Project : USDA ARS

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Research Project: Resilient, Sustainable Production Strategies for Low-Input Environments

Location: Crops Pathology and Genetics Research

2025 Annual Report

Objectives
Objective 1: Develop crop production strategies that integrate water and nutrient input management and the environment for healthy, sustainable vineyards. [NP 305, Component 1, Problem Statement 1B] • Subobjective 1.A. Characterize varied responses of grapevine genotypes to drought in order to improve detection and interpretation of water stress signals for local and remote proximal sensors and to develop precision irrigation techniques tailored to genotype- specific root responses. • Subobjective 1.B. Determine the molecular basis associated with the differential responses to drought stress among grapevine genotypes. • Subobjective 1.C. Identifying threshholds for organoleptic volatile phenols and their glycosidically-bound derivatives in wine grape varieties exposed to smoke taint across different growing regions. Expected benefits include standardized chemical analyses of smoke taint compounds in exposed and unexposed vineyards for the wine varietals growing in CA, OR, and WA with the goal of identifying and quantifying genotype-specific environmental threshold levels. Objective 2: Analyze the interaction of soil health and vineyard floor management for the enhancement of vine and fruit quality. [NP 305, Component 1, Problem Statement 1B] • Subobjective 2.A. Determine relationships among soil and grape must microbiomes and their structure in the wine grape production system. Objective 3: Develop improved strategies for controlling grapevine disease using preventative and post-infection management strategies. [NP 305, Component 1, Problem Statement 1B] • Subobjective 3.A. Characterize the role of wood-decay fungi in trunk diseases, to develop post-infection practices that return vines to productivity. • Subobjective 3.B. Identify when trunk pathogens sporulate and the infection courts by which they infect, to develop preventative practices that protect susceptible host tissues.

Approach
The approaches for each objective range from experimentation under controlled conditions in the greenhouse to experimentation under natural field conditions, with commercial vineyards making up the majority of field study sites. Prior to hypothesis testing, some level of methods development (e.g., imaging water flowing through the vessels of living plants, pathogen detection from environmental samples of microscopic spores) is required for each objective, in part because grape is not a model study system. For objective 1, parallel sets of physiological experiments are focused on measuring anatomical, physiological, and transcriptional responses of leaves and fine roots, under normal levels of irrigation versus under drought stress. Whole plants of Vitis vinifera wine-grape varieties (Cabernet-Sauvignon, Chardonnay) and rootstocks with differential drought tolerance will be examined by X-ray microCT, followed by sections of leaves and roots examined by transmittance electron microscopy and Laser Capture Microdissection. RNA-seq techniques will then be used to seek out transcriptional differences at a molecular scale. For Sub-Objective 1.C.-The approach will combine field experimentation in the vineyard, winemaking and distilling processes in the experimental winery, and laboratory analyses of smoke-related compounds using, for e.g., gas chromatography/mass spectrometry (GC/MS). Compositional changes in the fruit of different cultivars, with exposure to smoke, will be characterized and quantified. Smoke-related compounds in wines made from the smoke-exposed fruit will also be characterized and quantified. Grape and wine quality analytical methods will be developed to detect key smoke-related compounds in the fruit and the wine, and acceptable limits will be established. Further, endproduct processing methods will be developed to help mitigate such compounds. For objective 2, the interaction of host genotype by environment (soil and climate, specifically) by management is examined. High-throughput amplicon sequencing of soil fungi and bacterial communities will be used to compare those of vine rows under different floor-management practices. Samples from the must will evaluate whether vineyard floor management practices impact the microbiome during fermentation. Diffuse reflectance Fourier transformed mid-infrared spectroscopy (DRIFTS) will be used to characterize changes in SOM chemical composition in particulate organic matter and other soil C fractions. For objective 3, inoculations of potted plants in the greenhouse will be used to test hypotheses at the plant scale about which combinations of pathogens and sequences of infection cause disease symptoms, and also about how differential tissue susceptibility affects whether an infection spreads throughout an individual plant. At the vineyard scale, spore trapping in diseased vineyards and evaluations of pruning-wound susceptibility will be used to determine when grapevines are at greatest risk of infection.

Progress Report
This is the final report for project 2032-21220-008-000D, “Resilient, Sustainable Production Strategies for Low-Input Environments”, which has been replaced by new project 2032-30500-001-000D, “Sustainable Grape Production Under Emerging Climate Threats”. For additional information, see the new project report. The project, 2032-21220-008-000D expired in January 2025. The new project, 2032-30500-001-000D, began in January 2025. The project objectives focus on grapes and, to a limited extent, two other woody perennial crops in California (walnut, almond). Over the lifetime of the project the deliverables included practices that reduce the incident of grapevine trunk diseases, new technology to provide growers with precise water-use in real-time, methods to better examine drought tolerance in grapevine rootstocks, and tools to assess wildfire smoke impact in vineyards. Scientific advancements have been plentiful over the course of this project including ground-truthing datasets to better develop remote sensing tools to monitor vineyard evapotranspiration, understanding the physiological basis of drought tolerance in grape root systems, exploring interactions between soil type, climate, and microbial communities to identify region-specific strategies for soil management, and developing phenotyping assay for Phomopsis cane and leaf spot. The project also addresses the complex impacts of environmental pressures on California agriculture, namely wildfires, drought, changing rainfall patterns, less irrigation water, lower quality water, and heatwaves. In support of Sub-objective 1A, ARS researchers in Davis, California, in collaboration with other ARS locations, universities, and industry partners, made substantial progress over the past five years in developing and validating precision irrigation tools to manage drought and heat stress in vineyards and orchards. Through the long-term Grape Remote-sensing Atmospheric Profile and Evapotranspiration eXperiment (GRAPEX) and Tree crop Remote sensing of Evapotranspiration eXperiment (T-REX) projects, researchers collected multi-scale datasets from ground sensors, flux towers, and satellite platforms to quantify evapotranspiration and assess crop stress responses under commercial conditions and across varied irrigation regimes. A major advancement was the development of a rugged, ground-based method using infrared temperature sensors to estimate crop water use and stress at the single-plant level, offering continuous, real-time data and validated against research-grade standards. Researchers also applied solar-induced fluorescence (SIF) and lidar scanning to scale physiological responses from individual leaves to whole canopies, enabling detection of dynamic crop reactions to increasingly frequent and intense heatwaves. To address rising heat stress, supplemental irrigation was shown to reduce vine, fruit, and wine damage during extreme events helping growers fine-tune water applications. In addition, hyperspectral imaging research revealed that morning and late afternoon are optimal for detecting vine water stress, prompting changes in commercial monitoring practices. X-ray imaging further revealed that grapevine xylem collapses under mild drought, particularly in young leaves, reducing water loss but increasing vulnerability to heat. These insights into plant physiology and stress responses enhance the utility of both ground-based and remote-sensing tools. Together, these innovations are equipping growers with accurate, real-time information to improve irrigation scheduling, reduce water use, and maintain crop productivity and quality under challenging environmental conditions. For Sub-objective 1B, ARS researchers in Davis, California, made substantial progress in identifying molecular and genetic markers of drought tolerance in grapevine rootstocks through the development and deployment of a novel aeroponic culture system. This innovative system enabled the controlled growth of genetically identical grapevine rootstocks in a plant growth room, allowing the collection of high-quality root tissue for transcriptomic analysis and overcoming the long-standing challenge of obtaining suitable root samples from field-grown plants. Using this system, researchers conducted comparative transcriptomic analyses between drought-sensitive and drought-resistant genotypes, identifying key drought-responsive genes involved in hormone biosynthesis and transport that influence root system architecture and drought adaptation. A major accomplishment was the identification and functional characterization of drought stress-inducible transcription factors in both grapevine rootstocks and Myrothamnus flabellifolia, a highly drought-resistant desert plant. One such transcription factor from M. flabellifolia was cloned and overexpressed in Arabidopsis, resulting in transgenic plants that maintained higher water content and showed enhanced water-use efficiency compared to wild-type controls. These findings validate the role of transcriptional regulation in drought resilience and highlight the potential of leveraging genes from desert-adapted species to engineer crop tolerance. Orthologs of these regulatory genes were located in grapevine genomes, providing molecular markers for screening drought-tolerant germplasm. To further accelerate functional studies, a newly developed miniature CRISPR-associated protein was employed, improving gene-editing efficiency in grapevine. Together, these accomplishments establish a powerful foundation for breeding and engineering drought-resilient grapevine cultivars using advanced molecular tools and cross-species genomic insights. In support of Sub-objective 1C, an ARS researcher, in collaboration with university partners, identified practical and cost-effective methods to measure smoke-derived compounds that support grower decision-making during wildfire smoke events. Volatile phenols and their glycoconjugates are key indicators of smoke exposure to grapes and are linked to smoke taint in wines; however, current methods for quantifying these compounds are time-consuming and expensive. To address this, researchers evaluated cerium oxide nanoparticles (nanoceria) as an alternative detection method. Nanoceria react with phenolic compounds, producing a visible color change that corresponds to the composition and concentration of specific volatile phenols, and have been shown to successfully detect all phenols currently associated with smoke-exposed fruit. This approach provides a rapid, inexpensive, and portable tool for growers and winemakers to analyze grape samples before and after smoke events. Additionally, using a custom-built, greenhouse-scale smoking chamber, researchers identified passive sorbent samplers as another effective method for predicting volatile phenol concentrations in grapes and wines. Together, these tools offer fast, reliable, and accessible means to support harvest decisions and manage the risks of wildfire smoke exposure. In support of Sub-objective 2A, ARS researchers conducted a comprehensive spatial and functional analysis of soil and fermentation microbiomes in 15 Pinot noir vineyards spanning southern Oregon to southern California. Soil samples and fermentation samples were analyzed to evaluate how climate, vineyard management, and microbial communities interact to influence soil health and wine composition. Metagenomic sequencing revealed strong regional and management zone effects on microbial community structure and identified potential microbial markers for vineyard health and wine quality. Complementary research demonstrated that microbial communities in grape must also possess a unique identity based on vineyard location and climate, with fungal communities being especially influenced by local environmental conditions and dispersal limitations. These findings highlight the potential for using microbial community profiles as indicators of terroir and wine quality. In addition, a global structed review demonstrated that cover crops improve key soil health indicators such as soil organic carbon across a range of soil textures and production systems, although impacts on soil compaction were variable. Despite recognizing the value of soil health practices, many California growers hesitate to adopt them due to economic concerns and limited outcome data. Outreach and extension strategies are now being tailored to address these barriers. Collectively, these efforts inform the development of microbiome-based and management-driven strategies to enhance sustainability, soil health, and product value in viticultural systems. For Sub-objective 3A, significant progress was made toward detecting and managing grapevine trunk diseases that limit the profitable lifespan of vineyards. ARS researchers in Davis, California, demonstrated that hyperspectral imaging can detect unique reflectance patterns in asymptomatic leaves of grapevines infected with Botryosphaeria dieback and Esca pathogens, offering a promising non-destructive approach for early disease detection in young, nursery plants. Molecular techniques were designed for sensitive, species-specific detection of pathogens from spore traps, to evaluate the risk of infection in the vineyard. Long-term field studies in California and Washington identified fungicides to protect pruning wounds from infection. Also, a post-infection technique known as ‘trunk renewal’ was confirmed to manage Esca of highly susceptible wine-grape cultivar ‘Sauvignon blanc’’. To advance research on disease-resistant cultivars, phenotyping assays were developed for Eutypa dieback and Phomopsis cane and leaf spot, which impact vineyards across the US. Collectively, these advances deliver effective management tools for trunk diseases in U.S. vineyards and support adoption of preventative practices to sustain vineyard health and productivity.

Accomplishments
1. A real time irrigation management tool for woody perennial crops. Irrigation is critical to sustaining yields and quality of high value woody perennial crops in California such as grapes, almonds, pistachios and walnuts. Precision irrigation management requires the integration of ground-based sensors and remote sensing tools to guide grower management needs while accommodating the spatial and temporal variability in commercial settings. ARS researchers in Davis, California, worked with collaborators from the University of California, Davis, to deploy a novel ground-based sensor system to track crop water use and stress in real-time that will be made available to growers. These systems successfully tracked crop water use and stress throughout the growing season in commercial vineyards and orchards and provided site-specific data for integration into a management platform that pairs with remotely sensed data to improve crop water use models.

2. An inexpensive and rapidly deployable tool for monitoring vineyard smoke exposure. Wildfire smoke in vineyards can alter grape composition, resulting in unsalable wines and severe financial losses. As wildfires become more prevalent across the western United States, grape growers need reliable tools that can monitor smoke levels in their vineyards and assess potential damage. ARS researchers in Davis, California, in collaboration with researchers from the Desert Research Institute, identified passive sorbent samplers as an affordable and accessible solution for vineyard smoke risk assessment. These samplers passively absorb volatile organic compounds (VOCs) from the atmosphere, which can later be quantified using analytical instrumentation. Using a custom-built smoking chamber, researchers exposed the sorbent samplers and grapes to various levels of smoke and found a strong correlation between VOCs captured by the samplers and those absorbed by grapes and detected in wine. This work successfully demonstrated the potential of passive samplers as a practical and field-ready indicator of smoke impact in vineyards. In 2025, grape growers in Northern California have partnered with ARS to adopt this tool in their vineyards.

U.S. DEPARTMENT OF AGRICULTURE

Crops Pathology and Genetics Research: Davis, CA