Source: N Y AGRICULTURAL EXPT STATION submitted to
ACCELERATING GRAPE CULTIVAR IMPROVEMENT VIA PHENOTYPING CENTERS AND NEXT GENERATION MARKERS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
0225760
Grant No.
2011-51181-30635
Project No.
NYG-632532
Proposal No.
2011-01377
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2011
Project End Date
Aug 31, 2016
Grant Year
2012
Project Director
Reisch, B. I.
Recipient Organization
N Y AGRICULTURAL EXPT STATION
(N/A)
GENEVA,NY 14456
Performing Department
Geneva - Horticultural Sciences
Non Technical Summary
Grape industry surveys and scientist-stakeholder workshops repeatedly identify three traits of high importance to U.S. grape growers for cultivar improvement: powdery mildew resistance, cold tolerance, and fruit quality. This long term project will accelerate grape cultivar improvement by providing cutting-edge molecular marker technologies, rigorous centralized facilities to characterize traits, and molecular breeding expertise. To further facilitate industry- and consumer-driven development and adoption of improved cultivars, quantitative economic analyses will be conducted to evaluate the benefits for consumers, producers, and the economy as a whole from enhanced traits in new cultivars. This will inform breeding strategies to increase consumption of novel, desirable grape products - impacting nine stakeholder high-priorities in four SCRI focus areas. Outreach activities will focus on communication of results of consumer surveys as well as economic analyses of varieties with enhanced traits, and will be carried out with the ongoing national Grape Community of Practice project. Outreach will also work toward the development of a common vocabulary between the grape industry and scientists regarding the processes and applications of genomic technologies. The molecular breeding efforts will have two components: marker development and marker application. Marker development across 20 diverse breeding populations (with outreach to other specialty crops) will use the latest DNA sequencing technology to generate 50,000 DNA markers per plant - resulting in dozens of markers per trait-associated locus for mapping and marker-assisted breeding. In addition to traits scored at centrally developed project locations, breeders will use standardized practices to score additional traits locally, which will also be mapped to their chromosomal locations. Finally, existing markers will be applied across thousands of breeding lines, resulting in rapid impact. For example, existing markers for seedlessness and powdery mildew resistance can be screened following embryo rescue, and seeded, susceptible plantlets discarded years earlier than normal, resulting in planting of more seedlings with desired phenotypes, additional improved traits, improved resistance durability, and improved efficiency, all focused on industry and consumer priorities.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
50%
Developmental
50%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011139108040%
6031139301010%
6071139303010%
2121139108010%
2031139108010%
2041139108010%
2011139302010%
Knowledge Area
607 - Consumer Economics; 204 - Plant Product Quality and Utility (Preharvest); 212 - Pathogens and Nematodes Affecting Plants; 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms; 603 - Market Economics;

Subject Of Investigation
1139 - Grapes, general/other;

Field Of Science
1080 - Genetics; 3020 - Education; 3030 - Information and communication; 3010 - Economics;
Goals / Objectives
Within the scope of the current project, we aim to: 1. Develop breeding strategies for grape genetic improvement driven by consumer, industry, and broader market preferences, and documented economic, environmental, and social benefits. 2. Develop 35 new molecular markers associated with biotic and abiotic stress tolerance, fruit quality, and additional traits in germplasm relevant to U.S. grape breeding programs. Apply new and existing markers across thousands of breeding lines to accelerate the breeding and selection of improved cultivars combining biotic and abiotic stress tolerance with excellent fruit quality, directly resulting in new cultivars adapted to diverse regions of the U.S. 3. Optimize genotyping-by-sequencing (GBS) to increase to 50,000 the standard number of Single Nucleotide Polymorphism (SNP) markers for linkage mapping, decrease the per sample cost to 30 dollars, and train up to 30 geneticists from other specialty crops in GBS protocols and data analysis. 4. Enhance communication between grant participants and the industry and public and develop education resources on breeding and genetics.
Project Methods
Consumer and Industry Surveys. A consumer survey will explore general concepts such as improved environmental sustainability, health compounds, and quality characteristics, while comparing traditional breeding with other treatments such as chemical additives. A second survey will aim to understand perceptions about cultivars among stakeholders who directly interface with consumers. Surveys will be evaluated annually and revised accordingly. Economic Evaluation of Improved Grape Cultivars. We will estimate the value of improved cultivars. The evaluation includes a) the benefits to producers, b) the benefits to consumers, and c) other benefits associated with reduced use of pesticides. Centralized Genotyping and Mapping. The genotyping center will receive leaf samples for marker development or for marker application. DNA isolation will be completed using protocols optimized for Vitis to ensure sufficient quantity and quality. Genotyping-by-Sequencing (GBS). GBS combines multiplexing with unique barcoded adapter sequences and the generation of reduced representation libraries (RRLs) to provide the read-depth necessary for confidence in SNP calls. QTL Identification. Once the parameters for genotyping are established, 1920 DNA samples will be processed, and a linkage map developed for each population with marker-trait associations identified by standard QTL mapping procedures. Marker Application. Existing markers will be immediately applied for marker-assisted breeding. DNA from breeding populations will be sampled, screened, and the resulting data provided to the breeder for validation and/or selection. For new SNP markers developed during this project, a redundant, SNP haplotype signature will be developed using a multi-SNP technology. Centralized, Standardized Phenotyping Cold tolerance: The Fennell lab will assess freezing tolerance, dormancy status, and chilling fulfillment using replicated samples provided by breeders. Bud freezing tolerance will be determined by differential thermal analysis (DTA). Powdery mildew resistance: Avirulent isolates will be identified and used to phenotype each mapping population for resistance. On several resistant progeny of each population, we will conduct standardized phenotyping of the resistance mechanism and strength in the presence and absence of virulence. Negative fruit qualities: Phenotyping will be performed on 20 samples from 20 populations at two maturities in the Year 1, with phenotyping of selected populations in later years. Phenotyping will include targeted measurements of volatile and non-volatile compounds previously associated with undesirable characteristics of wild species (IBMP, IPMP, MA, o-AAP, C6 compounds, 1,8-cineole). Volatiles will be extracted by headspace solid phase microextraction (HS-SPME) coupled to gas chromatography time of flight mass spectrometry (GC-TOF-MS). Extension efforts will focus on developing materials targeted toward grape growers, grape geneticists, and the general public.

Progress 09/01/11 to 08/31/16

Outputs
Target Audience: During the collaboration we refer to as the VitisGen project, we targeted three main audiences: 1) researchers in biological sciences, chemistry, and economics; 2) the grape industry; and 3) the public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The project has provided several opportunities for training and professional development. Project participants provided training of more than 60 researchers and students in trait economics, trait evaluation, both modern and traditional breeding techniques, and genotyping-by-sequencing (GBS) analyses. Additionally, the project hosted seven GBS workshops to train more than 200 researchers how to apply GBS and make marker-trait associations in non-model organisms. Nine students took on VitisGen-related research projects as part of their master's or doctoral programs, seven of these students have already graduated. Project directors and participants have attended 70 scientific conferences, symposiums, meetings, colleges and universities (domestically and internationally) to deliver more than 175 oral or poster presentations, network with colleagues, and learn about research in their field. The annual project meetings of directors, collaborators, and the advisory panel has also offered the opportunity to bring researchers together for training and professional development. Three leading researchers representing Germany, Australia, and France presented seminars and participated in discussions at VitisGen annual project meetings, providing insight to the international grape research community and industry. How have the results been disseminated to communities of interest? The project disseminates results to communities of interest through presentations of data and research findings at scientific, industry, and extension meetings, research publications in peer-reviewed journals, extension articles in periodical publications, and the use of social media. Project directors and participants attended more than 70 scientific, industry, and extension meetings, giving more than 175 seminars, lectures, and poster presentations. Project brochures distributed at meetings provide contact information and additional material about the VitisGen vision and primary objectives. Researchers published research findings in 22 peer-reviewed journal articles to date and communicated project goals and accomplishments in 12 extension articles. Examples of research findings published include articles on the pipeline to identify single nucleotide polymorphisms and construct genetic maps using genotyping-by-sequencing (GBS) technology, powdery mildew disease resistance and race specificity, tannin extractability, amplicon sequencing (AmpSeq) as a method for marker-assisted selection, the economic benefits of virus screening, and the value of powdery mildew resistance in grapes. Annual project meetings, team reports, and meeting reviews helped to disseminate information internally across research and extension teams and to the advisory panel. The VitisGen project website (www.vitisgen.org), newsletter (the VitisGen Voice), and a suite of YouTube videos are also used to disseminate project goals and accomplishments. The website has general information regarding the project's vision, objectives, team members and accomplishments. It also hosts resources such as tools for marker-assisted selection, VitisGen publication lists, and a glossary defining several scientific terms used within the VitisGen project. Four issues of the VitisGen Voice were published and featured articles on the three trait evaluation centers for fruit quality, low temperature responses, and powdery mildew resistance. The project produced and published five videos on YouTube highlighting different aspects of the VitisGen project to reach researchers, industry, and the public. Project outputs have been distributed or made available on the internet through the Finger Lakes Grape Program Facebook page, Twitter, CornellCast, Grapes eXtension, and the project website. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Traditional grape cultivars are highly susceptible to biotic and abiotic stresses such as powdery mildew, cold winters, and temperature fluctuations in the spring. These cultivars have led to many of the economic and environmental costs associated with grape production in the US. As a result, grape breeders have adopted "marker-assisted breeding" to develop new cultivars with improved crop characteristics while increasing the efficiency and reducing the associated costs of production. The VitisGen project has strived to serve industry needs through a collaboration in trait economics, genotyping, trait evaluation, breeding, and extension. VitisGen agricultural economists conducted and analyzed a researcher survey, which identified powdery mildew disease resistance as the top priority trait nationally. Subsequent economic modeling projected a large cost benefit ($3.7 to $36.4 million/year) to adopting powdery mildew resistant varieties in a subset of table, wine, and raisin grape production in California, illustrating the economic benefit of developing new cultivars. Using next-generation sequencing technology and trait evaluation, VitisGen researchers worked to streamline the development of new cultivars, which can take twenty plus years. To speed up the process, they identified genetic markers (short sequences of DNA that serve as landmarks) associated with traits like powdery mildew resistance. Using genetic markers, breeders can select progeny from future crosses with specific traits through a simple DNA test. Thus far, VitisGen researchers have identified more than 75 marker-trait associations, which are being converted into new markers for biotic and abiotic stress tolerance, morphology, and fruit chemistry. VitisGen breeders have validated and applied existing markers across 16,501 breeding lines, enabling them to identify elite selections early in the breeding process. VitisGen project participants have also communicated results and distributed educational resources through 22 peer-reviewed journal publications; 12 extension articles; 5 videos published on social media; more than 180 domestic and international presentations; the project newsletter (the VitisGen Voice); and the VitisGen website (www.vitisgen.org). Through 8 workshops, the project has trained over 200 domestic and international geneticists on how to use new genotyping technology in non-model organisms. Not only has the VitisGen project created a foundation for future research in grape genomics and breeding, but results stemming from this body of work will also continue to contribute to the development of new grape cultivars for years to come. Obj. 1: Develop strategies for grape genetic improvement driven by documented societal benefits. The VitisGen trait economics team (TET) administered 2 surveys to establish priority traits and their value in viticulture. The analyses identified powdery mildew as the top research priority and assessed grower valuation of specific varietal traits. The TET also documented economic, environmental, and social benefits using a modeling approach. This approach approximated benefits from different types of varietal improvement across three sectors of the grape industry: wine, table, and raisin grapes. The TET established models of: 1) individual grower production budgets for sample growers; 2) aggregate benefits from adoption; and 3) likely adoption rates based on growers' valuation of individual varietal traits and perception of benefits from adoption of new varieties. They also evaluated environmental costs of disease management and potential benefits from adoption of resistant varieties. Obj. 2: Develop 35 new molecular markers. Apply new and existing markers to accelerate breeding and selection of improved cultivars, resulting in new cultivars adapted to diverse regions of the U.S. A coordinated effort in breeding, trait evaluation, and genetics developed more than 35 new molecular markers. Breeders maintained 17 core-mapping families in CA, MO, NY, SD and MN to provide samples for genetic analyses and trait evaluation and phenotyped more than 100 traits locally. Three centers phenotyped powdery mildew resistance (PM), low temperature responses (LT), and fruit quality (FQ). The PM center quantified powdery mildew severity in 7 mapping families; characterized race-specificity of Run1, Ren2, Ren3, and Ren4; discovered Ren10 (a novel locus conferring PM); and identified combinations of resistance genes for improved durability. The LT center assessed chilling fulfillment, rate of budbreak and freezing tolerance in 5 mapping families; discovered QTL and surveyed candidate genes underlying the loci; and identified extremes of budbreak and acclimation response types. The FQ center analyzed up to 30 fruit chemistry quality traits in 9 mapping families; discovered QTL for 8 quality traits such as malic acid and anthocyanins; and demonstrated that pathogenesis related proteins affect tannin extraction and retention in wild grape species. The genotyping center (GC) processed 18,774 DNA samples through a GBS pipeline developed within the project, including novel computational tools for analysis of GBS-derived SNPs in highly diverse, heterozygous species. The GC generated 16 high-resolution linkage maps and integrated them with trait data from the phenotyping facilities and breeding programs to discover more than 75 marker-trait associations. The GC worked with breeders to validate and apply markers. The GC developed a new NGS method called AmpSeq, with SNP and presence/absence AmpSeq marker pipelines for tracking high-diversity alleles in heterozygous species. Selection efforts primarily focused on PM and downy mildew resistance; seedlessness; flower sex; malic acid; and acylated anthocyanins. Breeders submitted more than 20,500 breeding lines and applied marker-assisted selection (MAS) on 16,501 seedlings from 144 families. Based on results from MAS, breeders retained approximately 39% of the seedlings for further nursery and/or field selection. Breeders also used marker-assisted parent selection to screen more than 2,000 potential parents in breeding programs and germplasm collections. One example out of the Cornell University grape breeding program is the disease resistant red wine grape selection, NY06.0514.06. This advanced selection is being distributed to nurseries for further propagation and testing and will be entered into NE1020 grape variety trials. Additional details and unanticipated outcomes are listed under Other Products. Obj. 3: Optimize GBS to increase density of SNP markers for linkage mapping, decrease cost per sample, and train geneticists from other specialty crops in GBS protocols and data analysis. Optimized protocols developed by the GC identify on average 150,000 raw SNPs (91,278 to 295,944) per family, at a typical cost of under $13/sample. Filtered genetic maps contain more than 10-fold the number of SNPs per linkage group than previous SSR maps. The GC conducted workshops training over 200 researchers to use GBS and AmpSeq tools for genetic analyses related to specialty crops. See Other Products for complete list of workshops hosted. Obj. 4: Enhance communication between grant participants and the industry and public and develop education resources on breeding and genetics. Five annual project meetings and quarterly internal communications maintained an open dialogue between researchers and industry. The project website (www.vitisgen.org) and social media served as an interface to communicate products to the industry and public. Project participants presented data and research materials at more than 70 academic and extension conferences. Educational resources developed include tools for MAS, a glossary of scientific terms, a project brochure, GBS training manuals, 4 issues of the VitisGen Voice newsletter, 5 project videos, 12 extension articles, and 22 peer-reviewed journal articles.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Teh, S.L., Fresnedo-Ram�rez, J., Sun, Q., Cadle-Davidson, L., Luby, J.J. (2016). Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps. Molecular Breeding (accepted)
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Springer, L.F., Chen, L-A., Stahlecker, A.C., Cousins, P., and Sacks, G.L. (2016). Relationship of Soluble Grape-Derived Proteins to Condensed Tannin Extractability during Red Wine Fermentation. Journal of Agricultural and Food Chemistry, 64(43), 8191-8199. doi: 10.1021/acs.jafc.6b02891
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Fresnedo-Ram�rez, J., Sun, Q., Hwang, C-F, Ledbetter, C.A., Ramming, D.W., Fennell, A.Y., Walker, M.A., Luby, J.J., Clark, M.D., Londo, J.P., Cadle-Davidson, L.E., Zhong, G-Y., and Reisch, B.I. (2016). Towards the elucidation of the cytoplasmic diversity of North American Grape Breeding Programs. Molecular Breeding, 36:116. doi: 10.1007/s11032-016-0538-z
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Cadle-Davidson, L., Gadoury, D., Fresnedo-Ram�rez, J., Yang, S., Barba, P., Sun, Q., Demmings, E.M., Seem, R., Schaub, M., Nowogrodzki, A., Kasinathan, H., Ledbetter, C., and Reisch B.I. (2016). Lessons from a Phenotyping Center Revealed by the Genome-Guided Mapping of Powdery Mildew Resistance Loci. Phytopathology, 106(10), 1159-1169. doi: 10.1094/PHYTO-02-16-0080-FI
  • Type: Other Status: Published Year Published: 2016 Citation: Levente Kiss, Imre J. Holb, Vittorio Rossi, Lance Cadle-Davidson, Michael J. Jeger. (2016). Foreword: Special issue on fungal grapevine diseases. European Journal of Plant Pathology 144:693694. doi: 10.1007/s10658-015-0844-z
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: S. Yang, J. Fresnedo-Ramirez, Q. Sun; D.C. Manns. G.L. Sacks; A.K. Mansfield, J.J. Luby, J.J. Londo, B.I. Reisch, L.E. Cadle-Davidson, A.Y. Fennell. (2016). Next generation mapping of enological traits in an F2 interspecific grapevine hybrid family. PLoS ONE 11(3): e0149560. doi: 10.1371/journal.pone.0149560
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Yang, S., Fresnedo, J., Wang, M., Cote, L., Schweitzer, P., Barba, P., Takacs, E.M., Clark, M., Luby, J., Manns, D., Sacks, G., Mansfield, A.K., Londo, J., Fennell, A., Gadoury, D., Reisch, B., Cadle-Davidson, L., and Sun, Q. (2016). A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker assisted selection in grapevine. Horticulture Research 3: 16002 http://dx.doi.org/10.1038/hortres.2016.2
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Springer, L.F., Sherwood, R.W., and Sacks, G.L. (2016). Pathogenesis-Related Proteins Limit the Retention of Condensed Tannin Additions to Red Wines. Journal of Agricultural and Food Chemistry, 64(6), 1309-1317. http://pubs.acs.org/doi/abs/10.1021/acs.jafc.5b04906
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Myles, S., Mahanil, S., Harriman, J., Gardner, K., Franklin, J.L., Reisch, B.I., Ramming, D.W., Owens, C.L., Li, L., Buckler, E.S., and Cadle-Davidson, L. (2015). Genetic mapping in grapevine using SNP microarray intensity values. Molecular Breeding, 35:88. doi: 10.1007/s11032-015-0288-3
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Michelle M. Moyer, Jason Londo, David M. Gadoury, and Lance Cadle-Davidson. (2015). Cold Stress-Induced Disease Resistance (SIDR): Indirect effects of low temperatures on host-pathogen interactions and disease progress in the grapevine powdery mildew pathosystem. European Journal of Plant Pathology, doi: 10.1007/s10658-015-0745-1.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Fuller, K.B., Alston, J.M., and Sambucci, O. (2015). The Benefits to California from Powdery Mildew Resistant Grape Varieties. Revues des Oenologues 157, 6466.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hyma, K.E., Barba, P., Wang, M., Londo, J., Acharya, C., Mitchell, S., Sun, Q. Reisch, B., and Cadle-Davidson, L. (2015). Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-by-Sequencing Markers: a case study in grapevine. PLoS ONE 10(8), e0134880. doi: 10.1371/journal.pone.0134880
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kono, A., Sato, A., Reisch, B.I., and Cadle-Davidson, L. (2015). Effect of Detergent on the Quantification of Grapevine Downy Mildew Sporangia from Leaf Discs. HortScience 50, 656660.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Barba, P., Cadle-Davidson, L., Galarneau, E., and Reisch, B. (2015). Mechanisms of quantitative resistance to Erysiphe necator in Vitis rupestris B38. Phytopathology 105, 1097-1103. Retrieved from http://apsjournals.apsnet.org/doi/pdfplus/10.1094/PHYTO-09-14-0260-R
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Feechan, A., Kocsis, M., Riaz, S., Zhang, W., Gadoury, D. M., Walker, M. A., Dry, I. B., Reisch, B., and Cadle-Davidson, L. (2015). Strategies for RUN1 deployment using RUN2 and REN2 to manage grapevine powdery mildew informed by studies of race specificity. Phytopathology 105, 1104-1113. Retrieved from http://apsjournals.apsnet.org/doi/pdfplus/10.1094/PHYTO-09-14-0244-R
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Alston, J.M., Anderson, K., and Sambucci, O.S. (2015). Drifting Towards Bordeaux? The Evolving Varietal Emphasis of U.S. Wine Regions. Journal of Wine Economics, 10(3), 349378. doi: 10.1017/jwe.2015.29
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Fuller, K.B., Alston, J.M., and Golino, D.A. (2015). The Economic Benefits from Virus Screening: A Case Study of Grapevine Leafroll in the North Coast of California. American Journal of Enology and Viticulture, 62(2), 112119.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Fuller, K.B., Alston, J.M., and Sambucci, O.S. (2014). The value of powdery mildew resistance in grapes: Evidence from California. Wine Economics and Policy, 3(2), 90107. doi: 10.1016/j.wep.2014.09.001
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Adhikari, P., Chen,L-L., Chen, X., Sapkota, S. and Hwang, C-F. (2014). Interspecific Hybrid Identification of Vitis aestivalis-derived Norton-Based Populations Using Microsatellite Markers. Scientia Horticulturae 179, 363-366.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Barba, P., Cadle-Davidson, L., Harriman, J., Glaubitz, J.C., Brooks, S., Hyma, K., and Reisch, B.I. (2014). Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. Theoretical and Applied Genetics 127(1), 73-84. doi: 10.1007/s00122-013-2202-x
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Springer, L.F., and Sacks, G.L. (2014). Protein-Precipitable Tannin in Wines from Vitis vinifera and Interspecific Hybrid Grapes (Vitis ssp.): Differences in Concentration, Extractability, and Cell Wall Binding. Journal of Agricultural and Food Chemistry 62 (30), 7515-7523.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Alston, J., Fuller, K., Kaplan, J., and Tumber, K. (2013). The Economic Consequences of Pierces Disease and Related Policy in the California Winegrape Industry. Journal of Agricultural and Resource Economics 38(2):269297.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Stafne, E.T., E. Hellman, R.K. Striegler, J.A. Wolpert, and J-M. Peltier. (2012). Industry involvement in the creation and funding of the eXtension Grape Community of Practice. HortTechnology 22:580-582.
  • Type: Journal Articles Status: Submitted Year Published: 2016 Citation: Barba, P., Lillis, J., Luce, R.S., Osier, M., Wilcox, W.F., Reisch, B.I., and Cadle-Davidson, L. (2016). Two dominant loci determine resistance to phomopsis cane lesions in half-sib families of hybrid grapevines. J. Exp. Botany (submitted)
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Demmings, E.M., Cadle-Davidson, L., Sacks, G., Fennell, A., Gadoury, D.M., Sun, Q., Schweitzer, P., Londo, P., Ledbetter, C., Clark, M., Luby, J., Teh, S.L., Mansfield, A.K., Manns, D., Springer, L., Chitwood, D., Barba, P., Hwang, C-F., Sapkota, S., Fresnedo, J., Yang, S., and Reisch, B.I. (2016). VitisGen discoveries in local and centralized trait evaluation. Acta Hort. (accepted)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Sagar, P., Swaminathan, P., Fennell, A., Zeng, E. (2015). De novo genome assembly tool comparison for highly heterozygous species Vitis vinifera cv. Sultanina. IEEE International Conference on Bioinformatics and Biomedicine, Washington, D.C. doi: 10.1109/BIBM.2015.7359957
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Xu X., J. Lu, Z. Ren, and F. Bradley (2013). Downy mildew disease resistance in F1 of C30-5-1 � Chardonnay. Proc. Fla. State Hort. Soc., 126, 14.
  • Type: Other Status: Published Year Published: 2016 Citation: Walter-Peterson, H. Editor. (2016, April). VitisGen Voice, Spring 2016, 1-9. Retrieved from: http://www.vitisgen.org/docs/newsletter/Spring2016.pdf
  • Type: Other Status: Published Year Published: 2015 Citation: Duren, J. (2015, June). Making Grapes Better: Collaboration Seeks to Speed Up Super-Grape Research. Snooth. Retrieved from http://www.snooth.com/articles/making-grapes-better-collaboration-seeks-to-speed-up-super-grape-research/?viewall=1
  • Type: Other Status: Published Year Published: 2015 Citation: Jeffries, A-M. (2015, June). Developing the Grapes of the Future. Growing Produce. Retrieved from http://www.growingproduce.com/fruits/grapes/developing-the-grapes-of-the-future/
  • Type: Other Status: Published Year Published: 2015 Citation: Walter-Peterson, H. Editor. (2015, June). VitisGen Voice, Spring 2015, 1-9. Retrieved from http://vitisgen.org/docs/newsletter/Spring2015.pdf
  • Type: Other Status: Published Year Published: 2015 Citation: Fellman, S. and Walter-Peterson, H. (2015, March). VitisGen: Mapping the Way to the Next Generation of Grapes. Appellation Cornell. Retrieved from http://grapesandwine.cals.cornell.edu/sites/grapesandwine.cals.cornell.edu/files/shared/Research%20Focus%202015-1.pdf
  • Type: Other Status: Published Year Published: 2014 Citation: Tumber, Kabir P., Alston, Julian M., Fuller, Kate B. (2014) Pierces disease costs California $104 million per year. California Agriculture, 68(1-2): 20-29.
  • Type: Other Status: Published Year Published: 2014 Citation: Fuller, K.B., Alston, J.M., and Sambucci, O.S. (2014). The Value of Powdery Mildew Resistance in Grapes: Evidence from California. Agricultural and Resource Economics Update, 17(5), 1-4. Retrieved from http://s.giannini.ucop.edu/uploads/giannini_public/7d/e7/7de78288-459d-497e-b7cd-f9eb447d0340/v17n5_1_ojkhjes.pdf
  • Type: Other Status: Published Year Published: 2013 Citation: Walter-Peterson, H. (2013, July). Mapping the Way to the Next Generation of Grapes. Growing Produce. Retrieved from http://www.growingproduce.com/fruits/mapping-the-way-to-the-next-generation-of-grapes
  • Type: Other Status: Published Year Published: 2014 Citation: Walter-Peterson, H. Editor. (2014, May). VitisGen Voice, Spring 2014, 1-6. Retrieved from: http://vitisgen.org/docs/newsletter/Spring2014.pdf
  • Type: Other Status: Published Year Published: 2014 Citation: Stafne, E.T. (2014). Online Grape Production Information via eViticulture. ASEV-ES News, Spring 2014, 4-5. Retrieved from: http://www.asev-es.org/pdf/2014%20asev-es%20newsletter%20spring14.pdf
  • Type: Other Status: Published Year Published: 2013 Citation: Walter-Peterson, H. Editor. (2013, November). VitisGen Voice, Winter 2013, 1-6. Retrieved from: http://vitisgen.org/docs/newsletter/Winter2013.pdf
  • Type: Other Status: Published Year Published: 2013 Citation: Stafne, E.T. (2013, April). The grape community of practice works to improve viticulture outreach education. Wines and Vines/Practical Vineyard and Winery Journal, 94(4), 72-74.
  • Type: Other Status: Published Year Published: 2013 Citation: Takacs, E.M. and H. Walter-Peterson. (2013, February). VitisGen: Mapping the Way to the Next Generation of Grapes. Northern Grapes Project Newsletter, 2(1), 5-7. Retrieved from http://northerngrapesproject.org/wp-content/uploads/2013/02/2013FebNGPnewsletter.pdf
  • Type: Other Status: Published Year Published: 2012 Citation: Thompson, S. (2012, October). Program Has $9 Million to Develop Better Grapes. Cornell Chronicle, October 24, 2012. Retrieved from http://www.news.cornell.edu/stories/2012/10/program-has-9-million-develop-better-grapes
  • Type: Other Status: Published Year Published: 2012 Citation: Fraser, R.L. (2012, August). DNA of the Vine: Grape Goes High Tech. Growing Magazine, 10(8), C8-C9. Retrieved from http://www.growing-digital.com/august2012/august2012/21/1#&pageSet=21
  • Type: Other Status: Published Year Published: 2012 Citation: Fraser, R.L. (2012, July). Grape Returns to its Wild Past. Growing Magazine, 10(7), B8-B10. Retrieved from http://www.growing-digital.com/july2012/july2012/12/0#&pageSet=12
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Springer, L.F. (2016). Taste of Terroir: the role of cultivar, region, and pathogenesis-related proteins in red wine astringency (Doctoral dissertation). Cornell University, Ithaca, NY.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Awale, M. (2016). Quantitative trait loci analysis of low temperature responses in grapevine F2 population (Masters Thesis). South Dakota State University, Brookings, SD.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Fortin, C. (2016). Development of a Data Management System for Grape Breeding Programs. (Masters Thesis). Rochester Institute of Technology, Rochester, NY.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Sambucci, O. (2015). Powdery Mildew Disease in the California Grape Industry (Chapter 2, Doctoral dissertation). UC Davis, Davis, CA.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Barba Burgos, P.L. (2015). Genetic Dissection of Disease Resistance and Pest Related Traits in Hybrid Grapevine Families (Doctoral dissertation). Cornell University, Ithaca, New York.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Adhikari, P. (2015). Molecular Genetic Study of Rooting Ability and Sulfur Sensitivity in Vitis aestivalis-derived Norton grapes (Masters Thesis). Missouri State University, Springfield, MO.
  • Type: Theses/Dissertations Status: Published Year Published: 2014 Citation: Lillis, J.A. (2014). Characterization of the Ren4 resistance locus through the integration of de novo assembly, expression analysis, and Genotyping-by-Sequencing data. (Masters Thesis). Rochester Institute of Technology, Rochester, NY.
  • Type: Book Chapters Status: Published Year Published: 2016 Citation: Stafne, E.T., S. Sleezer, and J.R. Clark. (2015). Grapevine breeding in the southern United States. In A.G. Reynolds (ed.), Grapevine breeding programs for the wine industry (pp. 379-408). Woodhead Publishing Ltd.
  • Type: Websites Status: Published Year Published: 2013 Citation: Walter-Peterson, H., Kogut, M., Stafne, E., Fellman, S., Monahan, J. and Demmings, E.M. (2013-2016). VitisGen: Mapping the way to the next generation of grapes. Retrieved from http://www.vitisgen.org


Progress 09/01/14 to 08/31/15

Outputs
Target Audience:The collaborative endeavor we refer to as the VitisGen project targeted three audiences during this reporting period, including scientific researchers, the grape industry, and the public. Project breeders and geneticists provided training for researchers and students in trait evaluation, both modern and traditional breeding techniques, and genotyping-by-sequencing (GBS) analyses. Project participants assisted the effort to reach other members of the research community and the grape industry by presenting seminars and posters at scientific, grower, and extension meetings. They also piloted group tours of research vineyards and facilities and distributed project brochures. Audience members of tour groups included researchers, extension associates, grape breeders, students, and grape industry members. Project geneticists also hosted a workshop for training in GBS analysis and mapping marker-trait associations. Additional extension efforts included publications in the quarterly newsletter Appellation Cornell, in Growing Produce magazine, and the Tannin Blog (http://blogs.cornell.edu/winechemistry/tanninblog/). The extension team has also posted material from the project on the websites www.extension.org , www.eviticulture.org, and www.vitisgen.org, authored another issue of the VitisGen Voice newsletter, and produced a YouTube video titled "Industry Voices in Support of VitisGen." Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has provided several opportunities for training and professional development. Project directors and participants have attended more than 25 scientific conferences, symposiums, meetings, colleges and universities to deliver oral or poster presentations, network with colleagues, and learn about research in their field. Additionally, the annual project meeting hosted a genotyping-by-sequencing (GBS) workshop to demonstrate how to use GBS data to construct genetic maps and perform QTL analysis. Project directors and participants have also trained scientists and students in trait evaluation and GBS analyses. Two students received graduate degrees in the current reporting period. How have the results been disseminated to communities of interest?The project disseminates results to communities of interest through presentations of data and research findings at scientific, industry, and extension meetings, research publications in peer-reviewed journals, extension articles in periodical publications, and the use of social media. Project directors and participants attended more than 25 scientific, industry, and extension meetings, giving more than 50 seminars, short talks, and poster presentations. Project brochures distributed at meetings provide contact information and additional material about the VitisGen vision and primary objectives. Project directors published seven research articles in peer-reviewed journals, which reported on the following topics: 1) the pipeline to identify single nucleotide polymorphisms and construct genetic maps using genotyping-by-sequencing technology; 2) powdery mildew disease resistance and race specificity; 3) methods to quantify downy mildew infection using a leaf disc assay; 4) the economic benefits of virus screening; and 5) the value of powdery mildew resistance in grapes. The extension team published the third issue of the 'VitisGen Voice' newsletter, wrote an article about the VitisGen powdery mildew phenotyping center for the Appellation Cornell newsletter, and published two additional articles in online trade magazines that provide an overview of the VitisGen project. The project also uses social media to host additional information about the VitisGen project and outcomes. A tannin blog (http://blogs.cornell.edu/winechemistry/tanninblog/) delivers updated information to the wine community and the public. In addition to the project website (www.vitisgen.org), project outputs are also posted on www.extension.org and www.eviticulture.org. The extension team also employs blogs, Facebook, Twitter, and YouTube to publicize project information and accomplishments. One example is the video "Industry Voices in Support of VitisGen" (https://www.youtube.com/watch?v=FAzIY70jfXI) published on YouTube. What do you plan to do during the next reporting period to accomplish the goals?We plan the following courses of action: TRAIT ECONOMICS 1) Complete the analysis of the online surveys administered to grape growers in the winter of 2014/2015 2) Publish the working paper on the pecuniary and non-pecuniary costs of powdery mildew managements, grower valuation of varietal traits and potential adoption of improved varieties BREEDING 1) Maintain core mapping populations 2) Collect final data to summarize marker-assisted breeding efforts in Year 4 3) Apply marker-assisted breeding in Year 5 4) Plant additional core populations in anticipation of continued funding for a successor project 5) Integrate a Norton linkage map with both SSR and GBS-SNP markers using JoinMap 4 software 6) Report outcomes to the scientific community and industry, including publications on local phenotyping efforts, which has identified markers for traits such as phylloxera resistance, powdery mildew resistance, black rot resistance, and leaf morphology; and the interpretation of sex markers in diverse Vitis germplasm TRAIT EVALUATION 1) Complete trait evaluation and data curation at the three phenotyping centers 2) Finish the development of a high-throughput protein quantification assay 3) Communicate results back to breeding programs and provide support for QTL analyses 4) Record, summarize, analyze, and integrate trait data into VitisGen breeding database 5) Report outcomes on trait evaluation to the scientific community and industry, including publications on tannin retention; tannin extractability during fermentation; high-throughput protein screening in grapes; and methods for rapid grape volatile analyses. GENETICS 1) Develop and validate Amplicon Sequencing (AmpSeq) markers for high-throughput, multi-locus marker-assisted selection 2) Report GBS-based genetic discoveries during the course of the project to the scientific community and industry , and work with breeders and phenotyping centers to publish on newly identified loci when data sets are complete EXTENSION 1) Continue to post research-related material on eXtension, eViticulture, and the project website 2) Hire a technical writer for the final year of the project to develop statements describing the accomplishments and impacts of VitisGen, write two to three articles about VitisGen for publication in trade journals, and content for the VitisGen Voice newsletter 3) Develop and release at least three more videos on a) VitisGen efforts to breed for improved quality; b) how VitisGen is helping to better understand the genetic control of grapevines' low temperature responses; and c) documenting what VitisGen has accomplished over its first five years 4) Host annual project meeting (scheduled in January 2016), which will advance collaborative efforts with industry; enable researchers to present findings; and allow project participants to share ideas and make plans

Impacts
What was accomplished under these goals? Grape cultivars developed 150-2000 years ago are highly susceptible to biotic and abiotic stresses such as powdery mildew, cold winters, and temperature fluctuations in the spring. These unimproved cultivars have led to many of the economic and environmental costs associated with grape production in the USA. As a result, grape breeders have adopted "marker-assisted breeding" to develop new cultivars with improved crop characteristics while increasing the efficiency and reducing the associated costs of production. The VitisGen project was designed to improve grape cultivars and serve industry needs through a collaboration in trait economics, genotyping, trait evaluation, breeding, and extension. VitisGen agricultural economists conducted and analyzed a researcher survey, which identified powdery mildew disease resistance as the top priority trait nationally. Subsequent economic modeling projected a large cost benefit ($3.7 to $36.4 million/year) to adopting powdery mildew resistant varieties in table grape, wine grape, and raisin production in California. Using next-generation sequencing technology and trait evaluation, VitisGen researchers identified 54 marker-trait associations for biotic and abiotic stress tolerance, morphology, and fruit chemistry. As researchers work toward developing new markers using these data sets, VitisGen breeders have applied existing markers across more than 12,000 breeding lines. VitisGen project participants have also communicated results and distributed educational resources through peer-reviewed journal publications, articles in trade and grower magazines, videos published on social media, presentations at national and international conferences, and the project website (www.vitisgen.org). Through workshops at meetings and conferences, project geneticists have trained domestic and international geneticists on how to use new genotyping technology in non-model organisms. In the final year of the project, participants will communicate findings to researchers, industry, and the public; and will continue to collaborate on the development of new cultivars addressing the critical needs of the grape industry. Objective 1: Develop breeding strategies for grape genetic improvement driven by consumer, industry, and broader market preferences, and documented economic, environmental, and social benefits. The trait economics team administered a survey developed to estimate grape grower attitudes towards improved varieties, the valuation of specific varietal traits, and grape grower's willingness-to-pay for these attributes. The team is analyzing the results of this survey and plan to incorporate the data in parallel economic modeling work on varietal adoption. Objective 2: Develop 35 new molecular markers associated with biotic and abiotic stress tolerance, fruit quality, and additional traits in germplasm relevant to U.S. grape breeding programs. Apply new and existing markers across thousands of breeding lines to accelerate the breeding and selection of improved cultivars combining biotic and abiotic stress tolerance with excellent fruit quality, directly resulting in new cultivars adapted to diverse regions of the U.S. Breeders continue to maintain 17 core mapping families at locations in California, South Dakota, Minnesota, Missouri, and New York. They also sent cuttings from three of the core families to E. & J. Gallo to establish backup plantings and evaluated a range of traits such as downy mildew resistance, leaf morphology, and foliar phylloxera resistance for marker development. The three phenotyping centers received shipments of canes, leaves, or fruit from breeders for trait evaluation. Traits assessed included: chilling fulfillment and freezing tolerance; powdery mildew resistance; and fruit quality (i.e. non-volatile and volatile analyses, grape tannin, tannin extractability, and macromolecular composition analyses). Trait data were transmitted to the genotyping center to identify marker-trait associations. Additionally, the fruit quality phenotyping center confirmed that pathogenesis related proteins are a major factor limiting tannin extraction during fermentation. Construction of genetic maps for 16 of the core mapping families using the genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) pipeline was completed. Using the trait data and genetic maps, 54 marker-trait associations were identified, including: 17 for fruit chemistry, 2 for low temperature responses, 3 for powdery mildew resistance, and 32 for locally phenotyped traits. In the previous field season, breeders applied markers from 13 loci across 5,660 seedlings within 27 breeding families. In the current season, the genotyping center extracted DNA from 4,085 samples for SSR processing for marker-assisted breeding. Outcomes will be reported in Year 5. The breeding and genetics teams are working on several additional projects to enhance marker development and application. First, the breeding team is investigating the use of a silica bead DNA extraction protocol for use in high throughput PCR based genotyping such as SSRs, indel, and KASP markers. Second, leaf samples from a diversity panel that includes key selections and ancestors in the University of Minnesota breeding program were submitted for GBS to enable parent selection, QTL discovery, and functional haplotype assessment. Third, cytoplasmic diversity (i.e. polymorphisms in chloroplast and mitochondria) was elucidated in VitisGen mapping families and a selective signature by Fst was detected among all breeding progeny. Fourth, GBS markers for sex determination and modified anthocyanin are being developed using an amplicon sequencing pipeline. Finally, both teams are working together to develop software for data management in grapevine breeding. Objective 3: Optimize GBS to increase to 50,000 the standard number of SNP markers for linkage mapping, decrease the per sample cost to 30 dollars, and train up to 30 geneticists from other specialty crops in GBS protocols and data analysis. The GBS SNP pipeline to construct genetic maps in F1 families was published and an additional method to construct a linkage map for an F2 family using GBS data was developed. A marker enrichment strategy was established to rescue additional markers within the confidence intervals of detected QTLs. This strategy increases the number of high-quality markers linked with QTLs of interest and the likelihood of targeting genes within these confidence intervals. Seventeen meeting participants attended a hands-on workshop about linkage and QTL mapping using GBS markers held during the January 2015 VitisGen meeting in San Diego, California. Objective 4: Enhance communication between grant participants and the industry and public and develop education resources on breeding and genetics. Project accomplishments and products were posted on www.vitisgen.org, www.extension.org, and www.eviticulture.org. One issue of the 'VitisGen Voice' and a video on how the industry supports the VitisGen project were published, distributed to project participants, and shared on social media. In January 2015, a project meeting of co-directors and industry advisory panel members assessed project progress and impacts, enhanced communications between researchers and industry, and outlined future plans. A workshop on QTL analysis using GBS data was held in conjunction with the annual meeting. Quarterly internal communications were distributed to project participants and the industry advisory panel to maintain an open dialogue throughout the year. Data and research materials from trait evaluation, genotyping, breeding, trait economics, and extension were presented at a multitude of academic and extension conferences and published online in industry or grower periodicals or peer-reviewed journals.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Adhikari, P., Chen,L-L., Chen, X., Sapkota, S. and Hwang, C-F. (2014). Interspecific Hybrid Identification of Vitis aestivalis-derived Norton-Based Populations Using Microsatellite Markers. Scientia Horticulturae 179, 363-366.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Barba Burgos, P.L. (2015) Genetic Dissection of Disease Resistance and Pest Related Traits in Hybrid Grapevine Families (Doctoral dissertation). Cornell University, Ithaca, New York.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Adhikari, P. (2015) Molecular Genetic Study of Rooting Ability and Sulfur Sensitivity in Vitis aestivalis-derived Norton grapes (Masters Thesis). Missouri State University, Springfield, MO.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hyma, K.E., Barba, P., Wang, M., Londo, J., Acharya, C., Mitchell, S., Sun, Q. Reisch, B., and Cadle-Davidson, L. (2015). Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-by-Sequencing Markers: a case study in grapevine. PLoS ONE 10(8), e0134880. doi:10.1371/journal.pone.0134880.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kono, A., Sato, A., Reisch, B.I., and Cadle-Davidson, L. (2015). Effect of Detergent on the Quantification of Grapevine Downy Mildew Sporangia from Leaf Discs. HortScience 50, 656660.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Barba, P., Cadle-Davidson, L., Galarneau, E., and Reisch, B. (2015). Mechanisms of quantitative resistance to Erysiphe necator in Vitis rupestris B38. Phytopathology 105, 1097-1103. Retrieved from http://apsjournals.apsnet.org/doi/pdfplus/10.1094/PHYTO-09-14-0260-R
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Feechan, A., Kocsis, M., Riaz, S., Zhang, W., Gadoury, D. M., Walker, M. A., Dry, I. B., Reisch, B., and Cadle-Davidson, L. (2015). Strategies for RUN1 deployment using RUN2 and REN2 to manage grapevine powdery mildew informed by studies of race specificity. Phytopathology 105, 1104-1113. Retrieved from http://apsjournals.apsnet.org/doi/pdfplus/10.1094/PHYTO-09-14-0244-R
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Fuller, K.B., Alston, J.M., and Sambucci, O.S. (2014). The value of powdery mildew resistance in grapes: Evidence from California. Wine Economics and Policy, 3(2), 90107.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Fuller, K.B., Alston, J.M., and Golino, D.A. (2015). The Economic Benefits from Virus Screening: A Case Study of Grapevine Leafroll in the North Coast of California. American Journal of Enology and Viticulture, 62(2), 112119.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Alston, J.M., Anderson, K., and Sambucci, O.S. (in press). Drifting Towards Bordeaux? The Evolving Varietal Emphasis of U.S. Wine Regions. Journal of Wine Economics.
  • Type: Other Status: Published Year Published: 2015 Citation: Fellman, S., Walter-Peterson, H. (2015, March). VitisGen: Mapping the Way to the Next Generation of Grapes. Appellation Cornell. Retrieved from http://grapesandwine.cals.cornell.edu/sites/grapesandwine.cals.cornell.edu/files/shared/Research%20Focus%202015-1.pdf
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Springer, L.F., Stahlecker, A.C., and Sacks, G.L. (2015). Disparate House Wines: The Role of Pathogenesis-related Proteins in Limiting Red Wine Astringency. Paper presented at the Proceedings of the American Society for Enology and Viticulture Eastern Section Meeting, Dunkirk, NY.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Springer, L.F., Stahlecker, A.C., Sherwood, R.W., and Sacks, G.L. (2015). Limits on Red Wine Tannin Extraction and Addition Part II: The Role of Pathogenesis Related Proteins in Terroir. Paper presented at the Proceedings of the American Society for Enology and Viticulture 66th National Conference, Portland, OR.
  • Type: Other Status: Published Year Published: 2015 Citation: Fellman, S., Walter-Peterson, H., and Londo, J. (2015). How Low Can You Go? Understanding the Genetics of Low Temperature Responses in Grapevines. VitisGen Voice, 1-5. Retrieved from http://vitisgen.org/docs/newsletter/Spring2015.pdf
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Sacks GL. (2015). Getting Consumer-Friendly Wine from Grower-Friendly Grapes: Challenges to Improving the Flavor Chemistry of New Sustainable Grape Varieties. Paper presented at the Proceedings of the American Chemical Society  Northeast Regional Meeting, Ithaca, NY.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Springer, L.F., and Sacks, G.L. (2015). Of Terroir and Tannins: The Role of Pathogenesis-Related Proteins in Red Wine Astringency. Paper presented at the American Chemical Societys 249th National Meeting, Denver, CO.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Springer, L.F., and Sacks, G.L. (2014). The Glass Ceiling on Red Wine Condensed Tannin: Limits Imposed by Soluble and Insoluble Binding Macromolecules. Paper presented at the Proceedings of the American Chemical Society 248th National Meeting, San Francisco, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Cadle-Davidson, L. (2015, August). Strategies for durable resistance to the grapevine powdery mildew fungus, Erysiphe necator. Poster presented at the American Phytopathological Society Annual Meeting, Pasadena, CA. Abstract retrieved from http://www.apsnet.org/meetings/Documents/2015_meeting_abstracts/aps2015abP486.htm
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Cadle-Davidson, L., Reisch, B., Sun, Q., Schweitzer, P., Sacks, G., Londo, J., Ledbetter, C., Luby, J., Hemstad, P., Hageman, A., Teh, S.L., Manns, D., Barba, P., Hyma, K., Lillis, J., Fresnedo, J., Yang, S., Takacs, E.M.. (2015). An update on VitisGen: recent advances in using DNA marker technologies in U.S. grape breeding programs. Paper presented at the International Plant and Animal Genome XXIII Conference, San Diego, CA. Abstract retrieved from https://pag.confex.com/pag/xxiii/webprogram/Paper14264.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Lillis, J.A., Majumdar, R., Ledbetter, C., and Lance Cadle-Davidson, L. (2015, January). Application of Genotyping-By-Sequencing for selection of locus-specific BAC clones to construct physical maps and identify candidate genes in Vitis. Poster presented at the International Plant and Animal Genome XXIII Conference, San Diego, CA. Abstract retrieved from https://pag.confex.com/pag/xxiii/webprogram/Paper15550.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Hyma, K.E., Barba, P., Wang, M., Londo, J., Hare, M.P., Acharya, C., Mitchell, S., Sun, Q., Reisch, B., and Cadle-Davidson, L. 2015. HetMappsS: Heterozygous Mapping Strategy for High Resolution Genotyping-by-Sequencing Markers. Paper presented at the International Plant and Animal Genome XXIII Conference, San Diego, CA. Abstract retrieved from https://pag.confex.com/pag/xxiii/webprogram/Paper14219.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Barba, P., Hyma, K.E., Wang, M., Londo, J., Acharya, C., Mitchell, S., Sun, Q., Reisch, B., and Cadle-Davidson, L. (2015, January). Fast and robust generation of high-resolution genetic maps in grapevine interspecific hybrid half-sib families using the HetMappS pipeline and R/qtl. Poster presented at the International Plant and Animal Genome XXIII Conference, San Diego, CA. Abstract retrieved from https://pag.confex.com/pag/xxiii/webprogram/Session3004.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Kovaleski, A., and Londo, J. (2015, August). Deacclimation rate in cultivated and wild grapes is dependent on dormancy stage and temperature. Paper presented at the American Society for Horticultural Science Annual Meeting, New Orleans, LA. Abstract retrieved from https://ashs.confex.com/ashs/2015/webprogramarchives/Paper21817.html Paper presentation retrieved from https://ashs.confex.com/ashs/2015/videogateway.cgi/id/1967?recordingid=1967
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Teh, S.L., Clark, M.D., Hemstad, P., Fresnedo Ramirez, J., Sun, Q., Cadle-Davidson, L., Hegeman, A., and Luby J. (2015, January). QTL Identification in an Interspecific Grapevine Cross Segregating for Resistance to Powdery Mildew, Downy Mildew, Black Rot, and Phylloxera. Poster presented at the International Plant and Animal Genome XXIII Conference, San Diego, CA. Abstract retrieved from https://pag.confex.com/pag/xxiii/webprogram/Paper16084.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Yang, S., Fresnedo, J., Takacs, E.M., Barba, P., Hyma, K., Lillis, J., Acharya, C., Fisher, A., Cote, L., Manns, D., Ryona, R., Gadoury, D., Seem, B., Sacks, G., Mansfield, A.K., Ledbetter, C., Luby, J., Hemstad, P., Fennell, A., Hwang, C-F., Walker, A., Riaz, S., Cousins, P., Londo, J., Buckler, E., Mitchell, S., Schweitzer, P., Sun, Q., Cadle-Davidson, L., and Reisch, B. (2015, January). VitisGen on the road: mapping the way to the next generation of grapes. Poster presented at the International Plant and Animal Genome XXIII Conference, San Diego, CA. Abstract retrieved from https://pag.confex.com/pag/xxiii/webprogram/Paper15597.html


Progress 09/01/13 to 08/31/14

Outputs
Target Audience: The target audiences during this reporting period were the general public, industry, and scientific researchers. Endeavors aimed toward reaching the public included the production and broadcast of a video entitled “VitisGen-Tracking Resistance,” distribution of two project newsletters via email and social media, continued circulation of the project brochure, and posted links to the project website on eViticulture.org and www.extension.org/grapes. Efforts to educate industry and scientific researchers involved hosting a poster session during the annual project meeting (open to the New York State Agricultural Experiment Station community and all meeting attendees), presenting seminars and posters at scientific meetings, and instructing two genotyping-by-sequencing (GBS) workshops. Both workshops used data generated within the project as a teaching tool. In addition, researchers (including visiting scientists, undergraduate students, graduate students, and postdoctoral associates) were trained in trait evaluation, GBS analyses, and in both modern and traditional breeding techniques. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The project has provided three main opportunities for training and professional development. First, project participants have assisted in coordinating and presenting two GBS workshops. Second, project directors and participants have helped to train other scientists and students in trait evaluation and GBS analyses at the three phenotyping centers, the genotyping center, and within individual breeding programs. Third, project directors and participants have traveled to more than 15 scientific conferences, extension meetings, and workshops to engage with the domestic and international grape research community and grape industry. How have the results been disseminated to communities of interest? The VitisGen website has provided a platform to disseminate information regarding the project, and breeding and genetics educational materials to the public, scientists/researchers, and industry. A link to the VitisGen website appears on the eViticulture website, which has provided increased visibility of the project to the public and grape industry. In addition, a tannin blog (http://blogs.cornell.edu/winechemistry/tanninblog/) was developed to educate the wine community and the public. Social media has also been employed to distribute educational materials to a broader public audience. For example, two issues of the ‘VitisGen Voice’ newsletter were distributed using email, the project website, and social media. In another example, the video “VitisGen: Tracking Resistance” was published on YouTube and the link to the video was distributed using email, the project website, and the Finger Lakes Grape Program Facebook page. Results stemming from the project have also been disseminated through a combined total of more than 40 seminars, short talks, and posters at domestic and international scientific, industry, and extension meetings and conferences. The project brochure has been distributed at several of these domestic and international meetings of scientists/researchers and industry. Two workshops using VitisGen data have provided the opportunity to train and educate geneticists about GBS in non-model organisms. Data and research materials have been published in conference proceedings and peer-reviewed journals. In addition, private and international grape breeders outside of the VitisGen project have expressed interest in VitisGen marker platforms. So that they can benefit from the VitisGen SSR expertise without using project-funded resources, VitisGen provided publicly available marker information to a private company and tested their service with 1,000 samples. The results indicated that the service provides a sufficient turnaround time, a reasonable cost, and an acceptable quality of data allowing non-VitisGen breeders to process SSRs using the VitisGen marker platform. What do you plan to do during the next reporting period to accomplish the goals? We plan the following courses of action: Trait Economics Administer and analyze the grower survey of the three main subsets of California grape growing industry (wine, raisin, and table) to determine grower preferences for genetic improvement and the market potential of new traits. Report results from the grower survey. Complete a second working paper on pecuniary and non-pecuniary costs of disease management, grower valuation of improved varietal traits, and adoption of improved cultivars. Trait Evaluation Complete the fourth year of phenotypic analysis of traits, both at breeding program locations and at phenotyping centers. Update low temperature response datasets to include 2 years of data of freezing tolerance and chilling fulfillment on five populations including the additional parameter information for both freezing tolerance and chilling fulfillment traits. Complete segregation analysis of the populations for resistance against powdery mildew (Erysiphe necator) and downy mildew (Plasmopara viticola). Complete raw data collection and reporting for non-volatiles at the fruit quality phenotyping center. Record, summarize, analyze, and integrate trait data into VitisGen breeding database. Communicate results from phenotyping centers back to the breeding programs. Report outcomes on trait evaluation to the scientific community. Genetics Complete genotype quality checks, discard contaminant vines, and construct high-resolution linkage maps for 16 VitisGen core populations. Develop a SNP map for an F2 population. Coordinate trait data and complete quality check and statistical analysis of phenotypic data representing 100 trait x population combinations, in preparation for QTL analysis. For a subset of high quality phenotypes, complete QTL analysis to identify marker-trait associations and share results with submitting breeder. Publicly release GBS pipeline for linkage map construction, which will be useful for organisms with heterozygosity. Provide outreach to geneticists working on GBS in other specialty crops. Breeding Maintain core populations. Provide samples for phenotyping and genotyping as needed. Apply marker-assisted breeding. Make crosses to develop populations for future research. Extension Develop additional videos and written materials, including the ‘VitisGen Voice’ newsletter and other articles. Improve the distribution of extension materials to industry members through a variety of means, including the network of viticulture and enology extension specialists throughout the US, and to relevant faculty members and researchers at institutions around the world. Host another project meeting (scheduled in January 2015), which will advance collaborative efforts with industry; enable researchers to present findings, and allow project participants to share ideas and make plans.

Impacts
What was accomplished under these goals? Many of the economic and environmental costs associated with grape production stem from the planting of unimproved cultivars developed 150-2000 years ago that are highly susceptible to biotic and abiotic stresses such as powdery mildew, cold winters, and autumn and spring freezes. To improve the efficiency and reduce the overall costs of grape production and improve crop characteristics, breeders have adopted "marker-assisted breeding" to develop new grape cultivars that incorporate consumer-driven top priority traits. This project has united grape breeders nationwide; established three phenotyping centers for trait evaluation; a genotyping center to identify new molecular markers; an economics team to establish models that measure the benefits of new traits and to identify top priority traits; and an extension team to enhance communication and develop educational materials on breeding and genetics. Using next-generation sequencing technology and three phenotyping centers, we are on our way to developing 35 new molecular markers associated with biotic and abiotic stress tolerance and fruit quality. We have already applied existing markers across over 10,000 breeding lines, trained domestic and international geneticists to use this new genotyping technology in non-model organisms, produced a project brochure, published videos on grapevine breeding and tracking disease resistance, and launched a project website www.vitisgen.org. In the remaining years of the project, participants will continue to collaborate on the development of new cultivars addressing the critical needs of the grape industry. Objective 1: Develop breeding strategies for grape genetic improvement driven by consumer, industry, and broader market preferences, and documented economic, environmental, and social benefits. A model was developed to approximate the benefits from varietal improvements for grape growers and industry data on costs and benefits associated with mitigation of different types of disease problems was compiled. Budgets for representative growers of wine, table and raisin grapes were used to evaluate benefits from hypothetical powdery mildew (PM) resistant cultivars accruing to California grape growers both statewide and for specific industry subsets. State-level costs of PM management using aggregate data on relevant fungicide applications were estimated and the net present value of economic benefits from PM resistance for 3 specific subsets of growers under various scenarios of varietal adoption was calculated. Based on the results of the analysis, a survey instrument was developed to determine whether grower valuation of improved varietals is consistent with estimates and to help quantify the environmental costs and benefits. The goal of the survey is to estimate growers’ acceptance of new genetic developments and to infer growers’ willingness-to-pay for attributes conveyed by genetics research. The data will be used in further economic modeling work on varietal adoption. Objective 2: Develop 35 new molecular markers in germplasm relevant to U.S. grape breeding programs. Apply new and existing markers to accelerate the breeding and selection of improved cultivars adapted to diverse regions of the U.S. Breeders maintain 19 core mapping populations at locations in CA, SD, MN, FL, MO, and NY. Breeders sent two of the core populations to E. & J. Gallo to establish backup plantings. The three phenotyping centers received shipments of canes, leaves, or fruit from breeders for trait evaluation. Traits assessed included: three populations for chilling fulfillment and freezing tolerance; six populations for powdery mildew resistance; six populations for fruit quality (non-volatile and volatile analyses); and individuals from three populations for grape tannin, tannin extractability, and macromolecular composition analyses. Breeders also evaluated a range of additional traits. Trait data were transmitted to the genotyping center to identify marker-trait associations and to begin QTL analyses. The genotyping center isolated DNA from 7,968 samples. Genotyping-by-sequencing (GBS) data was obtained for 2,592 of these samples. From the 11,425 grape breeding samples processed in Years 1 and 2, the GBS SNP pipeline discovered 2.9 million raw SNPs across the grape genome. Per population, 3,000 to 10,000 SNP markers were identified for assembling physical and linkage maps. For two core VitisGen populations, RNAseq differential expression analysis identified Phomopsis and powdery mildew disease resistance/susceptibility candidate genes within previously identified loci. Gene-specific markers are under development. In the previous field season, breeders applied markers from 10 unique loci across 3,814 seedlings within 50 mapping families. 58.7% of the seedlings were discarded based on marker data, field trait evaluation, or weak growth/mortality. In Year 3, the core genotyping facility processed 133 SSR plates multiplexed with four markers per plate, tracking twelve loci. Rapid turnaround allowed breeders to make selection decisions within two months of leaf sampling. Outcomes from marker application during the current field season will be reported in Year 4. Objective 3: Optimize GBS to increase the standard number of SNP markers for linkage mapping, decrease the cost per sample, and train geneticists from other specialty crops in GBS protocols and data analysis. Several new scripts, programs, and pipelines were developed to optimize GBS for mapping priority traits. First, a new pipeline for preparing genetic maps using GBS data in JoinMap was developed. Second, an error-correcting script was produced that identifies and corrects artifacts of GBS technology resulting in a 5-fold increase in marker density. Third, a script that infers parental alleles based on progeny data and reformats data was developed to convert variable call format data to input for linkage mapping analysis in JoinMap. Fourth, a quality control pipeline was constructed and automated to confirm and merge duplicated samples and to identify and discard contaminant samples resulting from self-hybridization, accidental outcrossing, or seed/cutting mix-ups. Fifth, a program was created to identify GBS tags that are predictive of a phenotype in the absence of a genetic map. In addition, two workshops and an in-house training were held to train researchers in GBS protocols and data analysis in non-model organisms using project data. Objective 4: Enhance communication between grant participants and the industry and public and develop education resources on breeding and genetics. The project website www.vitisgen.org remains an active site to communicate accomplishments. The eViticulture website hosts a link to the VitisGen website, which provides the project more public visibility. Project participants continue to circulate the VitisGen brochure at domestic and international meetings. Two issues of the ‘VitisGen Voice’ and an educational video on tracking disease resistance http://www.youtube.com/watch?v=eFSqfL946j4 were published, featured on the project website, distributed to project participants, and publicized using social media. A project meeting, including both a poster session and a GBS workshop, was held in February 2014 with the project team and the Industry Advisory Panel to enhance industry collaboration, input and dialogue; to assess current progress and improve project efficiency; and to share ideas and outline plans. An executive summary and review of the annual meeting and a spring update were distributed internally to all project participants. Data and research materials from trait evaluation, genotyping, breeding, trait economics, and extension were presented at a multitude of academic and extension conferences, shared informally on social media or with grower groups and local extension offices, and published in peer-reviewed journals.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Barba, P., Cadle-Davidson, L., Harriman, J., Glaubitz, J.C., Brooks, S., Hyma, K., and Reisch, B.I. (2014) Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. Theoretical and Applied Genetics 127(1), 73-84.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Springer, L.F., and Sacks, G.L. (2014) Protein-Precipitable Tannin in Wines from Vitis vinifera and Interspecific Hybrid Grapes (Vitis ssp.): Differences in Concentration, Extractability, and Cell Wall Binding. Journal of Agricultural and Food Chemistry 62 (30), 7515-7523.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Alston, J.M., Fuller, K.B., Kaplan, J.D., and Tumber, K.P. (2013) The Costs and Benefits of Pierces Disease Research in the California Winegrape Industry. Australian Journal of Wine Economics 58, 1-21.
  • Type: Other Status: Published Year Published: 2014 Citation: Fuller, K.B., Alston, J.M., and Sambucci, O.S. The Value of Powdery Mildew Resistance in Grapes: Evidence from California. Agricultural and Resource Economics Update 17(5) (2014): 1-4. Available from: http://giannini.ucop.edu/media/are-update/files/articles/V17N5_1_1.pdf
  • Type: Other Status: Published Year Published: 2014 Citation: Fuller, K.B., Alston, J.M., and Sambucci, O.S. The Value of Powdery Mildew Resistance in Grapes: Evidence from California. The Coffee Shop Blog by Lodi Winegrape Commission, Lewis Perdue/Wine Industry Insight and Wine Industry Advisor. Available at http://www.lodigrowers.com/the-value-of-powdery-mildew-resistance-in-grapes-evidence-from-california/
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Springer, L.F. and Sacks, GL. (2014). Limits on Red Wine Tannin Extraction and Addition: The Role of Pathogensis- related Proteins. American Society for Enology and Viticulture 65th National Conference, Austin, TX.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Springer, L.F. and Sacks, G.L. (2014) Tannin Management. Proceedings of the B.E.V. NY Conference, Waterloo, NY.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Manns, D. (2014) Challenges and Advances Regarding Selective Chemical Deacidification of Grape Musts and Wine. Proceedings of the B.E.V. NY Conference, Waterloo, NY.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Springer, L.F. and Sacks, G.L. (2014) Understanding tannins in hybrid wines, an explanation of why extraction and additions present particular challenges. Midwest Grape and Wine + Craft Brew Conference, St. Charles, MO.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2013 Citation: Sacks, G.L. (2013) Relating grape composition to wine flavor chemistry  or, why wine is more than grape juice diluted with vodka. Proceedings from the 246th American Chemical Society National Meeting, Indianapolis, IN.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Stafne, E.T., Burrows, R., Fidelibus, M., Greer, L., Jenkins, P., Ker, K., Moyer, M., Skinkis, P., and Walter-Peterson, H. (2014) A New Strategic Plan for the eXtension Grape Community of Practice. HortScience (in press)
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: Stafne, E.T., Burrows, R., Fidelibus, M., Greer, L., Jenkins, P., Ker, K., Moyer, M., Skinkis, P., and Walter-Peterson, H. (2014) Reach, Engagement, and Impact of eViticulture and the eXtension Grape Community of Practice. HortScience (in press)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Xu X., J. Lu, Z. Ren, and F. Bradley (2013). Downy mildew disease resistance in F1 of C30-5-1 � Chardonnay. Proc. Fla. State Hort. Soc., 126, 14.
  • Type: Other Status: Other Year Published: 2014 Citation: Fuller, K.B., Alston, J.M., and Sambucci, O.S. The Value of Powdery Mildew Resistance in Grapes: Evidence from California. Robert Mondavi Institute for Wine Economics Working Paper #1401. Available from: http://vinecon.ucdavis.edu/publications/cwe1401.pdf
  • Type: Other Status: Other Year Published: 2013 Citation: Fuller, K.B., Alston, J.M., and Golino, D.A. The Benefits from Certified Virus-Free Nursery Stock. Robert Mondavi Center for Wine Economics Working Paper #1306. Available from: http://vinecon.ucdavis.edu/publications/cwe1306.pdf
  • Type: Other Status: Published Year Published: 2013 Citation: Walter-Peterson, H. Editor. 2013, November. VitisGen Voice, Winter 2013:1-6. Available from: http://vitisgen.org/pubs.html.
  • Type: Other Status: Published Year Published: 2014 Citation: Walter-Peterson, H. Editor. 2014, May. VitisGen Voice, Spring 2014:1-6. Available from: http://vitisgen.org/pubs.html.
  • Type: Other Status: Other Year Published: 2014 Citation: Stafne, E.T. 2014. Online Grape Production Information via eViticulture. ASEV-ES News. Spring 2014: 4-5.


Progress 09/01/12 to 08/31/13

Outputs
Target Audience: There were three target audiences during this reporting period: the general public, industry and scientific researchers. Efforts to educate the general public and industry included the development and circulation of a project brochure, the re-design and launch of the project website <www.vitisgen.org>, and the production and distribution of a video “VitisGen: Breeding Crosses” <http://www.youtube.com/watch?v=z-Pranxd9fw>. National and international researchers and geneticists were the target audience for three genotyping-by-sequencing (GBS) workshops. Data generated in the project were used as an instructional tool to teach how to work with non-model organisms. Researchers were also the target audience for experiential learning opportunities by receiving training in trait evaluation, breeding, and GBS analyses. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The project has provided three main opportunities for training and professional development. First, project participants have assisted in coordinating and presenting three GBS workshops. Second, project directors and participants have helped to train other scientists and students in trait evaluation and GBS analyses at the three phenotyping centers, the genotyping center, and within individual breeding programs. Third, project directors and participants have traveled to more than 20scientific and extension meetings to engage with the domestic and international grape research community and grape industry. How have the results been disseminated to communities of interest? Results stemming from the project have been disseminated through a combined total of more than 30seminars, short talks, and posters at scientific, industry, and extension meetings and conferences. The website has provided a platform to disseminate information regarding the project, and breeding and genetics educational materials to the general public, scientists/researchers, and industry. Social media has also been employed to distribute educational materials to a broader public audience. A project brochure was designed and printed. It has been distributed at several meetings of scientists/researchers and industry. There is also an email account set-up for the project. The email address can be found on the project brochure and the website. What do you plan to do during the next reporting period to accomplish the goals? We plan the following courses of action: Administer and subsequently analyze the survey of grower and producer perceptions. Develop additional surveys (as needed) with guidance of the industry advisory panel. Generate economic models and measures of varietal innovations. Refine the automated pipeline to construct genetic maps using GBS data. Construct genetic maps for the 18 core mapping populations. Implement the marker discovery pipeline for the 3,990 DNA samples submitted for GBS fingerprinting. Create training materials to teach breeders in a workshop how to integrate GBS data with trait data. Apply marker-assisted breeding using rapid SSR fingerprinting in Year 3. Produce and distribute additional educational videos on breeding, genetics, and trait evaluation. Host another project meeting (scheduled in February 2014), which will advance collaborative efforts with industry, enable researchers to present findings, and allow project participants to share ideas and make future plans.

Impacts
What was accomplished under these goals? Many of the economic and environmental costs associated with grape production stem from the planting of unimproved cultivars developed 150-2000 years ago that are highly susceptible to biotic and abiotic stresses such as powdery mildew, cold winters, and autumn and spring freezes. To improve the efficiency and reduce the overall costs of grape production and improve crop characteristics, breeders have adopted “marker-assisted breeding” to develop new grape cultivars that incorporate consumer-driven top priority traits. This project has united grape breeders nationwide; established three phenotyping centers for trait evaluation; a genotyping center to identify new molecular markers; an economics team to establish models that measure the benefits of new traits and to identify top priority traits; and an extension team to enhance communication and develop educational materials on breeding and genetics. Using next-generation sequencing technology and three phenotyping centers we are on our way to developing 35 new molecular markers associated with biotic and abiotic stress tolerance and fruit quality. We have already applied existing markers across over 6,000 breeding lines, trained domestic and international geneticists to use this new genotyping technology in non-model organisms, produced a project brochure, published a video on grapevine breeding, and launched a project website <www.vitisgen.org>. In the remaining years of the project, participants will continue to collaborate to improve traditional grape breeding while addressing the critical needs of the grape industry. 1. Develop breeding strategies for grape genetic improvement driven by consumer, industry, and broader market preferences, and documented economic, environmental, and social benefits. Economic models and ways to measure the benefits to individual growers and market benefits from varietal technologies are being developed. Non-market benefits that include a reduction in the use of chemical pesticides and their associated environmental burdens are being measured. Two surveys were designed with guidance and feedback provided by a subcommittee of the Industry Advisory Panel. The first survey identified grape researcher perceptions of the priorities that should guide current and future grape research initiatives. The survey was administered to 718 researchers and completed by 140 individuals. A report summarized the findings and concluded that powdery mildew disease resistance was the most economically beneficial trait and could be developed most rapidly in new cultivars. It identified that 53% of the respondents currently use marker-assisted breeding and the primary source of difficulty in implementing breeding priorities is lack of funding. Lack of genetic information and agreement upon top priority traits were also identified as creating setbacks for the application of breeding priorities. The second survey, which will be administered and analyzed in Year 3, was devised to identify grower and producer perceptions toward adoption of new varieties and to identify their top priority traits. 2. Develop 35 new molecular markers associated with biotic and abiotic stress tolerance, fruit quality, and additional traits in germplasm relevant to U.S. grape breeding programs. Apply new and existing markers across thousands of breeding lines to accelerate the breeding and selection of improved cultivars combining biotic and abiotic stress tolerance with excellent fruit quality, directly resulting in new cultivars adapted to diverse regions of the US. Breeders maintain 18 core mapping populations at locations in CA, SD, MN, FL, MO, and NY. Breeders sent several of the core populations to E. & J. Gallo to establish backup plantings in the winter of 2012-13. In Year 2, the 3 phenotyping centers received shipments of canes, leaves, or fruit from breeders for trait evaluation. Traits assessed: 4 populations for low temperature responses (chilling fulfillment and freezing tolerance), 7 populations for powdery mildew resistance, and 5 populations for fruit quality. Breeders also evaluated a range of additional traits. In Year 2, the genotyping center performed computational analysis of GBS fingerprinting data from 8,256 individuals. Fifteen core mapping populations passed rigorous quality checks in the marker discovery pipeline, producing physical maps with ca. 20,000 SNPs per population. Leaf samples from an additional 6,935 individuals were submitted for DNA isolation and quantification. A total of 3,990 DNA samples were submitted for GBS fingerprinting and will be processed and computationally analyzed in Year 3. A subset of Year 1 samples submitted to the genotyping center were also processed for SSRs for marker-assisted breeding. Breeders screened up to 8 loci using SSR markers, totaling 65,664 single reactions. Processing this large number of reactions ultimately delayed the application of marker-assisted breeding. As a result, the protocol was adjusted, and certain markers were prioritized for rapid analysis, for the second round of submissions in Year 2. This reduced the total number of SSR reactions to ~12,000, which decreased the overall processing costs, allowed a higher number of individuals to be screened, and improved the turnaround time to deliver results back to breeders. 3. Optimize genotyping-by-sequencing (GBS) to increase to 50,000 the standard number of Single Nucleotide Polymorphism (SNP) markers for linkage mapping, decrease the per sample cost to 30 dollars, and train up to 30 geneticists from other specialty crops in GBS protocols and data analysis. To optimize GBS for linkage mapping, an algorithm was developed to automate construction of genetic maps with 2,000-4,000 SNP markers in F1 (pseudo-testcross) populations. This automated process needs to be further refined in Year 3, but has been used to generate 4 draft genetic maps. In addition to optimizing the GBS protocols, national and international geneticists were trained at three genotyping-by-sequencing (GBS) workshops. Two of the workshops were delivered in conjunction with Cornell University and USDA scientists on February 7-8, 2013 and June 17-18, 2013. The third workshop was held at the American Phytopathological Society and the Mycological Society of America Joint Meeting on August 10, 2013. 4. Enhance communication between grant participants and the industry and public and develop education resources on breeding and genetics. The project website www.vitisgen.org was launched to communicate project goals and results. Highlights of the website include: 1) a project description delineating project goals and outlining application of marker-assisted breeding; 2) a glossary defining key scientific terms used in breeding, trait evaluation, and genetics; and 3) a list of all project-related presentations. A brochure providing a general overview of the project goals and collaboration was designed, printed, and distributed. In addition to the website and the brochure, an educational video on grapevine breeding was produced and published on YouTube <http://www.youtube.com/watch?v=z-Pranxd9fw>. A link to the video was posted on the project website, the Cornell Cooperative Extension Finger Lakes Grape Program’s Facebook page, and distributed to project participants including the Industry Advisory Panel. A second educational video on the powdery mildew phenotyping center efforts is currently in production. An executive summary and review of the April 2012 project meeting of directors, collaborators, and industry advisory panel members was distributed to all meeting participants. A project meeting was held in March 2013 with the project team and the Industry Advisory Panel to further enhance continued industry collaboration, input and dialogue; to assess current progress and improve project efficiency; and to share ideas and outline future plans.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Stafne, E.T., E. Hellman, R.K. Striegler, J.A. Wolpert, and J-M. Peltier. 2012. Industry involvement in the creation and funding of the eXtension Grape Community of Practice. HortTechnology 22:580-582.
  • Type: Journal Articles Status: Accepted Year Published: 2013 Citation: Alston, J., Fuller, K., Kaplan, J., and Tumber, K.. 2013. "The Economic Consequences of Pierces Disease and Related Policy in the California Winegrape Industry." Journal of Agricultural and Resource Economics 38(2):269297.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Stafne, E.T., E. Hellman, R.K. Striegler, T. Martinson, B. Reisch, and J-M. Peltier. (2012) A Collaborative Research and Extension Outreach Model: the Grape Community of Practice. Amer. J. Enol. Viticul. 63(3): 431A-464A.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Springer L.F., E. Defnet, and G.L. Sacks. (2013) Tannin Extractability in Cool-Climate Cultivars: Variability and Regional Discrepancies. Abstracts from Presentations at the ASEVEastern Section 38th Annual Conference, 1518 July 2013, Winston-Salem, NC. Am. J. Enol. Vitic. 64(3), 416A-424A.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Stafne, E. (2013) eViticulture: A Multi-faceted International Platform for Viticulture Outreach. Abstracts from Presentations at the ASEVEastern Section 38th Annual Conference, 1518 July 2013, Winston-Salem, NC. Am. J. Enol. Vitic. 64(3), 416A-424A.
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2013 Citation: Fuller, Kate B. (2013) The Costs and Benefits of Pierces Disease Research in the California Winegrape Industry. Abstracts from Presentations at the ASEV 64th National Conference 2428 June 2013, Monterey, California. Am. J. Enol. Vitic. (in press)
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2013 Citation: Barba, P., L. Cadle-Davidson and B. Reisch. (2013) Genetic resistance to powdery mildew in Vitis rupestris: Mapping a way to generate durably resistant cultivars. Abstracts from Presentations at the ASEV 64th National Conference 2428 June 2013, Monterey, California. Am. J. Enol. Vitic. (in press)
  • Type: Conference Papers and Presentations Status: Submitted Year Published: 2013 Citation: Springer L.F., E. Defnet, and G.L. Sacks. (2013) Tannin Extractability among Hybrid and Vitis vinifera Grapes: Cultivar Variability and Differential Binding to Cell Walls. Abstracts from Presentations at the ASEV 64th National Conference 2428 June 2013, Monterey, California. Am. J. Enol. Vitic. (in press)
  • Type: Other Status: Accepted Year Published: 2012 Citation: Alston, J. M., Fuller, K., and Tumber, K. (2013) "The Costs of Pierces Disease in the California Winegrape Industry." California Agriculture. (in press)
  • Type: Other Status: Published Year Published: 2013 Citation: Walter-Peterson, H. (2013) Mapping the Way to the Next Generation of Grapes. American Fruit Grower.
  • Type: Other Status: Published Year Published: 2013 Citation: Takacs, E. and H. Walter-Peterson. (2013) "VitisGen: Mapping the Way to the Next Generation of Grapes." Northern Grapes Project Newsletter, February 2013.
  • Type: Other Status: Published Year Published: 2012 Citation: Thompson, S. (2012) Program Has $9 Million to Develop Better Grapes. Cornell Chronicle, October 24, 2012. http://www.news.cornell.edu/stories/2012/10/program-has-9-million-develop-better-grapes
  • Type: Other Status: Published Year Published: 2012 Citation: Fraser, R.L. (2012) "DNA of the Vine: Grape Goes High Tech." Growing Magazine, Vol 10(8): C8-C9.
  • Type: Other Status: Published Year Published: 2012 Citation: Fraser, R.L. (2012) "Grape Returns to its Wild Past." Growing Magazine, Vol 10(7): B8-B10.
  • Type: Other Status: Published Year Published: 2013 Citation: Stafne, E.T. (2013) The grape community of practice works to improve viticulture outreach education. Wines and Vines/Practical Vineyard and Winery Journal. April 2013, pp. 72-74.
  • Type: Websites Status: Published Year Published: 2013 Citation: http://www.vitisgen.org


Progress 09/01/11 to 08/31/12

Outputs
OUTPUTS: There are five overall goals to the "VitisGen" project: I. Develop consumer-driven breeding strategies for grape genetic improvement with documented impacts. Preliminary economic analysis has focused on understanding the traits being incorporated into new varieties and how to quantify the advantages of these traits. During a project meeting in April 2012, a subcommittee of the Industry Advisory Panel was formed to provide feedback on design and implementation of surveys. II. Develop and apply new molecular markers. Breeders are maintaining eighteen populations for genotypic and phenotypic analyses and have submitted leaf samples, fruit samples, or cuttings to genotyping and phenotyping centers. To date breeders submitted genotyping leaves from a total of 6,200 individuals of the 7,000 targeted for 2012 and additional leaves are arriving each week. The genotyping center is isolating and submitting DNA samples for GBS and SSR fingerprinting. In addition to receiving and processing samples from the breeders, the genotyping center has developed and started to implement a pipeline for computational analysis for both marker discovery and marker application. Three phenotyping centers, which measure powdery mildew resistance, low temperature tolerance, and fruit quality, have been established. Thus far, the powdery mildew center has received and processed samples from three VitisGen populations and is on track to meet its Year 1 goal. Breeders also sent four VitisGen populations to the low temperature tolerance center. Finally, the breeders sent fruit from two populations (200 accessions each) to the fruit quality center in the fall of 2011; analysis is underway. Breeders are also performing phenotypic analysis locally on a range of additional traits. III. Marker application across 20,000 breeding lines Both the breeders and the genotyping center are working toward applying markers across 20,000 breeding lines, approximately 5,000 per year for the first four years of the project. The genotyping center and breeders selected SSR markers from previous studies or designed and subsequently tested new markers in the spring of 2012. Eight loci of interest are being screened. Thus far, breeders have collected and submitted leaves (for DNA sampling) from 6,200 individuals. IV. Train in GBS for 50,000 markers per population. A GBS workshop was held on April 17, 2012 immediately following a VitisGen project meeting. A total of 25 participants attended the workshop from eight institutions. V. Communicate goals and results clearly. Two VitisGen project meetings have taken place. The first, a meeting of the breeders with the genotyping team, was held in January 2012 in San Diego, California. The second meeting was held in April 2012, gathering together the project team with the Advisory Committee. The meeting was held to assess current progress, to outline future plans, to share ideas, and to encourage continued industry collaboration, input, and dialogue. Several project directors have highlighted project goals at conferences and university seminar series. A project website is also being developed to communicate goals and results. PARTICIPANTS: Individuals: There are 25 Project Directors and Collaborators. Their roles within the project are described in the project narrative. In addition, there are the following individuals participating in the project: Anna Nowogrodzki: powdery mildew technician, Cornell University Peter Hemstad: grape breeder, U. Minnesota Michelle Schaub, powdery mildew technician, Cornell University George Wigsten, SSR technical support (student), Cornell University Kathy Mathiason, Research Associate, South Dakota State University Kas Deys, technical support, USDA-ARS, Geneva, NY Partner Organizations: National Grape and Wine Initiative (providing financial support as well as Advisory Committee input) Gallo Winery, Inc. (providing financial support as well as Advisory Committee input) California Table Grape Commission (providing financial support as well as Advisory Committee input) Collaborators: Jason Londo, Research Geneticist, USDA-ARS, Grape Genetics Research Unit, Geneva, NY Training, professional development: Atsushi Kono, Visiting Fellow at Cornell, National Institute of Fruit Tree Science, Japan Marianna Kocsis, Visiting Fellow at Cornell, Univ. of Pecs, Hungary Elizabeth Takacs, Postdoctoral Fellow, Cornell Univ. Katie Hyma, Postdoctoral Fellow, Cornell Univ. Paola Barba, Ph.D. student, Plant Breeding, Cornell Univ. Lindsay Springer, Ph.D. student, Food Science, Cornell Univ. TARGET AUDIENCES: At one level, our target audience includes grape breeders, who are actively developing new rootstocks as well as wine, raisin, and table grape cultivars. Beyond that our project will impact the grape and wine industry, tourism industry, as well as all consumers of grape and wine products. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
At this early stage of the project, the primary impact has been the adoption of marker-assisted selection practices by breeders associated with the program. Eight loci were available for analysis, based on genes known to be segregating in breeder populations. These loci were developed prior to the start of the VitisGen project both by PDs working with VitisGen and scientists not associated with VitisGen. Breeders are now changing their systems of seedling germination and handling to take advantage of the input of marker data, which will help to identify elite groups of seedlings in the first year. Of great importance to the overall success of the project is the development of a GBS data analysis pipeline to attain a goal of 50,000 SNP markers in each population, and to make sure that such markers are of high quality. Procedures includes rigorous quality control steps to detect unintentional outcrossing, sampling errors, or handling errors prior to data analysis. We are on-target for obtaining 50,000 markers per population. To date samples analyzed have had up to 300,000 markers, though we prefer to use a high stringency threshold, currently resulting in 10,000 to 20,000 markers per population. Over the course of the first four years, the goal was to develop GBS data for all eighteen project populations. In year one, DNA samples of all eighteen populations, and often more than the minimum 91 individuals per population, were submitted for analysis. In one population, nearly 400 individual seedlings were sampled. This is substantially ahead of the projected goal for year one.

Publications

  • Cadle-Davidson, L.E., Q. Sun, P. Barba, M. Wang, S. Brooks, A. Fennell, and B. Reisch. 2012. VitisGen: A coordinated effort in grape genotyping, phenotyping, and marker-assisted selection (abstract). Plant and Animal Genome XX. January 14-18, 2012.
  • Stafne, E.T. E. Hellman, R.K. Striegler, J. Wolpert, T. Martinson, B. Reisch, and J.-M. Peltier. 2012. A collaborative research and extension model: the Grape Community of Practice (abstract). Annual meeting of the American Society for Horticultural Science, July, 2012.
  • Cadle-Davidson, L., A. Nowogrodzki, M. Schaub, P. Barba, B.I. Reisch, R.C. Seem, and D.M. Gadoury. 2012. VitisGenPM: A precision phenotyping center for powdery mildew resistance breeding in grapevine (abstract). Annual meeting of the American Phytopathological Society, 4-8 August 2012, Providence, Rhode Island.
  • Reisch, B.I. and L. Cadle-Davidson. 2012. New(er) Grape and Wine Projects Funded by the SCRI: The VitisGen Project to Accelerate Grape Variety Development. In: Presentations from the 2012 New York Wine Industry Workshop & Finger Lakes Grape Growering Convention, March 1-3, 2012. (on CD-ROM)