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ARS Home Pacific West Area Davis, California Crops Pathology and Genetics Research Research





- Baumgartner, Kendra
- Steenwerth, Kerri
- McElrone, Andrew
- Jiang, Cai-Zhong
- Rumbaugh, Arran
- 2023
- 2022
- 2021
- 2020
- Publications
- Soil and Air (212)
- Crop Production (305)

Research Project: Resilient, Sustainable Production Strategies for Low-Input Environments **Location:
                            Crops Pathology and Genetics Research** 2022 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 report documents progress for project 2032-21220-008-000D "Resilient, Sustainable Production Strategies for Low-Input Environments", which started in March 2020 and continues research from 2032-21220-007-000D, "Sustainable Vineyard Production Systems". The project objectives focus on grapes and, to a limited extent, two other woody perennial crops in California. The deliverables include labor-saving practices for preventing grapevine trunk diseases and technology to give growers precise measurements of water-use in real-time. Scientific advances are also an important outcome of the project, with development of novel study tools for researchers to examine the physiological bases of drought tolerance in grape rootstocks and the diversity of microbes originating in the vineyard that contribute to the fermentation of wine. Some of the work also addresses the complex impacts of global climate change on California agriculture, including 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 a team made up of colleagues from other ARS locations, universities, and industry partners, continued validation of remote sensing-based water-use estimates, for commercial vineyards and orchards in California. Towers and sensor arrays replicated in different sites for the Grape Remote-sensing Atmospheric Profile and Evapotranspiration eXperiment (GRAPEX) and Tree crop Remote Sensing of Evapotranspiration eXperiment (T-REX) projects were installed and regularly maintained throughout the year. Ground-based physiological, micrometeorological, and biophysical data were collected along with airborne and satellite data, as part of the validation process. This team also evaluated the effectiveness of solar-induced fluorescence (SIF) to identify drought stress in GRAPEX vineyard sites.

In support of Sub-objective 1B, ARS researchers in Davis, California, successfully developed an aeroponic culture system for grapevine rootstocks. This new study tool allows researchers to grow genetically identical cuttings of rootstocks under controlled conditions, and to keep them clean for molecular studies on drought stress resistance by different varieties. A set of six rootstocks, including three drought-sensitive, (namely Riparia Gloire, 101-14 Mgt Millardet, 420 A Mgt), and three drought-resistant genotypes (110R, 140 Ruggeri, 1103 Paulsen), have successfully been tested in this culture system. Clean roots for DNA and Ribonucleic acid (RNA) extraction were harvested and stored for gene-expression analysis. Experiments identified 18 genes related to biosynthesis, transport and response of phytohormones, such as auxin, abscicic acid (ABA) and gibberellic acid (GA), which potentially regulate root system architecture and enhance drought resistance. These genes could be targeted for genome-editing, using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (CRISPR-CAS9) technology, and could serve as the molecular markers for screening drought stress resistance in different grape genotypes. Toward this goal, a newly developed miniature CRISPR-associated protein has been licensed, to improve the efficiency of functional gene analysis in grapevines.

In support of Sub-objective 2A, ARS researchers in Davis, California, examined the spatial distribution of soil microbial communities in 15 Vitis vinifera ‘Pinot noir’ vineyards, spanning southern Oregon to southern California. A goal of this research is to identify a soil microbial community that characterizes different aspects of both the soil and the quality of the wine from grapes at each vineyard. Microbial samples were collected from soil in the vine rows (in the irrigated ‘drip zone’ and non-irrigated dry zone) and from the alleys in between the rows. The roles of management histories and climatic conditions help us evaluate the interactive effects of climate, vineyard management and soil microbes on the chemical, biological and physical attributes of the soil. Ninety-six soil microbe metagenomes were sequenced in winter 2021 and will be analyzed to reveal how desirable soil microbe functions are associated with vineyard management practices. Taxonomic classification of these samples using Kaiju,a program for taxonomic classification of high-throughput sequencing reads from metagenomic sequencing, revealed initially that vineyard region and management zone (alley vs. vine row) influence the soil community structure. This analysis will inform next steps in the assembly process.

For Objective 3, ARS researchers in Davis, California, completed a 3-year field study in the southern San Joaquin Valley, to identify an effective fungicide for managing trunk diseases of modern (circa 2016) table-grape cultivars (in this case, ‘Autumn King’, which is a white, seedless table grape developed by USDA at Parlier, California. We identified the fungicide thiophanate-methyl as most effective against pathogens that cause Botryosphaeria and Eutypa-diebacks. Prior to this study, most materials were tested on wine grapes, in different viticultural regions (and climates), and as hand applications painted onto pruning wounds. Table grapes are genetically distinct from wine grapes and are grown in hotter, drier regions with a different pathogen community. Further, because it is not cost-effective to do hand applications, we evaluated tractor-spray applications. Also, all past work has been done in mature vineyards with widespread and severe trunk disease symptoms. Preventing trunk diseases in badly diseased vineyards will only go so far to prevent long-term yields losses. As such, we have been trying for years to convince growers to protect pruning wounds each year, starting in young vineyards. This study served as a good demonstration site, with cooperation from the ranch manager, and viticulture farm advisors from Tulare and Kern Counties. Field days are planned, once COVID restrictions are lifted. **Accomplishments**
                                

1. Mitigating heat-wave damage to wine grapes using supplemental irrigation. Heat-wave intensity and frequency are worsening across California, and irrigation is one of few practical mitigation methods to prevent crop damage to wine grapes during these extreme weather events. An ARS researcher in Davis, California, in collaboration with researchers from University of California, Davis, and industry, found that supplemental irrigation of wine grapes during heat waves mitigated damage to vines, fruit, and resulting wine. Supplemental irrigation was useful up to a certain level, but too much water had detrimental effects on fruit and wine quality. Under what seem to be persistent water-limited growing conditions of California, these results will help growers identify adequate watering that prevent plant and crop damage, while preventing overwatering, which can be detrimental to fruit and wine quality. 2. A new aeroponic culture system to grow grapes for molecular studies of abiotic stress. It is extremely challenging to obtain suitable plant materials especially root tissues from field-grown grapes for molecular studies, such as transcriptome analysis, which require high quality RNA preparation. To overcome these difficulties, ARS researchers in Davis, California, developed an aeroponic culture system to efficiently grow different grapevine rootstocks in a plant growth room. This new system allows researchers to grow plants to generate extremely clean root tissues for molecular studies on drought stress resistance of different grape varieties. 3. Cover crops improve soil-health indicators. ARS researchers in Davis, California, and faculty at the University of California, Davis, completed a global structured review of the effects of cover crops on soil biological, physical and chemical attributes, or soil health indicators. Given the priority of both USDA and various state of California agencies to support Climate Smart Agriculture, we examined the benefits of cover crops for soil health, crop productivity, economic and ecological factors. While cover crops were associated with soil organic carbon improvements – a prized soil-health indicator - soil texture class influenced the magnitude and frequency of the response of soil health indicators among studies. This work demonstrates that, in nearly all soil texture classes, cover crops tend to have beneficial impacts on the majority of soil health indicators, regardless of cover crop type, agricultural production system and region of the world where studies were conducted. However, a consistent effect of cover crops on reducing soil compaction across all soil textures was not strongly apparent, suggesting other mitigating practices for soil compaction are needed in combination with cover crops. Our findings suggest that cover crops improve and/or sustain soil health indicators, which may protect soils for crop production and promote Climate Smart Agriculture. 4. Protecting California table grapes from trunk diseases. ARS researchers in Davis, California, identified the fungicide thiophanate-methyl as effective for protecting pruning wounds from pathogens that cause Botryosphaeria dieback (Neofusicoccum parvum) and Eutypa dieback (Eutypa lata). These findings come after 3 years of research in a southern San Joaquin Valley vineyard of the seedless table-grape ‘Autumn King’. This young vineyard, planted in 2016, was a demonstrative setting to encourage growers to adopt preventative practices against trunk diseases, rather than wait as most growers do until the vineyard is mature and severely symptomatic. Given the high cost of labor in California vineyards, fungicides were spray-applied with a tractor to dormant grapevines immediately after pruning, rather than the more labor-intensive method evaluated in past studies of hand-painting fungicides onto individual pruning wounds. Although thiophanate-methyl was not effective in this study against a pathogen that causes the trunk disease Esca (Phaeoacremonium minimum), this is relatively rare in California vineyards, compared to Botryosphaeria dieback and Eutypa dieback. **Review Publications**
                            *Momayyezi, M., Borsuk, A., Brodersen, C., Gilbert, M., Theroux-Rancourt, G., Kluepfel, D.A., McElrone, A.J. 2022. Dessication of the leaf mesophyll and its implications for C02 diffusion and light processing. Plant, Cell & Environment. 45(5):1362-1381. https://doi.org/10.1111/pce.14287.*
                                *Ingel, B., Caldwell, D., Duong, F., Parkinson, D.Y., McCulloh, K.A., Iyer-Pascuzzi, A.S., McElrone, A.J., Lowe-Power, T.M. 2022. Revisiting the source of wilt symptoms: X-ray microcomputed tomography provides direct evidence that Ralstonia biomass clogs xylem vessels. Phytofrontiers. 2(1):41-51. https://doi.org/10.1094/PHYTOFR-06-21-0041-R.*
                                *Bartlett, M.K., Sinclair, G., Fontanesi, G., Knipfer, T.M., Walker, M.A., McElrone, A.J. 2021. Root pressure-volume curve traits capture rootstock drought tolerance. Annals Of Botany. 129(4):389-402. https://doi.org/10.1093/aob/mcab132.*
                                *Wong, C.Y., Bambach, N.E., Alsina, M.M., McElrone, A.J., Jones, T., Buckley, T.N., Kustas, W.P., Magney, T.S. 2022. Detecting short-term stress and recovery events in a vineyard using tower-based remote sensing of photochemical reflectance index (PRI). Irrigation Science. https://doi.org/10.1007/s00271-022-00777-z.*
                                *Bambach, N.E., Kustas, W.P., Alfieri, J.G., Prueger, J.H., Hipps, L., McKee, L.G., Castro-Bustamante, S., Volk, J., Alsina, M.M., McElrone, A.J. 2022. Evapotranspiration uncertainty at micrometeorological scales: The impact of the eddy covariance energy imbalance and correction methods. Irrigation Science. https://doi.org/10.1007/s00271-022-00783-1.*
                                *Bambach, N.E., Kustas, W.P., Alfieri, J.G., Gao, F.N., Prueger, J.H., Hipps, L., McKee, L.G., Castro-Bustamante, S., Alsina, M.M., McElrone, A.J. 2022. Inter-annual variability of land surface fluxes across vineyards: The role of climate, phenology, and irrigation management. Irrigation Science. https://doi.org/10.1007/s00271-022-00784-0.*
                                *Tang, Z., Jin, Y., Alsina, M.M., McElrone, A.J., Bambach, N.E., Kustas, W.P. 2022. Vine water status mapping with multispectral UAV imagery and machine learning. Irrigation Science. https://doi.org/10.1007/s00271-022-00788-w.*
                                *Fujiyoshi, P.T., Lawrence, D.P., Travadon, R., Cooper, M., Verdegaal, P., Schwebs, S., Baumgartner, K. 2021. Detection of spores of causal fungi of dieback-type trunk diseases in young, asymptomatic vineyards and mature, symptomatic vineyards. Crop Protection. 150. Article 105798. https://doi.org/10.1016/j.cropro.2021.105798.*
                                *Fujiyoshi, P.T., Lawrence, D.P., Travadon, R., Baumgartner, K. 2021. DNA-based detection of grapevine trunk-disease from environmental spore samples. MethodsX. 8. Article 101494. https://doi.org/10.1016/j.mex.2021.101494.*
                                *Wallis, C.M., Lawrence, D., Travadon, R., Baumgartner, K. 2021. Characterization of grapevine fungal canker pathogens using fatty acid methyl ester (FAME) profiles. Mycologia. 114(1):203-213. https://doi.org/10.1080/00275514.2021.1983396.*
                                *Devine, S.M., Steenwerth, K.L., O'Geen, A.T. 2021. A regional soil classification framework to improve soil health diagnosis and management. Soil Science Society of America Journal. 85(2):361-378. https://doi.org/10.1002/saj2.20200.*
                                *Devine, S.M., Steenwerth, K.L., O'Geen, A.T. 2022. Soil health practices have different outcomes depending on local soil conditions. California Agriculture. 76(1):46-55. https://doi.org/10.3733/ca.2022a0005.*
                                *Celikel, F., Zhang, Q., Zhang, Y., Reid, M., Jiang, C. 2021. A cytokinin analog Thidiazuron suppresses shoot growth in potted rose plants via the gibberellic acid pathway. Frontiers in Plant Science. 12. Article 639717. https://doi.org/10.3389/fpls.2021.639717.*
                                *Zhang, Y., Norris, A.M., Reid, M., Jiang, C. 2021. Improvement of drought resistance through manipulation of the gibberellic acid pathway. Ornamental Plant Research. 1. Article 11. https://doi.org/10.48130/OPR-2021-0011.*
                                *Wang, H., Zhang, Y., Norris, A.M., Jiang, C. 2022. S1-bZIP transcription factors play important roles in the regulation of fruit quality and stress responses. Frontiers in Plant Science. 12. Article 802802. https://doi.org/10.3389/fpls.2021.802802.*
                                *Dong, X., Ma, C., Xu, T., Reid, M., Jiang, C., Li, T. 2021. Auxin response and transport during induction of pedicel abscission in tomato. Horticulture Research. 8. Article 192. https://doi.org/10.1038/s41438-021-00626-8.*
                                *Liu, X., Cheng, L., Li, R., Cai, Y., Wang, X., Fu, X., Dong, X., Qi, M., Jiang, C., Xu, T., Li, T. 2022. The HD-Zip transcription factor S1HB15A regulates abscission by modulating jasmonoyl-isoleucine biosynthesis. Plant Physiology. 189(4):2396-2412. https://doi.org/10.1093/plphys/kiac212.*
                                *Zaini, P.A., Lee, S.H., Leslie, C.A., Walawage, S.L., Jiang, C., Browne, G.T., Dandekar, A.M., Kasuga, T. 2021. A rapid in vitro phenotypic assay of walnut shoots for prescreening resistance of Phytophthora pini. Plant Health Progress. 22(3):235-239. https://doi.org/10.1094/PHP-05-21-0078-FI.*
                                *Reiter, T., Montpetit, R., Byer, S., Frias, I., Leon, E., Viano, R., Mcloughlin, M., Halligan, T., Hernandez, D., Figueroa-Balderas, R., Cantu, D., Steenwerth, K.L., Runnebaum, R., Montpetit, B. 2021. Transcriptomics provides a genetic signature of vineyard site and offers insight into vintage-independent inoculated fermentation outcomes. mSystems. 6(2). Article e00033-21. https://doi.org/10.1128/mSystems.00033-21.*
                                *Sundaresan, S., Philosoph-Hadas, S., Ma, C., Jiang, C., Riov, J., Kochanek, B., Salim, S., Reid, M.S., Meir, S. 2022. Role of the KNOTTED1-LIKE HOMEOBOX protein (KD1) in regulating abscission of tomato flower pedicels at early and late stages of the process. Physiologia Plantarum. 173(4):2103-2118. https://doi.org/10.1111/ppl.13560.*
                                *Zhang, Y., Wu, Z., Feng, M., Chen, J., Qin, M., Wang, W., Bao, Y., Xu, Q., Ye, Y., Ma, C., Jiang, C., Gan, S., Zhou, H., Cai, Y., Hong, B., Gao, J., Ma, N. 2021. The circadian-controlled PIF8-BBX28 module regulates petal senescence in rose flowers by governing mitochondrial ROS homeostasis at night. The Plant Cell. 33(8):2716-2735. https://doi.org/10.1093/plcell/koab152.*


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