July 23-27, Madison, WI<br /> <br /> Volk G.M., Ann A. Reilley, Adam D. Henk, Christopher M. Richards, P.L. Forsline, and H.S. Aldwinckle. 2005. Ex situ conservation of vegetatively propagated species: Development of a seed-based core collection or Malus sieversii. J. Amer. Soc. Hort. Sci. 130: 203-210.<br /> <br /> Volk Gayle, Christopher M. Richards, Ann A. Reilley Adam D. Henk Patrick A. Reeves Philip L. Forsline Herb S. Aldwinckle. 2008. Genetic diversity and disease resistance of wild Malus orientalis from Turkey and southern Russia. Journal J. Amer. Soc. Hort. Sci. 133: 383-389<br /> <br /> Volk, G.M., Christopher M. Richards, Philip L. Forsline, and Herb Aldwinckle. <br /> 2008. Diversity of wild Malus germplasm available in the USDA-ARS National Plant Germplasm System. HortScience 43: 1136.<br /> <br /> Volk, Gayle M., Christopher M. Richards, Philip L. Forsline, and Herb S. Aldwinckle. 2008. Assessment of the genetic diversity and disease resistance of wild Malus orientalis seedlings from Turkey and Southern Russia. 4th International Rosaceae Genomics Conference.

Impact Statements

1. Both the seed and clonal crops for which Geneva has responsibility are important components of agriculture in the Northeast. Many Northeastern State Agricultural Experiment Stations (SAESs) have research and extension responsibilities for these valuable commodities. The vegetable crops maintained at Geneva account for about 48% of the value of U.S. fresh market production and the fruit crops account for 53% of the value of production of non-citrus fruit trees and vines.
2. Germplasm is maintained and distributed in accordance with standards for viability, genetic integrity, and accurate identity. Increased characterization of germplasm and the addition of digital images have increased the efficiency of use of the germplasm collections. Fingerprinting B. oleracea accessions may lead to diagnostic molecular tools to distinguish broccoli versus cauliflower seeds. Discovered genetic variation in tomato will enable breeders to target existing genetic variation. Genotyping the entire apple and grape collection is nearly complete and will be useful in assisting genomicists and breeders as existing genetic variation is targeted.
3. Combining genes from diverse sources into germplasm is more useful to plant breeders to produce improved germplasm and cultivars.
4. As biotechnology programs in the Northeastern U.S. have grown, plant genetic resource conservation has become more critical. Molecular biologists and genome researchers must have this reservoir of diversity available if they are to identify plants with useful genes that breeders can then exploit. Continuing progress in improving the performance of crop plants while simultaneously improving our understanding of plant biology will be accomplished by the integration of new technologies with the broadest possible array of genetic resources.
5. Development and testing of markers in tomato has led to a) designing molecular markers for mapping, breeding, germplasm characterization, taxonomy, and validation of genetic purity, b) markers that are useful for understanding evolutionary processes such as selection, genetic drift, and wild species introgression in tomato, c) an understanding and characterization of the genetic diversity present in cultivated tomato and d) identification of novel genes in the USDA, ARS germplasm collection in Geneva, NY.
6. Markers have been tested Brassica that are potentially useful to distinguish broccoli from cauliflower and polymorphisms found will also be valuable for marker-assisted breeding.
7. Development of improved vegetable varieties and improved fruit varieties and increased understanding of these crops through research.
8. Screening of the Malus germplasm collection has led to identification of novel fire blight resistance genes and insect resistance Malus germplasm in the USDA, ARS germplasm collection in Geneva, NY and to identification of Malus germplasm with red flesh and high levels of antioxidants in the USDA, ARS germplasm collection in Geneva, NY. This has also led to an understanding and characterization of the genetic diversity present in elite apple cultivars and wild Malus species.
9. Cryogenic storage of apple and cherry has been used as a model to test other commodities in the National Plant Germplasm System for a reliable backup system for clonal crops. Our results have shown this method to be a 50-fold savings over having duplicate plantings at another site.
10. As new genomic tools are developed for genetic improvement of apple we have collaborated with ARS, Cornell and New Zealand labs to develop two new genetic maps. These populations were developed by crossing scab resistant M. sieversii accessions with the susceptible cultivar &lsquo;Royal Gala&lsquo;. Correlation of the markers with phenotype indicated some M. sieversii parents likely had known resistance genes but, in some cases, exhibited patterns suggesting they also contained novel resistance loci. These populations also have traits for resistance to fire blight, post harvest diseases and tolerance to drought and cold temperatures. With the sequencing of the Malus genome by the international community nearly complete. These genetic maps will allow for more rapid introgressing of these genes into new varieties.

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