Crops Pathology and Genetics Research Unit

Davis, CA, United States

Crops Pathology and Genetics Research Unit

Davis, CA, United States
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Gambetta G.A.,University of California at Davis | Fei J.,University of California at Davis | Rost T.L.,University of California at Davis | Knipfer T.,University of California at Davis | And 5 more authors.
Plant Physiology | Year: 2013

To better understand water uptake patterns in root systems of woody perennial crops, we detailed the developmental anatomy and hydraulic physiology along the length of grapevine (Vitis berlandieri × Vitis rupestris) fine roots from the tip to secondary growth zones. Our characterization included the localization of suberized structures and aquaporin gene expression and the determination of hydraulic conductivity (Lpr) and aquaporin protein activity (via chemical inhibition) in different root zones under both osmotic and hydrostatic pressure gradients. Tissue-specific messenger RNA levels of the plasma membrane aquaporin isogenes (VvPIPs) were quantified using laser-capture microdissection and quantitative polymerase chain reaction. Our results highlight dramatic changes in structure and function along the length of grapevine fine roots. Although the root tip lacked suberization altogether, a suberized exodermis and endodermis developed in the maturation zone, which gave way to the secondary growth zone containing a multilayer suberized periderm. Longitudinally, VvPIP isogenes exhibited strong peaks of expression in the root tip that decreased precipitously along the root length in a pattern similar to Arabidopsis (Arabidopsis thaliana) roots. In the radial orientation, expression was always greatest in interior tissues (i.e. stele, endodermis, and/or vascular tissues) for all root zones. High Lpr and aquaporin protein activity were associated with peak VvPIP expression levels in the root tip. This suggests that aquaporins play a limited role in controlling water uptake in secondary growth zones, which contradicts existing theoretical predictions. Despite having significantly lower Lpr, woody roots can constitute the vast majority of the root system surface area in mature vines and thus provide for significant water uptake potential. © 2013 American Society of Plant Biologists. All Rights Reserved.


Brodersen C.R.,University of California at Davis | Brodersen C.R.,Crops Pathology and Genetics Research Unit | McElrone A.J.,University of California at Davis | Choat B.,Australian National University | And 2 more authors.
Plant Physiology | Year: 2010

Water moves through plants under tension and in a thermodynamically metastable state, leaving the nonliving vessels that transport this water vulnerable to blockage by gas embolisms. Failure to reestablish flow in embolized vessels can lead to systemic loss of hydraulic conductivity and ultimately death. Most plants have developed a mechanism to restore vessel functionality by refilling embolized vessels, but the details of this process in vessel networks under tension have remained unclear for decades. Here we present, to our knowledge, the first in vivo visualization and quantification of the refilling process for any species using high-resolution x-ray computed tomography. Successful vessel refilling in grapevine (Vitis vinifera) was dependent on water influx from surrounding living tissue at a rate of 6 × 104 μm s-1, with individual droplets expanding over time, filling vessels, and forcing the dissolution of entrapped gas. Both filling and draining processes could be observed in the same vessel, indicating that successful refilling requires hydraulic isolation from tensions that would otherwise prevent embolism repair. Our study demonstrates that despite the presence of tensions in the bulk xylem, plants are able to restore hydraulic conductivity in the xylem. © 2010 American Society of Plant Biologists.


Kasuga T.,Crops Pathology and Genetics Research Unit | Kozanitas M.,University of California at Berkeley | Bui M.,Crops Pathology and Genetics Research Unit | Huberli D.,University of California at Berkeley | And 2 more authors.
PLoS ONE | Year: 2012

The oomycete pathogen Phytophthora ramorum is responsible for sudden oak death (SOD) in California coastal forests. P. ramorum is a generalist pathogen with over 100 known host species. Three or four closely related genotypes of P. ramorum (from a single lineage) were originally introduced in California forests and the pathogen reproduces clonally. Because of this the genetic diversity of P. ramorum is extremely low in Californian forests. However, P. ramorum shows diverse phenotypic variation in colony morphology, colony senescence, and virulence. In this study, we show that phenotypic variation among isolates is associated with the host species from which the microbe was originally cultured. Microarray global mRNA profiling detected derepression of transposable elements (TEs) and down-regulation of crinkler effector homologs (CRNs) in the majority of isolates originating from coast live oak (Quercus agrifolia), but this expression pattern was not observed in isolates from California bay laurel (Umbellularia californica). In some instances, oak and bay laurel isolates originating from the same geographic location had identical genotypes based on multilocus simples sequence repeat (SSR) marker analysis but had different phenotypes. Expression levels of the two marker genes analyzed by quantitative reverse transcription PCR were correlated with originating host species, but not with multilocus genotypes. Because oak is a nontransmissive dead-end host for P. ramorum, our observations are congruent with an epi-transposon hypothesis; that is, physiological stress is triggered on P. ramorum while colonizing oak stems and disrupts epigenetic silencing of TEs. This then results in TE reactivation and possibly genome diversification without significant epidemiological consequences. We propose the P. ramorum-oak host system in California forests as an ad hoc model for epi-transposon mediated diversification.


Brodersen C.R.,University of Florida | Mcelrone A.J.,University of Florida | Choat B.,Crops Pathology and Genetics Research Unit | Lee E.F.,Crops Pathology and Genetics Research Unit | And 2 more authors.
Plant Physiology | Year: 2013

Long-distance water transport through plant xylem is vulnerable to hydraulic dysfunction during periods of increased tension on the xylem sap, often coinciding with drought. While the effects of local and systemic embolism on plant water transport and physiology are well documented, the spatial patterns of embolism formation and spread are not well understood. Using a recently developed nondestructive diagnostic imaging tool, high-resolution x-ray computed tomography, we documented the dynamics of drought-induced embolism in grapevine (Vitis vinifera) plants in vivo, producing the first three-dimensional, highresolution, time-lapse observations of embolism spread. Embolisms formed first in the vessels surrounding the pith at stem water potentials of approximately -1.2 megapascals in drought experiments. As stem water potential decreased, embolisms spread radially toward the epidermis within sectored vessel groupings via intervessel connections and conductive xylem relays, and infrequently (16 of 629 total connections) through lateral connections into adjacent vessel sectors. Theoretical loss of conductivity calculated from the high-resolution x-ray computed tomography images showed good agreement with previously published nuclear magnetic resonance imaging and hydraulic conductivity experiments also using grapevine. Overall, these data support a growing body of evidence that xylem organization is critically important to the isolation of drought-induced embolism spread and confirm that air seeding through the pit membranes is the principle mechanism of embolism spread. © 2013 American Society of Plant Biologists. All Rights Reserved.


Travadon R.,University of California at Davis | Baumgartner K.,Crops Pathology and Genetics Research Unit
Phytopathology | Year: 2015

Pathogen adaptation to different hosts can lead to specialization and, when coupled with reproductive isolation, genome-wide differentiation and ecological speciation. We tested the hypothesis of host specialization among California populations of Eutypa lata (causal fungus of Eutypa dieback of grapevine and apricot), which is reported from >90 species. Genetic analyses of nine microsatellite loci in 182 isolates from three hosts (grapevine, apricot, and willow) at three locations were complemented by cross-inoculations on cultivated hosts grapevine and apricot to reveal patterns of host specialization. The cultivated hosts are likely more important sources of inoculum than the wild host willow, based on our findings of higher pathogen prevalence and allelic richness in grapevine and apricot. High levels of gene flow among all three hosts and locations, and no grouping by clustering analyses, suggest neither host nor geographic differentiation. Cross-inoculations revealed diversified phenotypes harboring various performance levels in grapevine and apricot, with no apparent correlation with their host of origin. Such phenotypic diversity may enable this pathogen to persist and reproduce as a generalist. Regular genetic reshuffling through sexual recombination, frequent immigration among hosts, and the lack of habitat choice in this passively dispersed fungus may prevent fixation of alleles controlling host specialization. © 2015 The American Phytopathological Society.


Shapland T.M.,University of California at Davis | McElrone A.J.,Crops Pathology and Genetics Research Unit | Snyder R.L.,University of California at Davis | Paw U K.T.,University of California at Davis
Boundary-Layer Meteorology | Year: 2012

Structure functions are used to study the dissipation and inertial range scales of turbulent energy, to parametrize remote turbulence measurements, and to characterize ramp features in the turbulent field. Ramp features are associated with turbulent coherent structures, which dominate energy and mass fluxes in the atmospheric surface layer. The analysis of structure functions to identify ramp characteristics is used in surface renewal methods for estimating fluxes. It is unclear how commonly observed different scales of ramp-like shapes (i. e., smaller ramps and spikes embedded in larger ramps) influence structure function analysis. Here, we examine the impact of two ramp-like scales on structure function analysis using artificially generated data. The range of time lags in structure function analysis was extended to include time lags typically associated with isotropic turbulence to those larger than the ramp durations. The Van Atta procedure (Arch Mech 29:161-171, 1977) has been expanded here to resolve the characteristics of two-scale ramp models. This new method accurately, and in some cases, exactly determines the amplitude and duration of both ramp scales. Spectral analysis was applied to the structure functions for a broad range of time lags to provide qualitative support for the expanded Van Atta procedure results. The theory reported here forms the foundation for novel methods of analyzing turbulent coherent structures. © 2012 Springer Science+Business Media B.V.


Shapland T.M.,University of California at Davis | McElrone A.J.,Crops Pathology and Genetics Research Unit | Snyder R.L.,University of California at Davis | Paw U K.T.,University of California at Davis
Boundary-Layer Meteorology | Year: 2012

Ramp features in the turbulent scalar field are associated with turbulent coherent structures, which dominate energy and mass fluxes in the atmospheric surface layer. Although finer scale ramp-like shapes embedded within larger scale ramp-like shapes can readily be perceived in turbulent scalar traces, their presence has largely been overlooked in the literature. We demonstrate the signature of more than one ramp scale in structure functions of the turbulent scalar field measured from above bare ground and two types of short plant canopies, using structure-function time lags ranging in scale from isotropic to larger than the characteristic coherent structures. Spectral analysis of structure functions was used to characterize different scales of turbulent structures. By expanding structure function analysis to include two ramp scales, we characterized the intermittency, duration, and surface renewal flux contribution of the smallest (i. e., Scale One) and the dominant (i. e., Scale Two) coherent structure scales. The frequencies of the coherent structure scales increase with mean wind shear, implying that both Scale One and Scale Two are shear-driven. The embedded Scale One turbulent structure scale is ineffectual in the surface-layer energy and mass transport process. The new method reported here for obtaining surface renewal-based scalar exchange works well over bare ground and short canopies under unstable conditions, effectively eliminating the α calibration for these conditions and forming the foundation for analysis over taller and more complex surfaces. © 2012 Springer Science+Business Media B.V.


Kasuga T.,Crops Pathology and Genetics Research Unit | Gijzen M.,Agriculture and Agri Food Canada
Trends in Microbiology | Year: 2013

A feature of pathogenic and invasive organisms is their adaptability when confronted with host and environmental challenges. Recent studies have demonstrated that plant pathogens rely on epigenetic processes for this purpose. Epiallelic variation of effector genes that results in evasion of host immunity is one emerging phenomenon. Another is the epigenetically induced reprogramming and diversification of transcriptional patterns by de-repression of transposable elements. These observations indicate that epigenetic control of gene expression provides a versatile means of generating phenotypic diversity that is adaptable and heritable across generations. © 2013 .


McElrone A.J.,Crops Pathology and Genetics Research Unit
Journal of visualized experiments : JoVE | Year: 2013

Advanced micrometeorological methods have become increasingly important in soil, crop, and environmental sciences. For many scientists without formal training in atmospheric science, these techniques are relatively inaccessible. Surface renewal and other flux measurement methods require an understanding of boundary layer meteorology and extensive training in instrumentation and multiple data management programs. To improve accessibility of these techniques, we describe the underlying theory of surface renewal measurements, demonstrate how to set up a field station for surface renewal with eddy covariance calibration, and utilize our open-source turnkey data logger program to perform flux data acquisition and processing. The new turnkey program returns to the user a simple data table with the corrected fluxes and quality control parameters, and eliminates the need for researchers to shuttle between multiple processing programs to obtain the final flux data. An example of data generated from these measurements demonstrates how crop water use is measured with this technique. The output information is useful to growers for making irrigation decisions in a variety of agricultural ecosystems. These stations are currently deployed in numerous field experiments by researchers in our group and the California Department of Water Resources in the following crops: rice, wine and raisin grape vineyards, alfalfa, almond, walnut, peach, lemon, avocado, and corn.


Yakabe L.E.,Crops Pathology and Genetics Research Unit | Parker S.R.,Crops Pathology and Genetics Research Unit | Kluepfel D.A.,Crops Pathology and Genetics Research Unit
Plant Disease | Year: 2012

Greater than 75% of English walnut production in the United States occurs on the walnut rootstock Juglans hindsii × J. regia 'Paradox', which is highly susceptible to infection by Agrobacterium tumefaciens. When seed were germinated and grown in the presence of A. tumefaciens, in the absence of wounding, 94% of the seedlings exhibited tumors while 89% contained systemic A. tumefaciens populations. When seedlings were wound inoculated, A. tumefaciens established endophytic populations in stem tissue and often migrated from the site of infection. Distribution of A. tumefaciens in the stem was random and may exhibit seasonal variation. A. tumefaciens populations in root tissue were more readily detected than in stem tissue and may serve as a reservoir for subsequent infection of the aerial portions of the tree. Importantly, 7% of inoculated, asymptomatic seedlings contained endophytic populations of A. tumefaciens. In all, 17% of seedlings inoculated as seeds developed galls at secondary stem-wound sites. These results provide an ecological and epidemiological foundation upon which to modify existing tree-handling practices in both nursery and orchard production environments to manage crown gall incidence.

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