Bio


José Dinneny received his BS from UC Berkeley in Plant Biology and Genetics in the Department of Plant and Microbial Biology and PhD from UC San Diego working with Detlef Weigel at the Salk Institute for Biological Science and Martin Yanofsky in the Division of Biology, UCSD. His work focused on the cloning and characterization of JAGGED and NUBBIN in flower and fruit development. He then went to Duke University to do his post-doctoral studies with Philip Benfey. There he utilized Fluorescence Activated Cell Sorting (FACS) to develop the first tissue-specific map of transcriptional changes occurring during abiotic stress. José established his independent lab at the Temasek Lifesciences Laboratory (TLL) in Singapore with a joint appointment at the National University of Singapore, Department of Biological Sciences. He was an inaugural fellow of the National Research Foundation, Singapore. José moved his lab in 2011 to the Carnegie Institution for Science, Department of Plant Biology. In 2018 José joined the faculty at Stanford University in the Biology Department as an Associate Professor.

José Dinneny’s research focuses on the cellular and developmental mechanisms plants use to sense and respond to water limiting environments such as drought. He is a member of the editorial board for Plant Physiology. He currently serves on the Science Policy Committee for the American Society of Plant Biologists and is an elected member of the North American Arabidopsis Steering Committee. His work is science advocacy led to the organization of a petition to support plant biotechnology that garnered over 2,000 signatories and was published in Science. He is an HHMI-Simons Faculty Scholar and was a National Research Foundation of Singapore fellow, an NIH Ruth Kirschstein post-doctoral fellow and an HHMI predoctoral fellow. He was recognized in 2017 by Science News magazine’s 2017 SN 10: Scientists to Watch list.José is a member of the Science Policy Committee at the American Society of Plant Biologists, a elected member and Tressurer of the North American Arabidopsis Steering Committee, an Associate Editor at Plant Physiology, an HHMI-Simons Faculty Scholar and a 2017 Science News SN10 Scientists to Watch.

Academic Appointments


Honors & Awards


  • Leading Interdisciplinary Collaborations (LInC) Fellow, Stanford Woods Institute for the Environment (2018)
  • SN10: Scientists to Watch, Science News Magazine (2017)
  • Faculty Scholar, HHMI and Simons Foundation (2016)
  • National Research Foundation Fellowship, Singapore Government (2008)
  • Ruth L. Kirschstein National Research Service Award, National Institutes of Health (2005)
  • Babcock Prize, College of Natural Resources, UC Berkeley (2000)

Boards, Advisory Committees, Professional Organizations


  • Member, American Society of Plant Biologists, Science Policy Committee (2014 - 2018)
  • Treasurer, North American Arabidopsis Steering Committee (2015 - Present)
  • Associate Editor, Plant Physiology (2013 - Present)

Professional Education


  • Post-doc, Duke University, Plant Systems Biology (2008)
  • PhD, University of California, San Diego, Biology (2005)
  • BS, University of California, Berkeley, Plant Biology and Genetics (2000)

Current Research and Scholarly Interests


One of our greatest challenges in the next 50 years will be to realize a global society that is fully sustainable. Water is the most limiting resource for plant growth while agriculture uses between 70-80% of the fresh water supply. Despite its critical importance, key questions remain regarding how plants sense, transport and efficiently use water (Robbins and Dinneny, 2015). My research aims to understand plant-environment interactions using a holistic approach that emphasizes the importance of developmental pathways and molecular genetic mechanisms in guiding acclimation and homeostatic processes (Feng et al., 2016; Dinneny, 2015a). This work has led to the exploration of water-stress responses in plants at unparalleled spatial and temporal resolution (Duan et al., 2013; Geng et al., 2013; Dinneny et al., 2008), the discovery of novel adaptive mechanisms used by roots to capture water (Sebastian et al., 2016; Bao et al., 2014) and the invention of imaging methods that enable multidimensional studies of plant acclimation (Rellán-Álvarez et al., 2015). Today’s research goals focus on understanding the signaling mechanisms plants use to sense water availability and the characterization of the molecular-genetic basis for naturally occurring adaptive innovations that allow plants to survive water-limiting environments.

2018-19 Courses


Stanford Advisees


All Publications


  • Root branching toward water involves posttranslational modification of transcription factor ARF7. Science (New York, N.Y.) Orosa-Puente, B., Leftley, N., von Wangenheim, D., Banda, J., Srivastava, A. K., Hill, K., Truskina, J., Bhosale, R., Morris, E., Srivastava, M., Kumpers, B., Goh, T., Fukaki, H., Vermeer, J. E., Vernoux, T., Dinneny, J. R., French, A. P., Bishopp, A., Sadanandom, A., Bennett, M. J. 2018; 362 (6421): 1407–10

    Abstract

    Plants adapt to heterogeneous soil conditions by altering their root architecture. For example, roots branch when in contact with water by using the hydropatterning response. We report that hydropatterning is dependent on auxin response factor ARF7. This transcription factor induces asymmetric expression of its target gene LBD16 in lateral root founder cells. This differential expression pattern is regulated by posttranslational modification of ARF7 with the small ubiquitin-like modifier (SUMO) protein. SUMOylation negatively regulates ARF7 DNA binding activity. ARF7 SUMOylation is required to recruit the Aux/IAA (indole-3-acetic acid) repressor protein IAA3. Blocking ARF7 SUMOylation disrupts IAA3 recruitment and hydropatterning. We conclude that SUMO-dependent regulation of auxin response controls root branching pattern in response to water availability.

    View details for PubMedID 30573626

  • Suppression of Arabidopsis GGLT1 affects growth by reducing the L-galactose content and borate cross-linking of rhamnogalacturonan-II PLANT JOURNAL Sechet, J., Htwe, S., Urbanowicz, B., Agyeman, A., Feng, W., Ishikawa, T., Colomes, M., Kumar, K., Kawai-Yamada, M., Dinneny, J. R., O'Neill, M. A., Mortimer, J. C. 2018; 96 (5): 1036–50

    Abstract

    Boron is a micronutrient that is required for the normal growth and development of vascular plants, but its precise functions remain a subject of debate. One established role for boron is in the cell wall where it forms a diester cross-link between two monomers of the low-abundance pectic polysaccharide rhamnogalacturonan-II (RG-II). The inability of RG-II to properly assemble into a dimer results in the formation of cell walls with abnormal biochemical and biomechanical properties and has a severe impact on plant productivity. Here we describe the effects on RG-II structure and cross-linking and on the growth of plants in which the expression of a GDP-sugar transporter (GONST3/GGLT1) has been reduced. In the GGLT1-silenced plants the amount of L-galactose in side-chain A of RG-II is reduced by up to 50%. This leads to a reduction in the extent of RG-II cross-linking in the cell walls as well as a reduction in the stability of the dimer in the presence of calcium chelators. The silenced plants have a dwarf phenotype, which is rescued by growth in the presence of increased amounts of boric acid. Similar to the mur1 mutant, which also disrupts RG-II cross-linking, GGLT1-silenced plants display a loss of cell wall integrity under salt stress. We conclude that GGLT1 is probably the primary Golgi GDP-L-galactose transporter, and provides GDP-L-galactose for RG-II biosynthesis. We propose that the L-galactose residue is critical for RG-II dimerization and for the stability of the borate cross-link.

    View details for DOI 10.1111/tpj.14088

    View details for Web of Science ID 000451173000012

    View details for PubMedID 30203879

    View details for PubMedCentralID PMC6263843

  • Seeds of Science Why We Got It So Wrong on GMOs (Book Review) SCIENCE Book Review Authored by: Dinneny, J. R. 2018; 360 (6396): 1407
  • Organization out of disorder: liquid-liquid phase separation in plants. Current opinion in plant biology Cuevas-Velazquez, C. L., Dinneny, J. R. 2018; 45 (Pt A): 68–74

    Abstract

    Membraneless compartments are formed from the dynamic physical association of proteins and RNAs through liquid-liquid phase separation, and have recently emerged as an exciting new mechanism to explain the dynamic organization of biochemical processes in the cell. In this review, we provide an overview of the current knowledge of the process of phase separation in plants and other eukaryotes. We discuss specific examples of liquid-like membraneless compartments found in green plants, their composition, and the intriguing prevalence of proteins with intrinsically disordered domains. Finally, we speculate on the function of disordered proteins in regulating the formation of membraneless compartments and how their conformational flexibility may be important for molecular memory and for sensing perturbations in the physicochemical environment of the cell, particularly important processes in sessile organisms.

    View details for DOI 10.1016/j.pbi.2018.05.005

    View details for PubMedID 29859470

  • Q&A: How do gene regulatory networks control environmental responses in plants? BMC BIOLOGY Sun, Y., Dinneny, J. R. 2018; 16: 38

    Abstract

    A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana. Future studies will likely focus on how GRNs function in non-model plants and change over evolutionary time to allow for adaptation to extreme environments. This broader understanding will inform efforts to engineer GRNs to create tailored crop traits.

    View details for DOI 10.1186/s12915-018-0506-7

    View details for Web of Science ID 000429987700001

    View details for PubMedID 29642893

    View details for PubMedCentralID PMC5894133

  • Growth is required for perception of water availability to pattern root branches in plants. Proceedings of the National Academy of Sciences of the United States of America Robbins, N. E., Dinneny, J. R. 2018

    Abstract

    Water availability is a potent regulator of plant development and induces root branching through a process termed hydropatterning. Hydropatterning enables roots to position lateral branches toward regions of high water availability, such as wet soil or agar media, while preventing their emergence where water is less available, such as in air. The mechanism by which roots perceive the spatial distribution of water during hydropatterning is unknown. Using primary roots of Zea mays (maize) we reveal that developmental competence for hydropatterning is limited to the growth zone of the root tip. Past work has shown that growth generates gradients in water potential across an organ when asymmetries exist in the distribution of available water. Using mathematical modeling, we predict that substantial growth-sustained water potential gradients are also generated in the hydropatterning competent zone and that such biophysical cues inform the patterning of lateral roots. Using diverse chemical and environmental treatments we experimentally demonstrate that growth is necessary for normal hydropatterning of lateral roots. Transcriptomic characterization of the local response of tissues to a moist surface or air revealed extensive regulation of signaling and physiological pathways, some of which we show are growth-dependent. Our work supports a "sense-by-growth" mechanism governing hydropatterning, by which water availability cues are rendered interpretable through growth-sustained water movement.

    View details for PubMedID 29317538

  • The 6xABRE synthetic promoter enables the spatiotemporal analysis of ABA-mediated transcriptional regulation. Plant physiology Wu, R., Duan, L., Pruneda-Paz, J., Oh, D. H., Pound, M. P., Kay, S. A., Dinneny, J. R. 2018

    Abstract

    The water stress-associated hormone abscisic acid (ABA) acts through a well-defined signal transduction cascade to mediate downstream transcriptional events important for acclimation to stress. Although ABA signaling is known to function in specific tissues to regulate root growth, little is understood regarding the spatial pattern of ABA-mediated transcriptional regulation. Here we describe the construction and evaluation of an ABSCISIC ACID RESPONSIVE ELEMENT (ABRE)-based synthetic promoter reporter that reveals the transcriptional response of tissues to different levels of exogenous ABA and stresses. Genome-scale yeast-one-hybrid screens complemented these approaches and revealed how promoter sequence and architecture affect the recruitment of diverse transcription factors (TFs) to the ABRE. Our analysis also revealed ABA-independent activity of the ABRE-reporter under non-stress conditions, with activity being enriched at the quiescent center and stem cell niche. We show that the WUSCHEL RELATED HOMEOBOX 5 and NAC DOMAIN PROTEIN 13 TFs regulate QC/SCN expression of the ABRE-reporter, which highlights the convergence of developmental and DNA-damage signaling pathways onto this cis-element in the absence of water stress. This work establishes a tool to study the spatial pattern of ABA-mediated transcriptional regulation and a repertoire of TF-ABRE interactions that contribute to the developmental and environmental control of gene expression in roots.

    View details for DOI 10.1104/pp.18.00401

    View details for PubMedID 29884679

  • The FERONIA Receptor Kinase Maintains Cell-Wall Integrity during Salt Stress through Ca2+Signaling. Current biology : CB Feng, W., Kita, D., Peaucelle, A., Cartwright, H. N., Doan, V., Duan, Q., Liu, M. C., Maman, J., Steinhorst, L., Schmitz-Thom, I., Yvon, R., Kudla, J., Wu, H. M., Cheung, A. Y., Dinneny, J. R. 2018

    Abstract

    Cells maintain integrity despite changes in their mechanical properties elicited during growth and environmental stress. How cells sense their physical state and compensate for cell-wall damage is poorly understood, particularly in plants. Here we report that FERONIA (FER), a plasma-membrane-localized receptor kinase from Arabidopsis, is necessary for the recovery of root growth after exposure to high salinity, a widespread soil stress. The extracellular domain of FER displays tandem regions of homology with malectin, an animal protein known to bind di-glucose in vitro and important for protein quality control in the endoplasmic reticulum. The presence of malectin-like domains in FER and related receptor kinases has led to widespread speculation that they interact with cell-wall polysaccharides and can potentially serve a wall-sensing function. Results reported here show that salinity causes softening of the cell wall and that FER is necessary to sense these defects. When this function is disrupted in the fer mutant, root cells explode dramatically during growth recovery. Similar defects are observed in the mur1 mutant, which disrupts pectin cross-linking. Furthermore, fer cell-wall integrity defects can be rescued by treatment with calcium and borate, which also facilitate pectin cross-linking. Sensing of these salinity-induced wall defects might therefore be a direct consequence of physical interaction between the extracellular domain of FER and pectin. FER-dependent signaling elicits cell-specific calcium transients that maintain cell-wall integrity during salt stress. These results reveal a novel extracellular toxicity of salinity, and identify FER as a sensor of damage to the pectin-associated wall.

    View details for PubMedID 29456142

  • A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone. New phytologist Pruitt, R. N., Joe, A., Zhang, W., Feng, W., Stewart, V., Schwessinger, B., Dinneny, J. R., Ronald, P. C. 2017

    Abstract

    The biotrophic pathogen Xanthomonas oryzae pv. oryzae (Xoo) produces a sulfated peptide named RaxX, which shares similarity to peptides in the PSY (plant peptide containing sulfated tyrosine) family. We hypothesize that RaxX mimics the growth-stimulating activity of PSY peptides. Root length was measured in Arabidopsis and rice treated with synthetic RaxX peptides. We also used comparative genomic analyses and reactive oxygen species burst assays to evaluate the activity of RaxX and PSY peptides. Here we found that a synthetic sulfated RaxX derivative comprising 13 residues (RaxX13-sY), highly conserved between RaxX and PSY, induces root growth in Arabidopsis and rice in a manner similar to that triggered by PSY. We identified residues that are required for activation of immunity mediated by the rice XA21 receptor but that are not essential for root growth induced by PSY. Finally, we showed that a Xanthomonas strain lacking raxX is impaired in virulence. These findings suggest that RaxX serves as a molecular mimic of PSY peptides to facilitate Xoo infection and that XA21 has evolved the ability to recognize and respond specifically to the microbial form of the peptide.

    View details for DOI 10.1111/nph.14609

    View details for PubMedID 28556915

  • Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature plants Dietrich, D., Pang, L., Kobayashi, A., Fozard, J. A., Boudolf, V., Bhosale, R., Antoni, R., Nguyen, T., Hiratsuka, S., Fujii, N., Miyazawa, Y., Bae, T., Wells, D. M., Owen, M. R., Band, L. R., Dyson, R. J., Jensen, O. E., King, J. R., Tracy, S. R., Sturrock, C. J., Mooney, S. J., Roberts, J. A., Bhalerao, R. P., Dinneny, J. R., Rodriguez, P. L., Nagatani, A., Hosokawa, Y., Baskin, T. I., Pridmore, T. P., De Veylder, L., Takahashi, H., Bennett, M. J. 2017; 3: 17057-?

    Abstract

    Plants can acclimate by using tropisms to link the direction of growth to environmental conditions. Hydrotropism allows roots to forage for water, a process known to depend on abscisic acid (ABA) but whose molecular and cellular basis remains unclear. Here we show that hydrotropism still occurs in roots after laser ablation removed the meristem and root cap. Additionally, targeted expression studies reveal that hydrotropism depends on the ABA signalling kinase SnRK2.2 and the hydrotropism-specific MIZ1, both acting specifically in elongation zone cortical cells. Conversely, hydrotropism, but not gravitropism, is inhibited by preventing differential cell-length increases in the cortex, but not in other cell types. We conclude that root tropic responses to gravity and water are driven by distinct tissue-based mechanisms. In addition, unlike its role in root gravitropism, the elongation zone performs a dual function during a hydrotropic response, both sensing a water potential gradient and subsequently undergoing differential growth.

    View details for DOI 10.1038/nplants.2017.57

    View details for PubMedID 28481327

  • Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS genetics Feldman, M. J., Paul, R. E., Banan, D., Barrett, J. F., Sebastian, J., Yee, M. C., Jiang, H., Lipka, A. E., Brutnell, T. P., Dinneny, J. R., Leakey, A. D., Baxter, I. 2017; 13 (6): e1006841

    Abstract

    Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development.

    View details for DOI 10.1371/journal.pgen.1006841

    View details for PubMedID 28644860

    View details for PubMedCentralID PMC5507400

  • Setaria viridis: A Model for Understanding Panicoid Grass Root Systems GENETICS AND GENOMICS OF SETARIA Sebastian, J., Dinneny, J. R., Doust, A., Diao 2017; 19: 177–93
  • The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant physiology Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, C. R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R. J., Megraw, M., Meyers, B. C., Murray, J. A., Provart, N. J., Rhee, S., Smith, R., Spalding, E. P., Taylor, C., Teal, T. K., Torii, K. U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., Brady, S. M. 2017; 175 (4): 1499–1509

    View details for PubMedID 29208732

  • Understanding and engineering plant form. Seminars in cell & developmental biology Brophy, J. A., LaRue, T., Dinneny, J. R. 2017

    Abstract

    A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.

    View details for DOI 10.1016/j.semcdb.2017.08.051

    View details for PubMedID 28864344

  • Grasses suppress shoot-borne roots to conserve water during drought. Proceedings of the National Academy of Sciences of the United States of America Sebastian, J., Yee, M., Goudinho Viana, W., Rellán-Álvarez, R., Feldman, M., Priest, H. D., Trontin, C., Lee, T., Jiang, H., Baxter, I., Mockler, T. C., Hochholdinger, F., Brutnell, T. P., Dinneny, J. R. 2016; 113 (31): 8861-8866

    Abstract

    Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

    View details for DOI 10.1073/pnas.1604021113

    View details for PubMedID 27422554

    View details for PubMedCentralID PMC4978293

  • Grasses suppress shoot-borne roots to conserve water during drought PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Sebastian, J., Yee, M., Viana, W. G., Rellan-Alvarez, R., Feldman, M., Priest, H. D., Trontin, C., Lee, T., Jiang, H., Baxter, I., Mockler, T. C., Hochholdinger, F., Brutnell, T. P., Dinneny, J. R. 2016; 113 (31): 8861-8866

    Abstract

    Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

    View details for DOI 10.1073/pnas.1604021113

    View details for Web of Science ID 000380586600078

    View details for PubMedCentralID PMC4978293

  • Growing Out of Stress: The Role of Cell- and Organ-Scale Growth Control in Plant Water-Stress Responses. Plant cell Feng, W., Lindner, H., Robbins, N. E., Dinneny, J. R. 2016; 28 (8): 1769-1782

    Abstract

    Water is the most limiting resource on land for plant growth, and its uptake by plants is affected by many abiotic stresses, such as salinity, cold, heat, and drought. While much research has focused on exploring the molecular mechanisms underlying the cellular signaling events governing water-stress responses, it is also important to consider the role organismal structure plays as a context for such responses. The regulation of growth in plants occurs at two spatial scales: the cell and the organ. In this review, we focus on how the regulation of growth at these different spatial scales enables plants to acclimate to water-deficit stress. The cell wall is discussed with respect to how the physical properties of this structure affect water loss and how regulatory mechanisms that affect wall extensibility maintain growth under water deficit. At a higher spatial scale, the architecture of the root system represents a highly dynamic physical network that facilitates access of the plant to a heterogeneous distribution of water in soil. We discuss the role differential growth plays in shaping the structure of this system and the physiological implications of such changes.

    View details for DOI 10.1105/tpc.16.00182

    View details for PubMedID 27503468

  • Environmental Control of Root System Biology ANNUAL REVIEW OF PLANT BIOLOGY, VOL 67 Rellan-Alvarez, R., Lobet, G., Dinneny, J. R. 2016; 67: 619-642

    Abstract

    The plant root system traverses one of the most complex environments on earth. Understanding how roots support plant life on land requires knowing how soil properties affect the availability of nutrients and water and how roots manipulate the soil environment to optimize acquisition of these resources. Imaging of roots in soil allows the integrated analysis and modeling of environmental interactions occurring at micro- to macroscales. Advances in phenotyping of root systems is driving innovation in cross-platform-compatible methods for data analysis. Root systems acclimate to the environment through architectural changes that act at the root-type level as well as through tissue-specific changes that affect the metabolic needs of the root and the efficiency of nutrient uptake. A molecular understanding of the signaling mechanisms that guide local and systemic signaling is providing insight into the regulatory logic of environmental responses and has identified points where crosstalk between pathways occurs.

    View details for DOI 10.1146/annurev-arplant-043015-111848

    View details for Web of Science ID 000375803200025

    View details for PubMedID 26905656

  • GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems ELIFE Rellan-Alvarez, R., Lobet, G., Lindner, H., Pradier, P., Sebastian, J., Yee, M., Geng, Y., Trontin, C., LaRue, T., Schrager-Lavelle, A., Haney, C. H., Nieu, R., Maloof, J., Vogel, J. P., Dinneny, J. R. 2015; 4

    Abstract

    Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.

    View details for DOI 10.7554/eLife.07597

    View details for Web of Science ID 000373814300001

    View details for PubMedID 26287479

    View details for PubMedCentralID PMC4589753

  • Low Sugar Is Not Always Good: Impact of Specific O-Glycan Defects on Tip Growth in Arabidopsis PLANT PHYSIOLOGY Velasquez, S. M., Marzol, E., Borassi, C., Pol-Fachin, L., Ricardi, M. M., Mangano, S., Denita Juarez, S. P., Salgado Salter, J. D., Gloazzo Dorosz, J., Marcus, S. E., Knox, J. P., Dinneny, J. R., Iusem, N. D., Verli, H., Estevez, J. M. 2015; 168 (3): 808-U918

    View details for DOI 10.1104/pp.114.255521

    View details for Web of Science ID 000359307600007

    View details for PubMedID 25944827

    View details for PubMedCentralID PMC4741341

  • The divining root: moisture-driven responses of roots at the micro- and macro-scale JOURNAL OF EXPERIMENTAL BOTANY Robbins, N. E., Dinneny, J. R. 2015; 66 (8): 2145-2154

    Abstract

    Water is fundamental to plant life, but the mechanisms by which plant roots sense and respond to variations in water availability in the soil are poorly understood. Many studies of responses to water deficit have focused on large-scale effects of this stress, but have overlooked responses at the sub-organ or cellular level that give rise to emergent whole-plant phenotypes. We have recently discovered hydropatterning, an adaptive environmental response in which roots position new lateral branches according to the spatial distribution of available water across the circumferential axis. This discovery illustrates that roots are capable of sensing and responding to water availability at spatial scales far lower than those normally studied for such processes. This review will explore how roots respond to water availability with an emphasis on what is currently known at different spatial scales. Beginning at the micro-scale, there is a discussion of water physiology at the cellular level and proposed sensory mechanisms cells use to detect osmotic status. The implications of these principles are then explored in the context of cell and organ growth under non-stress and water-deficit conditions. Following this, several adaptive responses employed by roots to tailor their functionality to the local moisture environment are discussed, including patterning of lateral root development and generation of hydraulic barriers to limit water loss. We speculate that these micro-scale responses are necessary for optimal functionality of the root system in a heterogeneous moisture environment, allowing for efficient water uptake with minimal water loss during periods of drought.

    View details for DOI 10.1093/jxb/eru496

    View details for PubMedID 25617469

  • Traversing organizational scales in plant salt-stress responses CURRENT OPINION IN PLANT BIOLOGY Dinneny, J. R. 2015; 23: 70-75

    Abstract

    Modern society has developed in large part due to our ability to reliably grow plants for food and renewable resources. Predicted increases in environmental variability will impact agricultural productivity and may have extensive secondary effects on the stability of our society. Thus, a concerted effort to understand plant response strategies to stress is needed. High salinity is an agriculturally important environmental stress and generates complex effects on the physiology of the plant. The abiotic-stress-associated hormone, abscisic acid (ABA), mediates a major component of this response. I highlight recent work studying salt-stress responses at different spatial and organizational scales from the action of ABA in specific cell types to global networks of proteins that predict critical regulatory events during acclimation.

    View details for DOI 10.1016/j.pbi.2014.10.009

    View details for Web of Science ID 000349880900011

    View details for PubMedID 25449729

  • Salt-stress regulation of root system growth and architecture in Arabidopsis seedlings. Methods in molecular biology (Clifton, N.J.) Duan, L., Sebastian, J., Dinneny, J. R. 2015; 1242: 105-122

    Abstract

    In order to acclimate to the soil environment, plants need to constantly optimize their root system architecture for efficient resource uptake. Roots are highly sensitive to changes in their surrounding environment and root system responses to a stress such as salinity and drought can be very dynamic and complex in nature. These responses can be manifested differentially at the cellular, tissue, or organ level and between the types of roots in a root system. Therefore, various approaches must be taken to quantify and characterize these responses. In this chapter, we review methods to study basic root growth traits, such as root length, cell cycle activity and meristem size, cell shape and size that form the basis for the emergent properties of the root system. Methods for the detailed analysis of lateral root initiation and postemergence growth are described. Finally, several live-imaging systems, which allow for dynamic imaging of the root, will be explored. Together these tools provide insight into the regulatory steps that sculpt the root system upon environmental change and can be used as the basis for the evaluation of genetic variation affecting these pathways.

    View details for DOI 10.1007/978-1-4939-1902-4_10

    View details for PubMedID 25408448

  • Beyond the Barrier: Communication in the Root through the Endodermis PLANT PHYSIOLOGY Robbins, N. E., Trontin, C., Duan, L., Dinneny, J. R. 2014; 166 (2): 551-559

    Abstract

    The root endodermis is characterized by the Casparian strip and by the suberin lamellae, two hydrophobic barriers that restrict the free diffusion of molecules between the inner cell layers of the root and the outer environment. The presence of these barriers and the position of the endodermis between the inner and outer parts of the root require that communication between these two domains acts through the endodermis. Recent work on hormone signaling, propagation of calcium waves, and plant-fungal symbiosis has provided evidence in support of the hypothesis that the endodermis acts as a signaling center. The endodermis is also a unique mechanical barrier to organogenesis, which must be overcome through chemical and mechanical cross talk between cell layers to allow for development of new lateral organs while maintaining its barrier functions. In this review, we discuss recent findings regarding these two important aspects of the endodermis.

    View details for DOI 10.1104/pp.114.244871

    View details for Web of Science ID 000345071500010

    View details for PubMedCentralID PMC4213087

  • Plant roots use a patterning mechanism to position lateral root branches toward available water PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bao, Y., Aggarwal, P., Robbins, N. E., Sturrock, C. J., Thompson, M. C., Tan, H. Q., Tham, C., Duan, L., Rodriguez, P. L., Vernoux, T., Mooney, S. J., Bennett, M. J., Dinneny, J. R. 2014; 111 (25): 9319-9324

    Abstract

    The architecture of the branched root system of plants is a major determinant of vigor. Water availability is known to impact root physiology and growth; however, the spatial scale at which this stimulus influences root architecture is poorly understood. Here we reveal that differences in the availability of water across the circumferential axis of the root create spatial cues that determine the position of lateral root branches. We show that roots of several plant species can distinguish between a wet surface and air environments and that this also impacts the patterning of root hairs, anthocyanins, and aerenchyma in a phenomenon we describe as hydropatterning. This environmental response is distinct from a touch response and requires available water to induce lateral roots along a contacted surface. X-ray microscale computed tomography and 3D reconstruction of soil-grown root systems demonstrate that such responses also occur under physiologically relevant conditions. Using early-stage lateral root markers, we show that hydropatterning acts before the initiation stage and likely determines the circumferential position at which lateral root founder cells are specified. Hydropatterning is independent of endogenous abscisic acid signaling, distinguishing it from a classic water-stress response. Higher water availability induces the biosynthesis and transport of the lateral root-inductive signal auxin through local regulation of tryptophan aminotransferase of Arabidopsis 1 and PIN-formed 3, both of which are necessary for normal hydropatterning. Our work suggests that water availability is sensed and interpreted at the suborgan level and locally patterns a wide variety of developmental processes in the root.

    View details for DOI 10.1073/pnas.1400966111

    View details for Web of Science ID 000337760600071

    View details for PubMedCentralID PMC4078807

  • Methods to Promote Germination of Dormant Setaria viridis Seeds PLOS ONE Sebastian, J., Wong, M. K., Tang, E., Dinneny, J. R. 2014; 9 (4)

    Abstract

    Setaria viridis has recently emerged as a promising genetic model system to study diverse aspects of monocot biology. While the post-germination life cycle of S. viridis is approximately 8 weeks long, the prolonged dormancy of freshly harvested seeds can more than double the total time required between successive generations. Here we describe methods that promote seed germination in S. viridis. Our results demonstrate that treating S. viridis seeds with liquid smoke or a GA3 and KNO3 solution improves germination rates to 90% or higher even in seeds that are 6 days post-harvest with similar results obtained whether seeds are planted in soil or on gel-based media. Importantly, we show that these treatments have no significant effect on the growth of the adult plant. We have tested these treatments on diverse S. viridis accessions and show variation in their response. The methods described here will help advance research using this model grass species by increasing the pace at which successive generations of plants can be analyzed.

    View details for DOI 10.1371/journal.pone.0095109

    View details for Web of Science ID 000335226500058

    View details for PubMedID 24748008

    View details for PubMedCentralID PMC3991590

  • Circular RNA is expressed across the eukaryotic tree of life. PloS one Wang, P. L., Bao, Y., Yee, M., Barrett, S. P., Hogan, G. J., Olsen, M. N., Dinneny, J. R., Brown, P. O., Salzman, J. 2014; 9 (6)

    Abstract

    An unexpectedly large fraction of genes in metazoans (human, mouse, zebrafish, worm, fruit fly) express high levels of circularized RNAs containing canonical exons. Here we report that circular RNA isoforms are found in diverse species whose most recent common ancestor existed more than one billion years ago: fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), and protists (Plasmodium falciparum and Dictyostelium discoideum). For all species studied to date, including those in this report, only a small fraction of the theoretically possible circular RNA isoforms from a given gene are actually observed. Unlike metazoans, Arabidopsis, D. discoideum, P. falciparum, S. cerevisiae, and S. pombe have very short introns (∼ 100 nucleotides or shorter), yet they still produce circular RNAs. A minority of genes in S. pombe and P. falciparum have documented examples of canonical alternative splicing, making it unlikely that all circular RNAs are by-products of alternative splicing or 'piggyback' on signals used in alternative RNA processing. In S. pombe, the relative abundance of circular to linear transcript isoforms changed in a gene-specific pattern during nitrogen starvation. Circular RNA may be an ancient, conserved feature of eukaryotic gene expression programs.

    View details for DOI 10.1371/journal.pone.0090859

    View details for PubMedID 24609083

  • A gateway with a guard: How the endodermis regulates growth through hormone signaling PLANT SCIENCE Dinneny, J. R. 2014; 214: 14-19

    Abstract

    The endodermis is a defining feature of plant roots and is most widely studied as a differentially permeable barrier limiting solute uptake from the soil into the vascular stream. Recent work has revealed that this inner cell layer is also an important signaling center for hormone-mediated control of growth. Auxin, gibberellic acid, abscisic acid and strigalactones all appear to depend on the endodermis to regulate root biology and point to this cell type as having important inter-cell layer regulatory activity, as well. In this review I discuss recent work detailing the importance of the endodermis in growth control and how this function is affected during responses to the environment.

    View details for DOI 10.1016/j.plantsci.2013.09.009

    View details for Web of Science ID 000328725700003

    View details for PubMedID 24268159

  • Circular RNA Is Expressed across the Eukaryotic Tree of Life. PloS one Wang, P. L., Bao, Y., Yee, M., Barrett, S. P., Hogan, G. J., Olsen, M. N., Dinneny, J. R., Brown, P. O., Salzman, J. 2014; 9 (3)

    Abstract

    An unexpectedly large fraction of genes in metazoans (human, mouse, zebrafish, worm, fruit fly) express high levels of circularized RNAs containing canonical exons. Here we report that circular RNA isoforms are found in diverse species whose most recent common ancestor existed more than one billion years ago: fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), and protists (Plasmodium falciparum and Dictyostelium discoideum). For all species studied to date, including those in this report, only a small fraction of the theoretically possible circular RNA isoforms from a given gene are actually observed. Unlike metazoans, Arabidopsis, D. discoideum, P. falciparum, S. cerevisiae, and S. pombe have very short introns (∼ 100 nucleotides or shorter), yet they still produce circular RNAs. A minority of genes in S. pombe and P. falciparum have documented examples of canonical alternative splicing, making it unlikely that all circular RNAs are by-products of alternative splicing or 'piggyback' on signals used in alternative RNA processing. In S. pombe, the relative abundance of circular to linear transcript isoforms changed in a gene-specific pattern during nitrogen starvation. Circular RNA may be an ancient, conserved feature of eukaryotic gene expression programs.

    View details for DOI 10.1371/journal.pone.0090859

    View details for PubMedID 24609083

    View details for PubMedCentralID PMC3946582

  • A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology FRONTIERS IN PLANT SCIENCE Emami, S., Yee, M., Dinneny, J. R. 2013; 4

    Abstract

    Tools that allow for rapid, accurate and inexpensive assembly of multi-component combinatorial libraries of DNA for transformation into plants will accelerate the progress of synthetic biology research. Recent innovations in molecular cloning methods has vastly expanded the repertoire with which plant biologists can engineer a transgene. Here we describe a new set of binary vectors for use in Agrobacterium-mediated plant transformation that utilizes the Golden-Gate Cloning approach. Our optimized protocol facilitates the rapid and inexpensive generation of multi-component transgenes for later introduction into plants.

    View details for DOI 10.3389/fpls.2013.00339

    View details for Web of Science ID 000331109300001

    View details for PubMedID 24032037

    View details for PubMedCentralID PMC3759027

  • A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis PLANT CELL Geng, Y., Wu, R., Wee, C. W., Xie, F., Wei, X., Chan, P. M., Tham, C., Duan, L., Dinneny, J. R. 2013; 25 (6): 2132-2154

    Abstract

    Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these events is regulated. Here, we explored the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis thaliana seedling root to a rapid change in salinity. Using live-imaging analysis, we show that growth is dynamically regulated with a period of quiescence followed by recovery then homeostasis. Through the use of a new high-resolution spatio-temporal transcriptional map, we identify the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action, and link the activity of these pathways to the regulation of specific phases of growth. We use tissue-specific approaches to suppress the abscisic acid (ABA) signaling pathway and demonstrate that ABA likely acts in select tissue layers to regulate spatially localized transcriptional programs and promote growth recovery. Finally, we show that salt also regulates many tissue-specific and time point-specific transcriptional responses that are expected to modify water transport, Casparian strip formation, and protein translation. Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment.

    View details for DOI 10.1105/tpc.113.112896

    View details for Web of Science ID 000322371500020

    View details for PubMedID 23898029

    View details for PubMedCentralID PMC3723617

  • Endodermal ABA Signaling Promotes Lateral Root Quiescence during Salt Stress in Arabidopsis Seedlings PLANT CELL Duan, L., Dietrich, D., Ng, C. H., Chan, P. M., Bhalerao, R., Bennett, M. J., Dinneny, J. R. 2013; 25 (1): 324-341

    Abstract

    The endodermal tissue layer is found in the roots of vascular plants and functions as a semipermeable barrier, regulating the transport of solutes from the soil into the vascular stream. As a gateway for solutes, the endodermis may also serve as an important site for sensing and responding to useful or toxic substances in the environment. Here, we show that high salinity, an environmental stress widely impacting agricultural land, regulates growth of the seedling root system through a signaling network operating primarily in the endodermis. We report that salt stress induces an extended quiescent phase in postemergence lateral roots (LRs) whereby the rate of growth is suppressed for several days before recovery begins. Quiescence is correlated with sustained abscisic acid (ABA) response in LRs and is dependent upon genes necessary for ABA biosynthesis, signaling, and transcriptional regulation. We use a tissue-specific strategy to identify the key cell layers where ABA signaling acts to regulate growth. In the endodermis, misexpression of the ABA insensitive1-1 mutant protein, which dominantly inhibits ABA signaling, leads to a substantial recovery in LR growth under salt stress conditions. Gibberellic acid signaling, which antagonizes the ABA pathway, also acts primarily in the endodermis, and we define the crosstalk between these two hormones. Our results identify the endodermis as a gateway with an ABA-dependent guard, which prevents root growth into saline environments.

    View details for DOI 10.1105/tpc.112.107227

    View details for Web of Science ID 000315572400025

    View details for PubMedID 23341337

    View details for PubMedCentralID PMC3584545