Item No. 1 of 1

INVESTIGATOR: Clark, M.

PERFORMING INSTITUTION:
UNIV OF MINNESOTA
ST PAUL, MINNESOTA 55108

COMPLETING THE GRAPEVINE POWDERY MILDEW RESISTANCE PIPELINE: FROM GENES-ON-THE-SHELF TO STICKS-IN-THE-GROUND

NON-TECHNICAL SUMMARY: An unprecedented era of disease resistant grape cultivars is coming, bringing sustainability via reduced pesticide and fossil fuel use. Remarkable advances from VitisGen projects yielded more sources of resistance in 5 years than were discovered worldwide in the previous 50, and tools we developed will only accelerate this process. We now must learn how to best deploy the genetic resources. This project aims to advance grape breeding and sustainable grape production practices using cutting-edge technologies, completing the resistance pipeline from genes to vineyards to consumers. Objective 1 applies haplotype-resolved genomic resources to identify and test candidate genes - the final and often overlooked step in molecular breeding. Advanced gene editing and sequencing will perfect marker-assisted selection and improve clones. Objective 2 delivers advanced computer vision phenotyping, artificial intelligence, and DNA markers to all U.S. grape breeders. Objective 3 helps breeders discover important traits as they generate resistant cultivars and protects these investments by developing strategic and epidemiologically based management programs that are effective and sustainable. At the same time, we will train vineyard managers and Extension personnel across the US in their use, with the twin goals of maintaining plant health and preserving genetic resistance. Objective 4 will apply human-centered engineering and eye-tracking technologies to obviate information overloading while effectively engaging consumers to encourage the purchase of sustainably produced grape and wine products.

OBJECTIVES: Objective 1 applies haplotype-resolved genomic resources to identify and test candidate genes - the final and often overlooked step in molecular breeding. Advanced gene editing and sequencing will perfect marker-assisted selection and improve clones. Objective 2 delivers advanced computer vision phenotyping, artificial intelligence, and DNA markers to all U.S. grape breeders. Objective 3 helps breeders discover important traits as they generate resistant cultivars and protects these investments by developing strategic and epidemiologically based management programs that are effective and sustainable. At the same time, we will train vineyard managers and Extension personnel across the US in their use, with the twin goals of maintaining plant health and preserving genetic resistance. Objective 4 will apply human-centered engineering and eye-tracking technologies to obviate information overloading while effectively engaging consumers to encourage the purchase of sustainably produced grape and wine products.

APPROACH: OBJECTIVE 1:1a. Identify candidate PM resistance-associated genes: PM resistance loci will be reconstructed following the pipeline established in VitisGen2 (Massonnet et al. 2022). For each resistance locus, genomic sequences composing the locus will be identified within the genome assembly of the source of resistance by aligning resistance locus-associated rhAmpSeq local haplotype markers. Narrow down the genomic region associated with PM resistance and distinguish the two haplotypes of the PM resistance locus. In addition, RNA seqfrom mock- and PM-inoculated leaves of the siblings willrefine the gene models and assess the transcript abundance of the genes comprised in the two haplotypes of each PM resistance locus.1b. Identify candidate PM defense response-related genes and susceptibility factors: For each assembled grape genome, protein-coding genes with a putative function in host defense response and disease susceptibility will be identified based on protein homology with Arabidopsis thaliana and protein domain composition. RNA-seq datafrom inoculated leaves of PM-resistant and PM-susceptible breeding lines will be aligned on the combined transcriptomes of the Vitis species constituting the genetic background of the sibling vines. Transcriptomes of PM- and mock-inoculated leaves will be compared to identify defense-related genes with a constitutive expression or a transcriptional modulation that correlates with PM resistance or susceptibility.1c. Test the role of the candidate genes: Here we aim to assess the role of candidate PM resistance-associated and defense-related genes by introducing them in PM-susceptible V. vinifera plants and knocking them out in their corresponding PM-resistant wild grape species or introgression lines. Independent transgenic plants from all locations will be inoculated with E. necator locally in the greenhouse or controlled inoculations to validate genes involved in PM resistance and susceptibility.For each gene with a proven role in PM resistance or susceptibility, perfectly linked markers will be designed and tested on relevant grape accessions and/or populations theOBJECTIVE 2 :2a. Vineyard computer vision. Here, we aim to work directly with breeders to field-phenotype using effective computer vision tools. The outreach team will develop training materials in coordination with all parties to ensure that breeders and technical staff across sites are aware of proper installation and implementation of the necessary equipment. Vines will be imaged biweekly during the growing season, and weekly once susceptible checkshave more than 25% disease severity. Powdery mildew quantification will be refined and additional trait models built with expert annotation from participating breeders, pathologists, and graduate students. To improve PM detection below 5% severity, the spectral characteristics of PM hyphae and conidia will be considered.2b. Lab computer vision optimization to assess disease severity.Breeders sample leaves during the early growing season before vineyard PM confounds results. Leaf discs are surface sterilized, replicate leaf disks sampled, arrayed, and inoculated with pure isolates. Samples are imaged and disease severity estimated via convolutional neural networks and/or saliency mapping (Bierman et al. 2019; Qiu et al. 2021), by quantifying hyphae or conidia. Data are analyzed.2c. Molecular breeding support. Building on the logistics and analysis pipeline established in VitisGen2, we will: (1) Continue genetic map construction for new mapping families and translation of trait-associated markers and candidate genes into rhAmpSeq marker panels (Karn et al. 2021; Zou et al. 2020) for cross-family validation (2) Breeders will continue to make crosses consistent with local program goals, and incorporate marker technologies, especially in relation to disease resistance and fruit quality.Objective 3:3a.i) Field Studies: Here, we aim to a) demonstrate that a spray program driven by epidemiology will eliminate disease with only 1-2 sprays per year, and b) test over seasons the added benefit of stacked resistance genes in the context of a fungicide trial. Both studies will be in a vineyard with a 12-year history of virulence and overwintering on RUN1; there is likely no other such vineyard in the world (Cadle-Davidson et al. 2011). Goal 1 is to confirm our hypothesis that a limited spray program (not "no-spray") is sufficient for eliminating disease seasonally.Goal 2 will evaluate five spray programs year-over-year across seven varieties with different levels of resistance.3a.ii) Hyperspectral (HS) imaging: Here, we will obtain HS signatures indicative of infected vines having or lacking different resistance alleles, to 1) inform early detection in vineyards (signatures shared by all infected genotypes), 2) test whether HS signatures can be used for breeding selection of resistant vines (signatures specific to resistance alleles, as in Gold et al 2019), and 3) in coordination with previously obtained RNASeq data (Obj 1a), test whether HS signature can infer resistance mechanism and complementarity.3b: Grape breeding Support QTL mapping leading to gene discovery and MAS to enrich breeding pipelines with favorable alleles. We anticipate breeding teams to train graduate students as the main on-the-ground expert to implement and deploy CV for field characterization of PM resistance at each location. Coordination of sampling will be based on phenology so that CV devices can be moved during the growing season as growth and pathogen populations develop.?3c: Extension methods Deployment of new, PM resistant cultivars requires communication and training with our stakeholders to enhance adoption and promote long-term sustainability of deployed genes. Each project objective is suited for engagement with industry stakeholders and clear scientific communication for consumer or public audiences. Develop innovative approaches to promote the adoption of disease resistant grapevines in the US. We will distribute project materials. Outreach products include field days, webinars, or workshops as well as updates and results through communications to stakeholders through existing channels at each institution. Develop a calendar of the extension and outreach activities at quarterly team meetings.Objective 4:?4.a. Investigate consumer preferences for wine from disease-resistant cultivars in the context of information overloading. Following Lee and Lee (2004), we will design an experiment by combining both the traditional and structural approaches to the information overloading phenomenon by varying the number of wine alternatives and the number of wine attributes in a choice set, and/or the distribution of attribute levels across alternatives (the distribution is a function of the attribute levels and the probabilities these levels take place in a choice set). Participants will also be asked questions about their satisfaction, confidence, and confusion during wine shopping.4.b. Use eye-tracking technology to identify what information consumers pay most attention to. We will design different wine/raisin/table grape labels/advertisements that include various attribute designs and locations and track consumers' eyes while they are viewing the labels/advertisements. The attributes would include geographical region, vinifera denomination, disease-resistant grape variety, sweetness, vintage, price, etc. We will use a between-subject design where half of the participants are shown one version of the stimulus (label and/or advertisement) and the second half will be shown a modified version of the stimulus.A qualitative study (semi-constructed interviews) will be conducted immediately following the eye tracking study on about 20 of the MN participants to gain a deeper understanding of the participants' opinions regarding growing region, vinifera denomination, disease-resistant grape variety, sweetness, vintage, price, etc.

PROGRESS: 2022/09 TO 2023/08
Target Audience:Grape and muscadine breeders, geneticists, and pathologists; New York state legislatures including state senators and assembly members; Technology industries focusing on robotics and AI; Table grape and wine industry professionals; Grape and wine producers; Undergraduate and graduate students; Table grape, wine, and raisin consumers as well as the general public. Changes/Problems:Objective 1: NA Objective 2: Backordered parts have slightly delayed the timeline for shipping computer vision imaging equipment to participating sites. Equipment will be delivered and personnel trained in mid-July 2023. UMN was unable to hire a graduate student for this objective during this academic year, but will begin recruiting again during fall 2023 for the 2024 season. Objective 3a, & b (field trial & breeding): Three new co-Pis will be added to the project as of the 2024 reporting season, including Drs. Luis Diaz-Garcia (UCDavis), Soon Li Teh (UMN), and Sarah Lowder (University of Georgia). Due to the retirement of Dr. Bruce Reisch (Cornell) and the redefined role of Dr. Matthew Clark (University of Minnesota), new faculty have been hired for two of our major grape breeding programs. These hires at Cornell and UMN are, respectively, Dr. Madeline Oravec and Dr. Soon Li Teh. Dr. Clark will continue to serve as Project Director. Objective 4: We originally proposed to use only eye-tracking equipment to track people's eyes when they view the product labels, which will provide very useful information for label designing. But there is a lack of understanding about people's brain activities when experiencing the visual stimuli of product labels. To address this gap in knowledge, we will also scan participants' brains while they are viewing the labels using EEG equipment. The combination of eye-tracking and EEG technologies will help us get a deeper and more comprehensive understanding about people's behavior and provide marketing implications for the industry. What opportunities for training and professional development has the project provided?Objective 1: Manon Paineau, postdoc in the Cantu lab, has developed computational skills and has learned to perform pseudomolecule reconstruction of grape genomes. Dustin Guy Wilkerson, a new postdoc, joined the project VG3. He has learned genomic skills to narrow down candidate genes in the resistance loci. Objective 2: Eight international faculty and graduate students have visited VitisGen activities in Geneva, NY to be trained on Blackbird or rhAmpSeq technologies. The Jiang lab recruited two PhD students who are supported by this grant and will join the team Fall 2023 to develop and improve the proposed imaging robots and AI-based analysis algorithms for the phenotyping objective in this project. The Jiang and Cadle-Davidson groups have hired two summer undergraduate scholars in Summer 2023 for operating robots for field data acquisition and improving AI analytical pipeline for lab phenotyping. The Gold and Cadle-Davidson labs hired four summer undergraduate scholars in Summer 2023 to execute Blackbird microscopy robot experiments and learn computer vision approaches. Objective 3a (field trial): The installation of the vineyard has provided professional development for many of the technical staff, students and academics at Agritech, being involved in the physical placing of vines in the ground, irrigation installation and scouting for vine development. Included in these activities are: David Combs, Dr. Rocio Calderon, Dr. Saeed Hosseinzadeh, Kathleen Kanaley, Jaclyn Eller, Fernando Galvan, Angela Paul, Nicole D'Aurizio, Liam Crawley. Objective 3b (breeding): Dr. Luis Diaz-Garcia, at UCDavis, is mentoring 2 undergraduate students who are focusing on plant propagation and leaf sampling for rhAmpSeq genotyping, and 2 PhD students are being partially funded by VitisGen3. At UMN, PM Fessler has attended several conferences (PAG 2023, GiESCO 2023), developed skills in web design and development, and become rapidly familiarized with grape breeding and enology research. Two fruit breeding graduate students are being trained in vineyard management and are part of the discussion on vineyard design for the use of image acquisition at the Horticultural Research Center. In Arkansas, an undergraduate student has been training with Dr. Margaret Worthington, and will be transitioning to an MS program in the fall. An MS student and 2 undergraduate students are being trained by Dr. Anne Fennell at South Dakota State University. At Cornell AgriTech and USDA-ARS-Geneva, NY, a new PhD student (Aliyah Brewer) was recruited to focus on grapevine resistance breeding and genome-wide marker analyses. She is working this summer in ARS-Kearneysville, WV to help establish the new grape breeding program and learn about resistance sources and markers in that USDA breeding program. Objective 4: Two PhD students, Uma Parasuram (UMN, advisor: Dr. Chengyan Yue) and Qingwei Qiao (Washington State University, advisor: Dr. Karina Gallardo) have comprehensive training including conducting literature reviews, developing surveys, presenting their projects, designing experiments, and collaborating in a large team context. Undergraduate graphic design student, Nicholas Parkhill (supervisor: Dr. Garrett Steede) has developed the project logo, branded letterheads, promotional materials, and slide decks. He will also design visual stimuli for this fall's experiments. How have the results been disseminated to communities of interest?Project information has been disseminated to the general public and to any interested stakeholders via many channels. Popular press outlets include: SevenFiftyDaily (https://daily.sevenfifty.com/could-gene-editing-create-more-disease-resistant- grape-varieties/); CBC News (https://www.cbc.ca/news/canada/windsor/wine-future-hybrids-crispr-1.6766089); InsideHook (https://www.insidehook.com/article/booze/hybrid-grapes-wine-future); Wine Business Monthly (https://www.winebusiness.com/news/article/268948); Agri-Pulse (https://www.agri-pulse.com/articles/19534-scientist-new-epa-regulations-will-h inder-specialty-crop-breeding); and The Fence Post (https://www.thefencepost.com/news/senate-ag-subcommittee-holds-hearing-on-hort iculture/). These have been further promoted on VG3 digital platforms, including: Instagram (98 followers, 2719+ unique interactions); Twitter (1305 followers, 3269+ unique interactions); the website and blog (vitisgen3.umn.edu, 640 users and 8300+ events); and internal newsletter (69 subscribers). This amounts to over 6694 individuals reached via our digital platforms alone, who comprise more than half of our original proposed goal of reaching 12,000 individuals. Stakeholders: The general public, crop breeders, pathologists, geneticists, industry professionals, and grape and wine producers. Objective 1: NA Objective 2: Since Summer 2023, the Jiang lab has offered 6 tours to disseminate VG3 project vision as well as robots and AI tools developed from this project. Stakeholders: students from 4H programs, growers, researchers across the US, and New York state legislatures. Popular press articles: Autonomous Robots to Help Modernize Grape, Wine Industry. 2022. Tech Briefs by Sarah Thompson. https://www.techbriefs.com/component/content/article/tb/insiders/ra/stories/477 35 Seeing the light: innovation in powdery mildew treatment. 2022. Australian and New Zealand Grapegrower and Winemaker by Simone Madden-Grey. https://winetitles.com.au/gwm/articles/june-701/seeing-the-light-innovation-in- powdery-mildew-treatment/ In the Quest for a Healthier Grape, AI Uncorks a Defense. 2022. Vision Spectra by Jake Saltzman. https://www.photonics.com/Articles/In the Quest for a Healthier Grape AI Uncork s a/p21/vo212/i1366/a67730 Objective 3a (field trial): Gold, K. 2023. Plant Disease Sensing: Studying Plant-Pathogen Interactions at Scale. Kansas State University, Department of Plant Pathology, May 5, 2023. Stakeholders: Geneticists, pathologists, and plant scientists. Gold, K. 2023. Plant Disease Sensing: Studying Plant-Pathogen Interactions at Scale. University of Wisconsin-Madison, Department of Plant Pathology, April 19, 2023. Stakeholders: Geneticists, pathologists, and plant scientists. K.M. Gold, D.B. Combs. 2023. Grape disease control when chemical options are limited. E&J Gallo Spring Grape Grower Event. Geneva, NY. May 2, 2023. Stakeholders: Wine industry professionals and wine grape producers. K.M. Gold, D.B. Combs. 2023. Biopesticides for Grape Disease Control. BEV-NY 2023. Syracuse, NY, March 29, 2023. Stakeholders: Wine industry professionals and wine grape producers. Objective 3b (breeding): Clark, MD. 2023. UMN Research Updates. Minnesota Grape Growers Association Annual meeting. Chaska, MN. February 24th, 2023. Stakeholders: 100+ wine and grape producers. Clark, MD, Cadle-Davidson, L, Cantu, D, Gold, K, and Yue, C. 2023. VitisGen3: Advancing Powdery Mildew Resistance in Grape. Plant and Animal Genome Conference. San Diego, CA. January 15, 2023. Stakeholders: 50+ academic peers including crop breeders, geneticists, and pathologists. Diaz-Garcia, L. 2023. California Grape Rootstock Improvement Commission program visit. Davis, CA. June 21st, 2023. Stakeholders: Industry professionals. Duwadi, A., Chen, L., and Hwang, C. Genetic Study of Botrytis Bunch Rot Resistance in a Vitis aestivalis-derived 'Norton'-based Population. 2023. Show Me Grape and Wine Symposium. Columbia, MO. March 1, 2023. Oral Presentation. Stakeholders: Crop breeders, geneticists, and pathologists. Duwadi, A., Chen, L., and Hwang, C. 2023. Genetic Study of Postharvest Berry Rot Resistance in a Vitis aestivalis-derived 'Norton'-based Population, Annual Frank Einhellig Graduate Interdisciplinary Virtual Forum. Springfield, MO. April 29, 2023. Poster Presentation. Stakeholders: Crop breeders, geneticists, and pathologists. Duwadi, A., Chen, L., and Hwang, C. 2023. Genetic Study of Postharvest Berry Rot Resistance in a Vitis aestivalis-derived 'Norton'-based Population. 47th American Society for Enology and Viticulture-Eastern Section (ASEV-ES). Austin, TX. June 7th, 2023. Poster Presentation. Stakeholders: Grape and wine industry professionals, crop breeders, geneticists, and pathologists. Fennell, A. 2023. Publications (see #2). Stakeholders: Academic peers including crop breeders, geneticists, pathologists, and grape and wine producers. Hatterman-Valenti, H. 2023. North Dakota State University Field Days. Upcoming: July 25th, 2023 and September 9th, 2023. Stakeholders: Wine and table grape producers. Shahid, T., Chen, L., and Hwang, C. 2023. Cold Hardiness in Chambourcin-based Hybrids. Show Me Grape and Wine Symposium. Columbia, MO. March 1, 2023. Oral Presentation. Stakeholders: Crop breeders, geneticists, and pathologists. Shahid, T., Chen, L., and Hwang, C. 2023. Cold Hardiness in 'Chambourcin' X 'Cabernet Sauvignon' Grapevine Population. Annual Frank Einhellig Graduate Interdisciplinary Virtual Forum. Springfield, MO. April 29, 2023. Poster Presentation. Stakeholders: Crop breeders, geneticists, and pathologists. Shahid, T., Chen, L., and Hwang, C. 2023. Cold Hardiness in 'Chambourcin' X 'Cabernet Sauvignon' Hybrids. 47th American Society for Enology and Viticulture-Eastern Section (ASEV-ES). Austin, TX. June 7th, 2023. Oral Presentation. Stakeholders: Grape and wine industry professionals, crop breeders, geneticists, and pathologists. Schneider, J., Chen, L., and Hwang, C. 2023. Marker Discovery for Adventitious Rooting Ability in Dormant Hardwood Cuttings of Grapevine. Show Me Grape and Wine Symposium. Columbia, MO. March 1, 2023. Oral Presentation. Stakeholders: Crop breeders, geneticists, and pathologists. Objective 4: NA What do you plan to do during the next reporting period to accomplish the goals??Objective 1: During the upcoming reporting period, we plan to finish the chromosome-scaled assembly of the Ren1+ and Ren1- Vitis vinifera ssp. vinifera and Vitis vinifera ssp. sylvestris. RNA-seq data will be used to identify candidate genes in the Ren4U and Ren11 loci. The skim-seq, phenotyping replication, and transcriptome analysis will be conducted for Ren13. Transgenic plants expressing the candidate genes of Run1.2b (4 genes), Run2.2 (1 gene), Ren6 (4 genes), and Ren7 (2 genes) will be produced by the UC Davis Plant Transformation Facility (David Tricoli). We will also aim to initiate stable knock-out of the candidate genes identified for Ren4U, Ren11, and Ren12. Objective 2: Our genotyping focus will be on identifying candidate genes (eg Ren1, Ren4U, Ren4D, Ren11, Ren12, Ren13, RPV27) for testing in objective 1, providing rhAmpSeq data for genetic analysis and accelerated trait introgression, and providing low cost DNA markers with fast turnaround time. Our computer vision focus will continue execution of 8 precisely controlled laboratory experiments per year on Blackbird microscopy robot, and implementation of computer vision imaging and analysis in all public grape breeding programs where interest is expressed and infrastructure is compatible. We also aim to start the design of a next-gen imaging system dedicated to powdery mildew detection and quantification and start the design of additional robots to increase the throughput of current lab phenotyping robots. Objective 3a (field trial): Observe and record vine and disease developments in its first year of growth. Incorporate human, remote and robotic sensing devices to determine these factors. Objective 3b (breeding): In the next reporting period, all programs participating in MAS (UCDavis, UMN, NDSU, Cornell, MoSU, ARS) plan to complete local phenotyping, analyze rhAmpSeq marker datasets for use in informing 2024 crosses, participate in 2024 genotyping and phenotyping, and continue with genetic map construction and QTL analysis. The NDSU program intends to specifically make crosses between extremely cold hard breeding lines and lines carrying known resistance to powdery and downy mildew for later selection. At South Dakota State University, there are further plans to explore rootstock population traits through scion phenotype plasticity. The University of Arkansas group plans to genotype their Vitis germplasm and Muscadinia x Vitis hybrid selections to determine segregation of known resistance alleles and phenotype these populations for cold hardiness, fruit quality, seedlessness, and disease resistance (including about 1200 Muscadinia x Vitis seedlings). Missouri State University researchers plan to preserve the existing mapping populations of 'Norton' x 'Cabernet Sauvignon' and 'Chambourcin' x 'Cabernet Sauvignon' and 'Jaeger 70/Munson' x 'Vignoles'. ARS-Geneva/Kearneysville strives to obtain early flowering to attain the second generation of crosses in that new breeding program. Objective 4: We will analyze the focus group discussion question and pre-survey results. Based on the results, the formal experiments will be designed to explore the effective labeling for wine, table grapes, and raisins made from disease-resistant cultivars through eye-tracking and brain scanning.

IMPACT: 2022/09 TO 2023/08
What was accomplished under these goals? Objective 1: Efforts were focused on identifying candidate genes responsible for grape powdery mildew (PM) resistance among genetic loci identified in wild Vitis species: Ren1, Ren4U, Ren6, Ren7, Ren11, Ren12, Ren13, Run1.2b, and Run2.2. This included chromosome-scaled genome assembly of 19 grapevines (Vitis vinifera ssp. vinifera Husseine (Ren1+), Karadzhandal (Ren1+), Khalchili (Ren1+), Sochal (Ren1+), Late Vavilov (Ren1+); V. vinifera ssp. sylvestris DVIT3603.16 (Ren1+) and its sib-line DVIT3603.07 (Ren1-); six F1 vines from the crossing of Vitis vinifera ssp. vinifera F2-35 and V. piasezkii DVIT2027 (Ren6+/Ren7+); V. romanetii C166-026 (Ren4U+) and V. romanetii C166-043 (Ren4D+); Tamiami (Ren11), Vitis amurensis PI 588631 (Ren12), Norton (Ren13), and Muscadinia rotundifolia Trayshed (Run1.2b and Run2.2). Combined with allele-specific gene expression via RNA sequencing data of hundreds of full-sibling progeny, these genomes have enabled identification of 2 or more candidate NLR (Nucleotide-Binding Leucine-rich repeat protein) genes for functional characterization, per resistance locus. Cloning of the binary vectors for knock-in of candidate genes in the PM-susceptible Vitis vinifera ssp. vinifera Thompson Seedless is ongoing for Ren6, Ren7, Run1.2b and Run2.2. Binary vectors have been designed to express the candidate genes under their native promoter. The one exception to the NLR story is the Ren11 locus, for which no NLR gene has been identified within the candidate region. This discovery highlights a potentially unique mechanism of resistance against PM in this locus. Objective 2: Blackbird phenotyping was successful during this reporting period and included 19 experiments totaling 27,448 leaf discs and 107,768 images. This included imaging of 800 National Plant Germplasm System (NPGS) accessions, as well as leaf tissue from 211 'Norton' x 'Cabernet Sauvignon' progenies (plus parents) and 146 'Jaeger 70/Munson' x 'Vignoles' progenies (plus parents) from the University of Missouri, both for powdery mildew and/or downy mildew resistance. ARS researchers in Geneva, New York germinated a total 4000 grapevine seedlings segregating for resistance to downy mildew and/or powdery mildew. ARS-Geneva then collected vineyard disease ratings from 3 mapping families, including images and ground truth data. The genome-wide rhAmpSeq markers developed by VitisGen continue to be widely used for marker assisted selection (MAS) in public and private breeding programs, tracking 18 disease resistance loci and 7 fruit quality traits. In FY23, these rhAmpSeq markers were applied to 19,000 grape samples from 11 research programs on three continents, including running rhAmpSeq markers on both NPGS national Vitis repositories with collaboration from Breeding Insight. We have also developed new low-cost DNA markers (KASP) for quick screening of eleven high-priority grapevine traits. The Jiang lab is also working to deliver custom imaging and AI-based analysis systems for high throughput plant phenotyping of grape diseases. The Jiang lab developed three sets of custom strobe-light based cameras with needed hardware and computer programs for field data collection in three collaborating breeding programs (California, South Dakota, and New York) in this project. Establishment of a new grape breeding program for the Mid-Atlantic US located at The Innovative Fruit Production, Improvement, and Protection is located in Kearneysville, WV which included new vineyard infrastructure, new irrigation, and permanent planting of 4000 grapevines. Deploy custom, strobe light-based imaging acquisition systems for three collaborative breeding programs within the project for field data collection. Objective 3a (field trial): Under Objective 3, we made significant progress towards "developing strategic and epidemiologically based management programs that are effective and sustainable," by establishing the two aforementioned new research vineyards at Cornell AgriTech to develop strategic management programs based on varying numbers of stacked resistance gene with conventional and biological fungicide applications to determine disease control. Two research vineyards were planted at Cornell AgriTech: 2 acres of NY06.0514.06, that will be blocked in to a spray/no spray experiment to test the resistance genes against powdery and downy mildews; 1 acre of a variety trial consisting of Arandel, NY06.514.06, La Cresent, NY06.512.01, NY10.0910.01 and NY15.0414.01. Each cultivar will serve as a replicate for timed fungicide applications to determine optimum timing for disease control. Coordination of grape pathologists to attend multistate VG3 variety trial "SCRI planning" workshop in March 2024. Pre-workshop meeting was held June 6, 2023, with 10 attendants. Objective 3b (breeding): Breeders at University of California, Davis (UCDavis), University of Minnesota (UMN), Cornell University, North Dakota State University (NDSU), the University of Arkansas, and the USDA at Kearneysville, WV and Parlier, CA, submitted over 12,000 samples for genotyping for using rhAmpSeq. These materials included breeding materials for marker assisted selection (MAS), mapping populations for marker-trait discovery, and diverse germplasm which will be used to generate rhAmpSeq data for identifying disease resistant material and novel resistance alleles. These cross-institutional results have been coordinated by PD Clark and PM Fessler at the UMN. At the University of Arkansas, Vitis x Muscadinia hybrid populations are under development, which segregate for disease resistance and seedlessness. Local phenotyping has occurred at South Dakota State University (SDSU) for shoot growth parameters and fruitful node position. At the University of Missouri local phenotyping has occurred for winter cold hardiness of a 'Chambourcin' x 'Cabernet Sauvignon' mapping population, as well as for Penicillium chrysogenum resistance and rooting ability from hardwood cuttings for a 'Norton' x 'Cabernet Sauvignon' mapping population. Objective 4: The socio-economic team has conducted a comprehensive literature review on consumer preferences for wine, table grapes, and raisins. The team has developed the focus group discussion questions and met with the industry advisory panel members on the question development. The questions were finalized and the focus group discussions were conducted in late June/early July, 2023. Pre-survey questions for table grapes and raisins have been developed and the team is polishing the questions and the pre-survey will be distributed in September, 2023.

PUBLICATIONS (not previously reported): 2022/09 TO 2023/08
1. Type: Journal Articles Status: Published Year Published: 2023 Citation: Alahakoon, D., & Fennell, A. (2023). Genetic analysis of grapevine root system architecture and loci associated gene networks. Frontiers in Plant Science, 13. doi: 10.3389/fpls.2022.1083374. PMID: 36816477; PMCID: PMC9932984.
2. Type: Journal Articles Status: Published Year Published: 2023 Citation: Clark, M. D., Luby, J. J., & Atucha, A. (2023). âClarionâ Grapevine: A Cold Climate Wine Cultivar for Midwest United States Production. HortScience, 58(2), 231-233. https://doi.org/10.21273/HORTSCI16849-22
3. Type: Journal Articles Status: Published Year Published: 2022 Citation: Gadoury, D.M., Sapkota, S., Cadle-Davidson, L., Underhill, A., McCann, T., Gold, K., Gambhir, N., & Combs, D. (2022). Effects of Nighttime Applications of Germicidal Ultraviolet Light upon Powdery Mildew (Erysiphe necator), Downy Mildew (Plasmopara viticola), and Sour Rot of Grapevine. Plant Disease, First Look. https://apsjournals.apsnet.org/doi/10.1094/PDIS-04-22-0984-RE
4. Type: Journal Articles Status: Published Year Published: 2022 Citation: Alahakoon, D., Fennell, A., Helget, Z., Bates, T., Karn, A., Manns, D., Mansfield, A. K., Reisch, B. I., Sacks, G., Sun, Q., Zou, C., Cadle-Davidson, L., & Londo, J. P. (2022). Berry anthocyanin, acid, and volatile trait analyses in a grapevine-interspecific F2 population using an integrated GBS and rhAmpSeq genetic map. Plants, 11, 696. https://doi.org/10.3390/plants11050696
5. Type: Journal Articles Status: Published Year Published: 2022 Citation: Liu, E., Gold, K. M., Combs, D., Cadle-Davidson, L., & Jiang, Y. (2022). Deep semantic segmentation for the quantification of grape foliar diseases in the vineyard. Frontiers in Plant Science, 13. https://doi.org/10.3389/fpls.2022.978761
6. Type: Websites Status: Published Year Published: 2023 Citation: Gold, K. M., & Kanaley, K. (2023). Grape Disease Control, June 2023. Pg 4. Retrieved from https://blogs.cornell.edu/grapes/ipm/diseases/grape-disease-control-spring-2023 /
7. Type: Book Chapters Status: Published Year Published: 2023 Citation: Conner, P., & Worthington, M. (2023). Muscadine grape breeding. Plant Breed. Rev., 46, 31-119. ISBN: 978-1-119-87412-6
8. Type: Journal Articles Status: Published Year Published: 2023 Citation: Jenkins, D., Juba, N., Crawford, B., Worthington, M., & Hummel, A. (2023). Regulatory frameworks for plant varieties developed using new breeding techniques must focus on the product to ensure societal benefit. Nature Plants. https://doi.org/10.1038/s41477-023-01403-2
9. Type: Conference Papers and Presentations Status: Accepted Year Published: 2023 Citation: Liu, E., Monica, J., Gold, K., Cadle-Davidson, L., Combs, D., & Jiang, Y. (2023). Vision-based Vineyard Navigation Solution with Automatic Annotation. In 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), Detroit, USA (Accepted).
10. Type: Journal Articles Status: Published Year Published: 2022 Citation: Massonnet, M., Riaz, S., Pap, D., Figueroa-Balderas, R., Walker, M. A., & Cantu, D. (2022). The grape powdery mildew resistance loci Ren2, Ren3, Ren4D, Ren4U, Run1, Run1.2b, Run2.1, and Run2.2 activate different transcriptional responses to Erysiphe necator. Frontiers in Plant Science, 13, 1096862.
11. Type: Journal Articles Status: Published Year Published: 2022 Citation: Reshef, N., Karn, A., Manns, D. C., Mansfield, A. K., Cadle-Davidson, L., Reisch, B., & Sacks, G. L. (2022). Stable QTL for malate levels in ripe fruit and their transferability across Vitis species. Horticulture Research. https://doi.org/10.1093/hr/uhac009
12. Type: Journal Articles Status: Published Year Published: 2023 Citation: Patel, S., Harris, Z. N., Londo, J. P., Miller, A., & Fennell, A. (2023). Genome assembly of the hybrid grapevine Vitis âChambourcinâ. Gigabyte: gigabyte84. doi: 10.46471/gigabyte.84
13. Type: Journal Articles Status: Published Year Published: 2023 Citation: Sapkota, S., Zou, C., Ledbetter, C., Underhill, A., Sun, Q., Gadoury, D., & Cadle-Davidson, L. (2023). Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew. Horticulture research, 10(5), uhad052. https://doi.org/10.1093/hr/uhad052
14. Type: Journal Articles Status: Published Year Published: 2022 Citation: Qiu, T., Underhill, A., Sapkota, S., Cadle-Davidson, L., & Jiang, Y. (2022). High throughput saliency-based quantification of grape powdery mildew at the microscopic level for disease resistance breeding. Horticulture Research, uhac187. https://doi.org/10.1093/hr/uhac187
15. Type: Journal Articles Status: Published Year Published: 2022 Citation: Nigar, Q., Cadle-Davidson, L., Gadoury, D. M., & Hassan, M. U. (2022). First Report of Colletotrichum fioriniae Causing Grapevine Anthracnose in New York. Plant Disease. https://doi.org/10.1094/PDIS-03-22-0604-PDN
16. Type: Websites Status: Published Year Published: 2023 Citation: VitisGen3 Project Website: vitisgen3.umn.edu (Published 2023) ed. K. Fessler.