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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Research Project #437846

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

Location: Crops Pathology and Genetics Research

2020 Annual Report

1a. Objectives (from AD-416):
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.

1b. Approach (from AD-416):
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.

3. Progress Report:
This report documents progress for project 2032-21220-008-00D Resilient, Sustainable Production Strategies for Low-Input Environments, which started March 2020 and continues research from 2032-21220-007-00D Sustainable Vineyard Production Systems. A major focus of Sub-objective 1A is to develop precision-irrigation tools and to identify new and existing cultivars and rootstocks, which better tolerate drought stress. ARS researchers in Davis, California, in collaboration with researchers at University of California, Davis and Los Angeles, and Yale University, measured similar physiological responses of Vitis vinifera varieties ‘Chardonnay’ and ‘Cabernet Sauvignon’ to drought stress, where stomatal closure was associated with lower hydraulic permeability outside the xylem in their leaves. ARS researchers in Davis, California, in collaboration with a team of other ARS, university, and industry partners, continued work on the multi-scale, remote sensing-based modeling system for California vineyards ‘Grape Remote-sensing Atmospheric Profile and Evapotranspiration eXperiment (GRAPEX)’. Physiological, micrometeorological, and biophysical data were collected at the plant scale, along with airborne and satellite data at the vineyard scale. At one site, the team built Solar-Induced Fluorescence towers, to identify irrigation practices that mitigate heat waves. Water-use and stress models generated real-time data, which, in turn, was used to schedule irrigations. A major focus of Sub-objective 1B is to characterize the molecular response of grape to drought stress. ARS researchers in Davis, California, evaluated a simple and efficient genome-editing technology (CRISPR/CAS9- Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9) for grape. The CRISPR target was overexpression of the plant hormone abscisic acid (ABA), which plays an important role in the regulation of stomatal aperture and thus tolerance of drought stress, under the control of a drought stress-inducible promoter. Experiments are in progress to generate expression constructs and transformants. In support of Sub-objective 2A, ARS researchers in Davis, California, examined the relationship between microbial communities in vineyard soil and during fermentation, with samples from 15 Vitis vinifera ‘Pinot noir’ vineyards, which are located along a transect extending from southern Oregon to southern California. An outcome of this research is to cultivate a soil microbial community that maximizes wine quality. Microbial samples were collected from soil from under the vinerows (in the irrigated ‘drip zone’) and in between the rows, and from fermenting grape juice at three days after the onset of fermentation and just prior to addition of yeast. The roles of management histories and climatic conditions will be taken into account, using a Parameter-elevation Relationships on Independent Slopes Model, to determine the interactive effects of climate, vineyard management, soil microbes, and juice microbes on the chemical composition of the juice, namely compounds that are indicative of wine quality. In support of Objective 3, ARS researchers in Davis, California, compared single versus mixed infections by the pathogens that cause the grapevine trunk disease Esca, under controlled conditions in the greenhouse. An outcome of this research is a reliable infection assay to create the leaf symptoms of Esca, the absence of which is a bottleneck to screening for Esca-resistant germplasm and for fungicides/biocontrol agents that protect nursery stock from infection. Fungi not yet reported as causal pathogens of trunk diseases, which were isolated from symptomatic vines during 2019 surveys of California table grapes and Washington wine grapes, were evaluated in the greenhouse for pathogenicity. Further, pathogens found to be common in Washington vineyards (e.g., Cytospora viticola), which have not previously been evaluated in published studies, were included in a field study to identify pruning-wound protectants. The USDA Climate Hub’s program of work in Davis, California, is aligned with one of three synthetic themes: 1) research and information synthesis, 2) tool and technology development, and 3) stakeholder outreach and education. ARS researchers in Davis, California, are examining extreme heat and frost risk (extreme frost) on several high-value perennial crops in California. They continued work on climate extremes, and also how such events impact the broader landscape at the interface of California agriculture, namely riparian and meadow communities. The ARS researchers in Davis, California, evaluated climate impacts to the wildland-urban interface for forests and rangelands in the Southwest region of the United States. They also continued to co-design the Cal-AgroClimate website - a web-based, decision support tool for agriculture producers statewide (modeled after the Agro Climate toolkit for the Southeastern United States) – in partnership with collaborators from University of California Division of Agriculture and Natural Resources and University of California, Merced. In response to large stand-replacing wildfires and tree mortality, ARS researchers in Davis, California, co-developed the climate-wise reforestation toolkit (a web-based decision support toolkit). To address the topic of farming in the context of climate change, they developed three stakeholder factsheets, which are focused on several aspects of climate impacts (e.g., chill hours, extreme heat) on agriculture. To extend technical knowledge to stakeholders, ARS researchers in Davis, California, serve on several advisory and technical steering committees, including the Forest Management Task Forces’ Science Advisory Panel, helping guide actions that support forest management, backed by California Climate Investments – of which other USDA agencies are engaged (namely USDA-Forest Service and USDA-Natural Resource Conservation Service).

4. Accomplishments
1. Transcriptional regulation of the drought-stress response in a model plant system. Molecular responses to drought stress in a desert plant could provide genetic material and knowledge of genetic pathways for genetically engineering and breeding drought-tolerant crops. For example, ‘Resurrection plants’, such as Myrothamnus (M.) flabellifolia, can withstand extreme drought. However, the mechanisms by which they survive and revive after drought are not well characterized. ARS researchers in Davis, California, in collaboration with researchers at Sichuan Agricultural University, China, characterized a transcription factor in M. flabellifolia, which controls when other genes are switched on, and transformed the model plant Arabidopsis with this gene. Transgenic Arabidopsis plants with over-expression of this gene maintained higher water content and exhibited better water-use efficiency than non-transformed control plants. In the future, this technology could be incorporated into important agricultural crops such as wheat and corn.

5. Record of Any Impact of Maximized Teleworking Requirement:
For Objective 1B, the maximized telework requirement had a negative impact on the lab’s ability to perform greenhouse and field experiments relating to molecular studies using VIGS and CRISPR-mediated genome editing technologies. Due to the safety concern, only the plants were maintained in the greenhouse with limited time allowed (1.5 hours per week). We have not been able to collect leaf, fine root tissues, neither to generate any testing constructs, and inoculation on the grape plants for VIGS studies. The tests will be rescheduled when safe to do so. For Objective 2, the maximized telework requirement that began on March 19 continues to limit the ability to analyze soil characteristics and extract genomic DNA in preparation for targeted metagenomic analysis of Pinot noir vineyard soils. This creates a corresponding delay in the next steps: sequencing and data analysis. In lieu of this laboratory-based work in Objective 2, existing datasets from vineyard microbiomes have been analyzed and are being prepared for publication. In accordance with NP305’s mission, a preliminary effort in biogeochemical modeling of carbon, nitrogen and water flows has been established, building on existing collaborations between USDA-ARS and UC Davis partners. The long-term goal is to adapt the DayCent model to include novel practices for almonds, grapes and other specialty crops using existing datasets. A working group to establish proficiency with the model and support data analysis was established in March 2020, meeting weekly via Zoom.

Review Publications
Knipfer, T., Grom, J., Reyes, C., Momayyezi, M., McElrone, A.J., Kluepfel, D.A. 2020. A comparative study on physiological responses to drought in walnut genotypes (RX1, Vlach, VX211) commercially available as rootstocks. Trees. 34(3):665-678.
Parker, L.E., McElrone, A.J., Ostoja, S.M., Forrestel, E.J. 2020. Extreme heat effects on perennial crops and strategies for sustaining future production. Plant Science. 295.