Table of Contents
- PROJECT ACCOMPLISHMENTS
- FUTURE DIRECTIONS
- PROJECT OUTPUTS
This report serves as the summary of first year project updates for VitisGen2. The following is an excerpt from the annual report submitted to the USDA-NIFA Research, Extension, and Education Project Online Reporting system (REEport) for the project entitled “VitisGen2: Application of Next Generation Technologies to Accelerate Grapevine Cultivar Development”. The report is cumulative from all project team members and covers the period from September 1, 2017 through August 31, 2018 and was submitted on November 30, 2018. The report has been reformatted for readability prior to distribution to project directors, collaborators, and the advisory panel.
Recent analyses have emphasized the economic and environmental importance of developing new grape cultivars with high fruit quality (FQ) and resistance to powdery mildew (PM). An Advisory Panel of table, juice, raisin and wine grape industry members concurs that high-quality, PM-resistant cultivars are a top priority. The VitisGen2 project seeks to 1) expand on VitisGen1 progress in developing novel economic, phenotyping and genetics knowledge and tools related to new grape cultivars, and 2) translate these and previous VitisGen1 innovations into new applications for improving grape breeding programs and managing existing vineyard plantings. The Economics team objectives are to evaluate the consequences of introducing new grape traits, including impacts upon cost, yield, revenue, profit, pesticide use, and the environment. The Phenotyping and Breeding teams are developing novel high-throughput methods, and applying these along with proven approaches to characterize a range of phenotypes, such as PM resistance durability and undesirable fruit qualities, as well as locally important traits. The Genetics Team is utilizing phenotyping results with high-resolution genetic maps, which can be combined with genome assembly and RNA-Seq analyses to develop inexpensive, high-resolution markers spanning key genes. Finally, the Outreach team will communicate scientific opportunities and discoveries, and provide stakeholders with knowledge of the benefits of adopting new high-quality PM resistant cultivars along with new tools for characterizing PM and FQ in their existing plantings. The proposed work utilizes plant breeding and genomics approaches to improve grape characteristics and enhance the economic and environmental sustainability of grape production. This work expands upon the VitisGen1 project which created a foundation for research in grape genomics and breeding, and the results from VitisGen2 will also continue to contribute to the development of new grape cultivars.
Powdery mildew (PM) resistance consistently ranks as a top research priority facing the U.S. grape industry, based on more than a dozen stakeholder meetings focused on research priorities since 2005 and numerous industry surveys. PM is the most significant grape disease in California, and likely worldwide, in terms of expenses for control and losses in quality and yield. In an international survey of grape scientists, PM was statistically significant in being both the most important and the most genetically tractable of twelve key traits. However, breeding for PM resistant cultivars via traditional methods frequently results in negative fruit quality trait introgression from wild Vitis. Winemakers report that poor sensory attributes and color are major challenges to using interspecific hybrids, particularly the presence of high acidity, low tannin and color stability, and off aromas. To address the need for PM resistant cultivars with desirable fruit quality, the long-term objectives and progress and the progress being are listed in the next section.
Objective 1: Technological Innovations Driven by Trait Economics
Two sub-objectives are focusing on integrating genome-wide data with innovations in phenotyping powdery mildew (PM) resistance, and table and wine grape quality for genetic characterization of high-priority traits. Specific goals focus on gene discovery and trait assays using de novo annotations of relevant wild genomes, conducting RNA-Seq of all VitisGen2 parents, using low-cost AmpSeq markers for marker assisted selection (MAS), automating PM quantification, and developing multiple high throughput phenotyping screens for key fruit quality traits, and identification of candidate genes for PM resistance and fruit quality. All of this work is expected to be completed along with a complete economic analysis of several key agronomic and quality traits relevant to grape research and breeding.
Teams have worked collaboratively to complete de novo assembly of 16 Vitis genomes, which has led to the construction of a Vitis pan-core genome, identifying regions that are structurally stable and well conserved across the genus. PCR primers were developed from the core genome regions and will be used as markers in hybrid grape breeding. In collaboration with a U.S. company, IDT-DNA, the genetics team developed an improved low-cost, genotyping marker platform using rhAmpSeqTM technology, which focused on the core genome and existing molecular markers. The core genome set of 2,000 amplicon sequencing markers are evenly distributed across all 19 chromosomes. Initial analyses indicated that over 90% of the markers successfully returned data for marker assisted selection as well as construction of draft genetic maps and resulted in high correlations between physical and genetic positions. To manage and analyze the new marker platform, a computational data analysis pipeline was set up to process both Ampseq and rhAmpSeq data, which includes sample and data management systems, software tools to process sequencing data, and a full pipeline from genotyping data to produce genetic maps or for marker-assisted selection.
Across all institutional breeding programs, marker assisted selection analysis was conducted on ~6,000 progeny using previously validated markers. Additionally, several wild grape genomes are in the process of being sequenced using PacBio. Libraries have been prepared for PacBio sequencing for V. piasezkii, V. romanetii and the PS11-5 breeding line that carries two qualitative loci (REN1 and RUN1) conferring powdery mildew resistance.
For disease resistance phenotyping, the PM team developed an automated robotic system for high-throughput phenotyping of living, unstained samples. The system is based on an XYZ robotic stage to manipulate a pre-arranged and large array of leaf disc samples. Images are captured on a high resolution 50 MP full-frame DSLR camera at 3.5X actual size. The great depth of field paired with high resolution allows a minimal number of images to be assembled to form a completely focused 3D image from which a convolutional neural network can correctly identify presence or absence of the relevant pathogen (E. necator) within 800 subsampled areas of each disk with 94.3% accuracy compared to human expert screening. Infection (+ or -) of each sub-sampled area allowed quantitation of infection severity on each replicate disc. The system can process up to 2,000 samples per 8 hr day. The latest system will have increased sample processing speed and flexibility. Using this automated robotic system, laboratory-based powdery mildew or downy mildew phenotyping was completed for 6 VitisGen2 families and QTL analyses were completed. Tissues have been collected from four mapping families for RNAseq. These studies are designed to identify disease resistance candidate gene loci based on gene expression data. Currently, phenotypes and genotypes are being quality checked before RNA extraction is conducted.
Over 700 samples from seven mapping populations and four grape breeders were received at the Cornell FQ/WineCenter (Ithaca, NY) from the 2016 and 2017 harvests. Routine protocols for analysis of acids, sugars, volatiles, tannin, and other components have been developed, and will be applied to the grape samples in the coming year. Time-resolved sampling of berries from accessions of wild V. cinerea and V. riparia species (USDA-PGRU Cold HardyGrape Collection) and V. vinifera (Finger Lakes, NY) was conducted during 2017 and 2018. Samples are in preparation for metabolic and transcriptomic analyses. At the Parlier FQ/Table Grape Center, high-throughput 2D phenotyping of cluster architecture and berry shape algorithms for analyses were developed using a subset of images from the previous year (collaborator: Dr. Amy Tabb (USDA ARS)). A high-throughput 3D reconstruction phenotyping of cluster architecture algorithm was developed (Amy Tabb), and fruit phenotyping evaluation methods for texture and juice production were developed. In addition, Breeding Team members have made extensive efforts to maintain core mapping families for continued sampling.
For purposes of addressing the economic analysis of several key agronomic and quality traits to drive research and breeding, the Trait Economics Team has begun working on evaluating economic returns from varietal improvements in table grapes using both historical data and producer surveys. Concurrently, they are developing a set of instruments to use with consumers and market intermediaries of wine and table grapes to evaluate the attitudes towards varieties developed using conventional breeding vs. genetically edited varieties. This work has involved several conference calls with project member and advisory panelists.
Objective 2: Knowledge Extension and Application
Sub-objectives within this goal focus on incorporating technological innovations and economics-oriented priorities in the generation of grapevine seedlings in breeding programs and the selection of elite breeding lines. This will lead to publicly released grapevines, pollen, and/or seed lots with various combinations of RUN1, REN1, REN2, REN3, REN4, REN6, REN7 and REN10 PM resistance. All of the work accomplished in VitisGen2 will be disseminated to show of these advances to grape growers, enologists, and specialty crop researchers.
To achieve these goals, approximately 7,000 genotypes were screened for the presence of multiple alleles for powdery mildew resistance, downy mildew resistance, leaf phylloxera resistance, phomopsis resistance, seedlessness, muscat characters, mono- vs. diglucosides, and more. Based on the presence of favorable alleles, seedling retention during the first year of growth ranged from 29 to 44%. In some cases, both haplotypes at a locus were saved to validate markers, and the Breeding and Genetics teams successfully transitioned all marker screening to AmpSeq analyses.
The automated imaging robot described under Objective 1 was a major technological innovation used for laboratory based powdery mildew or downy mildew phenotyping in 6 VitisGen2 core families. This innovation enabled higher throughput than previously possible and repeated measures of live images, in contrast to previous methods that required destructive sampling for disease severity assessment.
The Breeding Team also carried out phenotyping for the following traits in 2018: powdery mildew (field and lab), phomopsis, flower sex, flowering time, time to veraison, downy mildew (including cooperative work with CSIRO and an NSF project), red skin quality on berries for future work with our red color population, leaf trichomes, budbreak (field an greenhouse), volatiles at anthesis, and veraison through maturity. As data are accumulated, QTL analyses will be run to locate alleles controlling trait variation.
Pollen from a number of new PM resistant sources were incorporated into the breeding programs in 2018. Team members from Cornell, Minnesota, USDA-Parlier, and Davis, California, combined to make multiple crosses with five distinct combinations of the following PM resistance loci: Run1, Ren1, Ren2, Ren3, Ren4, Ren6, Ren7, Ren9, and Ren10. One cross also included three loci for downy mildew resistance (Rpv1, Rpv3, and Rpv10). These seedlings will be screened with genetic markers and selected for different combinations of resistance alleles. Additionally, crosses were performed between a new V.amurensis PM resistance source for both high quality table grapes and NDOV raisin grapes. Additional breeding work included analyses of a family segregating for all combinations of 0 to 4 resistance genes (Run1,Ren1, Ren6, Ren7), which was developed in 2016 and then genotyped and phenotyped to study the effects of gene stack combinations with the ultimate goal of developing breeding lines with stacked loci that will beleased for public use.
Previous economic analyses under VitisGen1 highlighted the economic importance of powdery mildew resistance. With this knowledge, all participating grape breeders are using powdery mildew resistant germplasm and markers in their breeding programs. The impact of VitisGen2 was demonstrated to grape growers, enologists, and specialty crop researchers through a series of webinars, trade publications, the project website, workshops, field days, and peer-reviewed publications.
The project has provided several opportunities for training and professional development. Project participants, cooperators, and visitors received on-site training in diverse topics such as: grape hybridization, propagation, and production; laboratory phenotyping of disease resistance; fruit chemistry, and physical fruit quality; genotyping and marker-assisted selection; linkage mapping and QTL analysis, genome assembly and annotation; RNA-seq analysis; economic analysis and surveys; and communication and outreach. In total, these on-site training activities benefited 19 faculty, 22 technicians, 9 postdocs, 17 graduate students, 11 undergrad students, and 39 high school students. In addition, off-site training was executed via workshops, project meetings, seminars, and webinars. Undergraduate students as well as graduate students and postdocs have been trained in abiotic stress phenotyping and QTL analysis, have worked on experimental design related to understanding differences in metabolite accumulation and degradation between wild Vitis and V. vinifera, have been trained in computational methods in core genome identification, marker design, and downstream data analysis, and trained for evaluating the economic returns from new technology in agriculture. Undergraduate training focused on: mass spectrometry, automation of data collection, and evaluation of variegation in grape seedlings, learning about berry sampling and analytical approaches, and training in viticultural practices and specialized equipment. Educational efforts and outreach activities were conducted via webinars, the VitisGen2 website, and trade publications to educate the grape industry community on the need and potential for genetic improvement to incorporate disease resistance and improved fruit quality traits in new varieties.
Results from this project have been disseminated to a broad range of communities of interest including the general public, industry members, stakeholders, extension, and scientists through national and international conferences. Conferences that project members attending and presented their work included the 69th Annual Conference of the American Society for Enology and Viticulture (ASEV) in Monterey, CA, the International Plant &Animal Genome XXVI Conference in San Diego, CA, the American Society for Enology and Viticulture-Eastern Section 43rd Annual Conference in King of Prussia, PA, the XII International Conference on Grapevine Breeding and Genetics, Bordeaux, France, and the International Congress of Plant Pathology Conference, Boston, MA. Additionally, results have been disseminated through peer reviewed publications, trade publications, news articles, fact sheets, field days, seminar presentations, workshop presentations, stakeholder board meetings, the VitisGen2 website https://www.vitisgen2.org/, the https://enology.umn.edu website, social media via Twitter, and one-on-one communications. Specifically, targeted audiences were reached through several products and publications resulting from this project. Online webinars focused on a target audience consisting of grape scientists and grape industry members who are potential producers and users of new, disease resistant varieties and scientists and industry members interested in computer vision based laboratory evaluation of traits. The data and research materials produced from this project targeted grape industry members and USDA funding agencies. Seminars, conference presentations, and workshop materials were delivered to scientists and grape industry members interested in breeding for disease resistance, management of new disease resistant varieties, and cutting-edge genotyping technologies. The databases that were disseminated were aimed at targeting project participants involved in genetic analyses or application of genetic results and all scientists who generate data on grapevines. Surveys and models that were developed targeted scientists and industry members interested in the economics of grape production. Lastly, plant patents targeted grape industry members interested in cold-hardy, disease resistant wine grapes with excellent fruit quality.
For the Breeding and Genetics teams, goals for year 2 include further development of LIMS for more efficient streamlined automation of primer pair and sample submission and tracking information for MAS to decrease the data turnaround time. This goal will be met by simplifying submission protocols. Additional work will help finish the design of the core rhAmpSeq amplicon sequencing probe set. This goal is being met by identifying core genomic regions where currently designed probes are failing to sequence. Placement of new markers in these gaps will help increase the utility of the core set. Additionally, the team will design new core rhAmpSeq makers in genomic regions where QTL have been identified to help fine map traits. This goal will be met by following the same core methods used to design the larger 2,000 core probe set. The only difference will be to design probes based on the family information for the specific QTL being elucidated. Additional wild, hybrid, and cultivated genomes will be sequenced to help cover the diversity represented in the VitisGen1 and 2 mapping families and to increase the utility of the 2,000 core amplicon probe set. This goal will be met by simply continuing to sequence and analyze genomic data as it becomes available off the sequencers. The genetics team plans to initiate RNA extraction and gene expression analysis from segregating disease resistance families. These families have been identified and a major goal of year 1 was to quality check phenotypes to makes sure only the most rigorous contrasts are initiated. In year 2, the team plans to move past QC and onto bulk segregant transcriptomics. As appropriate families are determined, parental tissue will be collected for isoSeq reference sequencing as well to further increase the probability of identifying the underlying SNPs controlling contrasting phenotypes. Genes in the three genome assemblies will be annotated to serve as a reference for the full sibling transcriptomic analysis that we will conducted in the second year of the project.
Additional future work will include collaborating with USDA-ARS scientist Edward Buckler to adopt the practical haplotype graph (PHG) system, and develop a new genotyping pipeline to process rhAmpSeq data. Migration of the genotyping data processing pipeline to the PHG based system will improve both quality and speed of the MAS analysis pipeline.
Breeding work will continue to generate and analyze combinations of fruit quality traits including plans to quantify the red skin color of all fruiting vines in the red color population growing in Parlier, CA. Additionally, plans are scheduled to collect leaf tissues from the red color population as well as from the new PM resistance source populations for genotyping. Additional work will focus on powdery mildew resistance loci challenged with a range of strains of the pathogen. Plant samples will continue to be supplied to the phenotyping centers, and analyzed locally for additional traits of interest. Plant samples will also be supplied to the genetics team for DNA analyses leading to genetic maps covering all 19 linkage groups. At the Missouri State Fruit Experiment Station (MSFES) efforts will continue to preserve the existing mapping populations of ‘Norton’ x ‘Cabernet Sauvignon’, ‘Chambourci’n x ‘Cabernet Sauvignon’ and Jaeger 70/Munson x Vignoles and further work will continue to construct a ‘Chambourcin’ linkage map with SSR markers using JoinMap 4 software.
The Trait Economics Team’s future plans will involve administering surveys to market intermediaries and consumers to evaluate preferences with respect to varietal traits and breeding methods used on wine and table grapes. Additional plans include completing the analysis of returns to prior varietal improvements in table grapes.
The Extension and Outreach Team’s future plans and goals include: continuing highlighting scientific advances from VitisGen2 through trade articles, webinars, and the VitisGen2 website. Specific topics will include economics of powdery mildew resistant varieties; challenges of durable genetic disease resistance; focus on table grape breeding and use of embryo rescue for seedless varieties; how the MN breeding program created a new cold-hardy grape industry; and DNA markers for fruit quality. Collaborative efforts will be made with the Breeding and Genetics Teams to contribute to the development of extension and outreach efforts. Specifically, writing content to discuss the application of technologies to a breeding program; the history of the cold-climate wine industry in the Midwest; how plant breeding for resistance does not necessarily mean “no spray”grape varieties; and a focus on developing and harmonizing the traits evaluated in the grape community. Additional work will include networking with colleagues in curation of ontologies for grape genomics, and applying it to the VitisGen2 community.
- Sapkota, S.,Chen, L., Yang, S., Hyma, K., Cadle-Davidson, L., Hwang, C-F. 2018. Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived ‘Norton’. Theoretical and Applied Genetics. doi: 10.1007/s00122-018-3203-6
- Burzynski-Chang EA, Ryona I, Reisch BI, Gonda I, Foolad M, Giovannoni JJ and Sacks GL (2018). HS-SPME-GC-MS Analyses of Volatiles in Plant Populations – Quantitating Compound × Individual Matrix Effects. Molecules. 23(10), 2436. https://www.mdpi.com/1420-3049/23/10/2436
- Divilov, K.D., P. Barba, L. Cadle-Davidson, and B.I. Reisch. 2018. Single and multiple phenotype QTL analyses of grapevine downy mildew resistance in interspecific grapevines. Appl. Genet. 131(5):1133-1143. DOI: 10.1007/s00122-018-3065-y
- Barba, P., J. Lillis, R.S. Luce, R. Travadon, M. Osier, K. Baumgartner, W.F. Wilcox, B.I. Reisch, and L. Cadle-Davidson. 2018. Two dominant loci determine resistance to phomopsis cane lesions in F1 families of hybrid grapevines. Theor. Appl. Genet. 131(5):1173-1189. DOI: 10.1007/s00122-018-3070-1
- Cadle-Davidson, L. A perspective on breeding and implementing durable powdery mildew resistance. Acta Hort (In press)
- Clark, M., Teh, S. L., Burkness, E., Moreira, L., Luby, J., Watson, Yin, L., G., Hutchison, W. 2018. QTL Identified For Foliar Phylloxera Resistance in A Hybrid Grape Population. Australian Journal of Grape and Wine Research 24(3): 292-300
- Divilov, K.D., T. Wiesner-Hanks, P. Barba, L. Cadle-Davidson, and B.I. Reisch. 2017. Computer vision for high-throughput quantitative phenotyping: A case study of grapevine downy mildew sporulation and leaf trichomes. Phytopathology 107: 1549-1555. DOI: 10.1094/PHYTO-04-17-0137-R
- Fresnedo-Ramírez, J., S. Yang, Q. Sun, L.M. Cote, P.A. Schweitzer, B.I. Reisch, C.A. Ledbetter, J.J. Luby, M.D. Clark, J.P. Londo, D.M. Gadoury, P. Kozma, and L. Cadle-Davidson. 2017. An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci. Molec. Breeding 37:145 doi: 10.1007/s11032-017-0739-0
- Fresnedo-Ramírez, J.,Yang, S., Sun, Q., Karn, A., Reisch, B., Cadle-Davidson, L. Computational analysis of AmpSeq data for targeted, high-throughput genotyping of amplicons. Frontiers in Plant Science. (Submitted July 5, 2018).
- Martinson, T. and B. Reisch (2018). Is Europe Starting to Embrace Hybrid Wine Grapes? Wines and Vines, August 2018. 78-80. Online at: https://www.winesandvines.com/news/article/201942/Will-Europe-Embrace-Hybrid-Wine-Grapes
- Martinson, T. (2018). Grape breeders No Longer Flying Blind. Wines and Vines, March, 2018. 64-65. Online at: https://www.winesandvines.com/features/article/196083/Grape-Breeders-No-Longer-Flying-Blind
- Martinson, T. (2017). The Frozen Genetics of International Wine Cultivars. Wines and Vines, December, 2017. 28-29. Online at: https://www.winesandvines.com/columns/section/26/article/192690/The-Frozen-Genetics-of-International-Wine-Cultivars
- Londo, JP., Gutierrez, B., Martinez, D., Sapkota, S., Cadle-Davidson, L. (Submitted 2018). From phenotyping to phenomics: Present and future approaches in grape trait analysis to inform grape gene function. The Grape Genome
- Alston, J.M., Sambucci, O. (2019) Grapes in the World Economy. Chapter for Dario Cantu and Andrew M. Walker, eds., The Grape Genome
- Alston, J.M., Lapsley, J.T., Sambucci, O. (2018) “Grape and Wine Production in California.” In Goodhue, R., Martin, P. and Wright, B., eds, California Agriculture: Dimensions and Issues). Giannini Foundation of Agricultural Economics, Berkeley, CA. Available at: https://s.giannini.ucop.edu/uploads/giannini_public/a1/1e/a11eb90f-af2a-4deb-ae58-9af60ce6aa40/grape_and_wine_production.pdf
- Sapkota,S. (2018) Ph.D. dissertation “High Density Mapping and Quantitative Trait Loci Analysis for Fungal Diseases in Vitis aestivalis-Derived ‘Norton’”. Missouri State University, Springfield, MO.
- Carl Knuckles (2018). MS dissertation “The Identification of Intraspecific Hybrids Between Jaeger 70 x Vignoles Grapes Using SSR Markers”. Missouri State University, Springfield, MO.
- Adams,D . (2017) MS dissertation “Genetic Analysis of Cold Hardiness in a Population of Norton (Vitis aestivalis) and Cabernet Sauvignon (Vitis vinifera) Hybrids”. Missouri State University, Springfield, MO.
- Divilov, K. (2017). D. Dissertation. “Phenotypic and genetic studies of grapevine.”, Cornell University, Ithaca, NY, USA
The extension team produced two VitisGen2 videos in collaboration with the Breeding and Genetics Teams highlighting different aspects of the VitisGens project to educate the public and researchers.
- Reisch, B. and T. Martinson (2018) Europe is Starting to Embrace New, Disease Resistant Varieties. VitisGen2 Webinar, live broadcast March 13, 2018. Audience: 70 online participants, Recorded and posted at: https://www.youtube.com/watch?v=z1RjMSq2LkU&list=PLBTN_VCK49BmEaDcU82daoZEQ4eyfC61F&index=2. The target audience was grape scientists and grape industry members who are potential producers and users of New, Disease Resistant Varieties.
- Cadle-Davidson, L., R. Naegele and A. Underhill (2018). Automated Evaluation of Grape Breeding Progeny to Reduce the Phenotyping Bottleneck VitisGen2 Webinar, live broadcast April 19, 2018. Audience: 55 online participants. Posted at: https://www.youtube.com/watch?v=C_w5wEBEz5Q . The target audience was scientists and industry members interested in computer vision-based laboratory evaluation of traits.
- The Trait Economics team assembled a detailed database on the production of major table grape varieties using USDA acreage reports, and are currently in the process of collecting and adding pricing information. The target audience was grape scientists and industry members interested in the economics of grape production.
- The existing Vitisgen database was updated in 2018 by the Genetics Team in order to manage AmpSeq and rhAmpSeq database. The new database will manage the primer sets used in each genotyping experiment, and two software tools were developed to access the database and produce data files to run the genotyping and map construction pipeline. The target audience was project participants involved in genetic analyses or application of genetic results.
- The Genetics Team created custom perl scripts used for amplicon analysis. The script was updated in 2018 for processing rhAmpSeq data, including bug fixing and parallelization. A new script to_lep_map.pl was developed to create file formats that can be used for genetic mapping tool LepMap3. The software can be accessed through github. https://github.com/qisun2/analyze_amplicon. The target audience was scientists interested in cutting-edge genotyping technologies.
- A web based database system http://Vitisbase.org was setup in collaboration with Dr. Lukas Mueller at Boyce Thompson Institute. The system is used to manage germplasm accessions, field trial, genotyping and phenotyping data. The target audience was all scientists who generate data on grapevine.
- The Powdery Mildew team successfully developed and implemented the use of a robotic PM imaging system (PMbot v3) that mproved efficiency of processing 2,000 samples per day with 94% accuracy in quantifying PM growth. They also use of a new robotic leaf sampling arm
- The Genetics team developed two software tools to access databases and produce data files to run the genotyping and map construction pipeline and process AmpSeq and rhAmpSeq data.
- The FQ Team has drafted new workflows and protocols to develop new high-throughput phenotyping platforms for multi-trait analysis and introduce new phenotyping content such as ionomics and be able to detect tannins, juice proteins, pH, volatiles, tannins, malic and tartaric acid, titratable acidity and metal compounds.
- Clark, M. PP 29847 Itasca Grapevine 11/20/2018. The target audience was grape industry members interested in cold-hardy, disease resistant winegrapes with excellent quality.
- The Trait Economics team developed the first round of draft surveys to administer to producers of table grapes and market intermediaries to evaluate their attitudes towards improved varieties. The target audience was grape scientists and industry members interested in the economics of grape production.
- The Trait Economics Team began work on a model that can be used to evaluate economic returns from varietal improvements in table grapes using historical data on production and prices of table grape varieties. The target audience was grape scientists and industry members interested in the economics of grape production.
- Seminars with PowerPoint presentations and demonstrative plant materials were routinely provided to interested parties at ARS-Parlier to highlight the long-term breeding efforts at this location. During the past year, laboratory tours and presentations on grape breeding efforts have been provided to:
- FARMS Leadership program consisting of 12 high school juniors interested in agriculture, Feb. 12, 2018
- Sunnyside high school Ag program students,- 26 high school juniors, Feb. 28, 2018
- Eight Cochran fellows from Bosnia were hosted on June 19, 2018
- ~ 6 interns from the RJ Gallo Winery working with the NSF Vitis rootstock project, July 27, 2018
- Chilean table grape growers (12) on an educational tour in their offseason, July 31, 2018
- Gavin Sacks provided training of two undergraduate students in chemical trait evaluation on grape accessions at the FQ/Wine Center (June to August 2018), and provided training for three undergraduate students at FQ/Table Grape Center in trait evaluation, data collection, and breeding (September 2017 to August 2018).
- Chin-Feng Gwang provided training of two undergraduate students (summer interns; Rayann Bailey and Bryce Bentley) in breeding and trait evaluation of grapevine in June and July 2018.
- Lance Cadle-Davidson provided training on powdery mildew biology and disease resistance assessment for 1 high school student, 4 graduate students, 2 postdoctoral scientists, 6 technicians, and 5 faculty-level scientists.
- Martinson, T. and R. Kallas (2018) VitisGen2 website. http://www.Vitisgen2.org/
- Lance E. Cadle-Davidson. VitisGen2 Approaches to Powdery Mildew Resistance. USDA-ARS Grape Industry Workshop. Portland, OR. November 18, 2017. The target audience was scientists and grape industry members interested in breeding for disease resistance and cutting-edge genotyping technologies.
- Lance E. Cadle-Davidson, Jonathan Fresnedo Ramirez, Avinash Karn. WORKSHOP: Hands-On Analysis of Amplicon Sequence (AmpSeq) Data for Targeted Multiplexed Genotyping presented at International Congress of Plant Pathology. July 29, 2018. The target audience was scientists interested in cutting-edge genotyping technologies.
- Reisch, B.I. and L. Cadle-Davidson. 2018. Perspectives from the VitisGen projects. SCRI Project Directors Workshop. 30 July 2018. Washington, D.C. (presentation) The target audience was the USDA funding agency.
- Hwang, C-F. (2017). Expanding Research on Berry and Juice Chromatographic Analysis to Expedite Grape Cultivar Improvement and Build Education Capacity, 2017 USDA-NLGCA Project Directors’ Meeting, Morro Bay, California, October 3, 2017. The target audience was the USDA funding agency.
- Burzynski, EA. and Sacks, GL. (2017) Sour notes on the finish: malic acid behavior during ripening of wild Vitis Cornell Recent Advances in Viticulture and Enology (CRAVE) Meeting, Nov. 14, 2017, Ithaca, NY
- Reisch, B.I. and L. Cadle-Davidson. (2017). Grapevine breeding for resistance in the era of cheap sequencing technology. Section of Plant Pathology and Plant-Microbe Biology, December 12, 2017. Geneva, NY, USA. (seminar) The target audience was scientists interested in breeding for disease resistance and cutting-edge genotyping technologies.
- Burzynski, E.A., B.I. Reisch, I. Gonda, M.R. Foolad, J.J. Giovannoni and G.L. Sacks. (2018). Internal standards roulette: Best practices for HS-SPME-GC-MS volatile analyses in plant populations. International Plant and Animal Genome Conference XXVI. January 13-17, 2018. San Diego, California
- Underhill, A., C. Hirsch, and M. Clark. (2018). Image-based phenotyping and genetic control of cluster density traits in interspecies grapevine hybrids. Plant & Animal Genome XXVI, San Diego, CA. Jan. 13-17, 2018. Poster.
- Reisch, B.I. 2018. VitisGen2: Application of next generation technologies to accelerate grapevine cultivar development. Board Meeting of the National Grape and Wine Initiative. January 25, 2018. Sacramento, CA, USA. (presentation) The target audience was grape industry members.
- Cadle-Davidson, L. (2018). Design and Analysis of Amplicon Sequencing (AmpSeq) for Targeted Multiplexed Genotyping. Gulf Coast Research Center, Wimauma, FL. January 31, 2018. Invited speaker. The target audience was scientists interested in cutting-edge genotyping technologies.
- Sacks, GL. (2018) “Know your wine chem basics (and acidics)” BEV-NY 2018 Conference. March 1, 2018. Rochester, NY.
- Cadle-Davidson, L. (2018). Tools and strategies for breeding new grape varieties with durable powdery mildew resistance. ICVV, Longrono, Spain. April 2018. Invited keynote speaker. The target audience was grape scientists interested in breeding or management of new disease resistant varieties.
- Zou, C. (2018). Building pan-genome to assist marker development in the breeding practice. Plant Pathology Department Seminar at Cornell University, Geneva, NY, May 1, 2018. The target audience was scientists interested in cutting-edge genotyping technologies.
- Hwang, C-F. (2018). Optimization of Chambourcin Grape Breeding Using Molecular Genetic Approaches, Missouri Grape and Wine Research Board Meeting, Columbia, Missouri, May 9, 2018. The target audience was grape industry members. Oral Presentation
- Burzynski, EA Sacks, GL. (2018) “Acids in Wine” Rochester Area Home Wine Committee. June 16, 2018. Rochester, NY.
- Burzynski EA, Brown EJ, and Sacks GL. (2018). Sour grapes indeed! Malic acid increases in certain Vitis spp. during maturation. 69th Annual Conference of the American Society for Enology and Viticulture, June 18-24, 2018, Monterey, CA.
- Yin, L. (2018) Characterization of leaf trichome for its potential role in resistance to foliar phylloxera in a cold-hardy hybrid grape population (e-poster & Student Ignite Competition). American Society of Horticultural Science.
- Underhill, A., A. Diering, D. Tork, D. Freund, A. Hegeman, S. L. Teh, and M. Clark. (2018). Multiple phenotyping methods find QTL for berry color in an interspecific hybrid grape (Vitis) population. Taming High pH in the East. American Society for Enology and Viticulture-Eastern Section 43rd Annual Conference, King of Prussia, PA. July 9-11, 2018. Paper Presented
- Fennell, A., Alahakoon, D., Awale, M., Luby, J., Clark, M. (2018). Mapping the genetic architecture of grapevine bud dormancy and chilling fulfillment traits XII International Conference on Grapevine Breeding and Genetics. July 15-20, 2018. Bordeaux, France. Oral Presentation
- Hwang, C-F. (2018). QTL mapping of downy mildew and botrytis bunch rot resistance in a Vitis aestivalis-derived ‘Norton’-based population”, XII International Conference on Grapevine Breeding and Genetics, Bordeaux, France, July 18, 2018.
- Cantu, D., Minio, A., Zhou, Y., Vondras, A., Gaut, B., Delledonne, M., Cramer, G., Massonnet, M., Figueroa-Balderas, R. (2018). Uncovering the wealth of grapevine genetic diversity through whole genome sequencing and assembly. XII International Conference on Grapevine Breeding and Genetics, July, 15-20, 2018, Bordeaux, France. Invited keynote speaker
- Cadle-Davidson, L. (2018). A perspective on breeding and implementing durable powdery mildew resistance. XII International Conference on Grapevine Breeding and Genetics, Bordeaux, France. July 15-20, 2018. Invited keynote speaker
- Fresnedo-Ramírez, J., S. Yang, Q. Sun, J. Londo, M. Clark, B. Reisch, and L. Cadle-Davidson. (2018). AmpSeq as a tool for genetics and breeding of grapevine. XII International Conference on Grapevine Breeding and Genetics. July 15-20, 2018. Bordeaux, France.
- Reisch, B. (2018). Genetic resources and breeding: current status and shifting paradigms. XII International Conference on Grapevine Breeding and Genetics, Bordeaux, France, July 15-20, 2018. Invited keynote speaker
- Kisselstein, B., Cadle-Davidson, L., Gadoury, M (2018). Investigation of Erysiphe necator Population Structure using Amplicon Sequencing (AmpSeq) without Clonal Isolation. International Congress of Plant Pathology. July 30, 2018. Poster. The target audience was scientists interested in cutting-edge genotyping technologies, powdery mildew, or population genetics.
- Cadle-Davidson, L. (2018). Genetic tools for the study of light and circadian processes in microbial plant pathogens. International Congress of Plant Pathology. August 1, 2018. Oral Presentation. The target audience was scientists interested in cutting-edge genotyping technologies.
- Sun, Q. (2018). Towards more complex crops: marker technologies and bioinformatics in grape. Presented at GOBII Annual Meeting at International Rice Research Institute, Philippines, Aug 14-16, 2018. Seminar. The target audience was scientists interested in cutting-edge genotyping technologies. Seminar