About

While plants are sedentary, their bodies often traverse long distances as they explore their local environment in search of resources necessary for growth. The biology of root systems is governed by both micro-scale and systemic signaling that allows the plant to integrate these complex variables into growth and branching decisions that ultimately determine the efficiency resources are captured. Research in the Dinneny lab is aimed at understanding the response of roots to water-limiting conditions and is exploring this process at different organizational scales from the individual cell type to the level of the whole plant.

Research topics

• Computer Science
• Biology
• Botany
• Biochemistry
• Cell biology
• Computational biology
• Sociology
• Genetics
• Engineering
• Political Science
• Horticulture
• Chemistry
• Nanotechnology
• Biotechnology
• Materials science
• Biochemical engineering
• Engineering ethics
• Neuroscience
• Biophysics
• Public relations
• Ecology

Selected publications

• Shaping with water: linking moisture perception to development in plant roots

  BMC Biology · 2026-01-17

  articleOpen accessSenior author

  Water is the most limiting resource for plant growth and development. Heterogeneity in the environmental distribution of water requires plants to direct root growth toward water and to avoid investing resources in areas that lack water. Roots use hydrosignaling pathways-hydrotropism, hydropatterning, and xerobranching-to sense and respond to water availability. While molecular mechanisms of water perception remain unclear, recent studies suggest that organ-level processes using proxies like ethylene help detect spatial water patterns. This review summarizes advances in hydrosignaling and identifies key knowledge gaps to address how plants sense water. Understanding these processes will guide strategies to improve root water capture for sustainable agriculture.

  PublisherDOI

• BPS2026 – Correlating physiology and structure with fluorescent biosensors and cryo-ET

  Biophysical Journal · 2026-02-01

  article
  PublisherDOI

• Rhizobacterial Biosensors Spatially Map Natural and Engineered Sucrose Exudation

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-16

  articleOpen accessSenior author

  Abstract Root exudation mediates the delivery of plant primary and secondary metabolites into soil, where they regulate plant–microbe interactions and terrestrial carbon cycling. Conventional exudate analyses quantify total root-released carbon yet obscure the spatial origin and rhizosphere influence of individual compounds. Here, we develop a rhizobacterial biosensor platform, named Suc-MAPP, to map local exudate profiles along the surface of colonized root tissues. Focusing on sucrose, we engineered sfGFP-based, sucrose-responsive gene circuits in Pseudomonas putida KT2440 for live imaging of exudate concentrations in the micromolar range. These biosensors reveal spatially structured sucrose exudation patterns across eudicots and monocots and implicate photoassimilated source–sink dynamics as a major determinant. We further apply this platform to phenotype exudation modulated by synthetic gene circuitry in Arabidopsis thaliana , identifying genetic design rules for graded sucrose release and quantifying how engineered export sculpts rhizosphere assembly of a defined bacterial community. Together, these results establish programmable rhizobacterial biosensors as tools to spatially resolve plant–environment carbon exchange in situ and provide a framework for extending this approach to diverse exudate targets.

  PublisherDOI

• Moisture-responsive root-branching pathways identified in diverse maize breeding germplasm

  Science · 2025-02-06 · 23 citations

  articleOpen accessSenior authorCorresponding

  Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by root tips, leading to the patterning of new root branches toward available water in a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis in crop plants. Here, we developed an assay to measure hydropatterning in maize and revealed substantial differences between tropical/subtropical and temperate maize breeding germplasm that likely resulted from divergent selection. Genetic analysis of hydropatterning confirmed the regulatory role of auxin and revealed that the gaseous hormone ethylene locally inhibits root branching from air-exposed tissues. Our results demonstrate how distinct signaling pathways translate spatial patterns of water availability to developmental programs that determine root architecture.

  PublisherDOI

• Cellulose Synthase Complexes and Remorins Mediate Stress Resilience Through Cell Wall-Plasma Membrane Attachments

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-02 · 2 citations

  preprintOpen accessSenior author

  The outer cell surface of an organism is the frontline for detecting and responding to environmental stimuli. In plants, this interface consists of the plasma membrane that lies beneath the cell wall and remains associated with it through attachment sites. These wall-membrane attachments become evident upon hyperosmotic shock, when severe water loss causes the membrane to retract from the wall. Despite their long-standing observation, the molecular identity and function of these attachments remain poorly understood. Here, we identified two nanodomain-mediated mechanisms governing wall-membrane attachments: one dependent on the Cellulose Synthase Complex (CSC), whose density at the plasma membrane positively correlates with resistance to hyperosmotic stress, and the other on REMORIN (REM), which acts antagonistically to the CSC mechanism. Using proximity-labeling proteomics, we identified SHOU4/4L as REM-associated proteins that mediate this antagonism. Together, our findings reveal how membrane nanodomains pattern wall-membrane attachments to mediate plant cell resilience under water stress.

  PublisherOA PDFDOI

• Plant biology: Soil compaction rewires gene expression across root cell types

  Current Biology · 2025-07-01

  articleOpen accessSenior author

  Soil compaction affects crop productivity by limiting root growth. A recent single-cell transcriptomic study in rice roots uncovers plant responses to compaction stress through cell type-specific reprogramming of nutrient transport, cell wall remodeling, and ABA-triggered barrier formation.

  PublisherDOI

• Moisture-responsive root-branching pathways identified in diverse maize breeding germplasm

  UNC Libraries · 2025-10-15

  articleOpen access

  Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by root tips, leading to the patterning of new root branches toward available water in a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis in crop plants. Here, we developed an assay to measure hydropatterning in maize and revealed substantial differences between tropical/subtropical and temperate maize breeding germplasm that likely resulted from divergent selection. Genetic analysis of hydropatterning confirmed the regulatory role of auxin and revealed that the gaseous hormone ethylene locally inhibits root branching from air-exposed tissues. Our results demonstrate how distinct signaling pathways translate spatial patterns of water availability to developmental programs that determine root architecture.

  PublisherDOI

• Rooting for survival: how plants tackle a challenging environment through a diversity of root forms and functions

  PLANT PHYSIOLOGY · 2024-12-05 · 43 citations

  reviewOpen accessSenior author

  The current climate crisis has global impacts and will affect the physiology of plants across every continent. Ensuring resilience of our agricultural and natural ecosystems to the environmental stresses imposed by climate change will require molecular insight into the adaptations employed by a diverse array of plants. However, most current studies continue to focus on a limited set of model species or crops. Root systems are particularly understudied even though their functions in water and nutrient uptake are likely pivotal for plant stress resilience and sustainable agriculture. In this review, we highlight anatomical adaptations in roots that enable plant survival in different ecological niches. We then present the current state of knowledge for the molecular underpinnings of these adaptations. Finally, we identify areas where future research using a biodiversity approach can fill knowledge gaps necessary for the development of climate-resilient crops of the future.

  PublisherOA PDFDOI

• Discovering Innovations in Stress Tolerance through Comparative Gene Regulatory Network Analysis and Cell-Type Specific Expression Maps (Final Technical Report with Cover Page)

  2024-10-17

  reportOpen access1st authorCorresponding

  Through this grant, we developed a comparative framework to elucidate the mechanisms behind variations in environmental stress responses among a diverse group of species within the Brassicaceae family. Our focus was on the differences in physiological and transcriptomic responses to abscisic acid (ABA), a hormone associated with water stress. We examined the differential growth responses of four Brassicaceae species, finding that most exhibited reduced root growth correlated with smaller meristem size. In contrast, Schrenkiella parvula showed accelerated growth due to increased root cell elongation. We employed RNA sequencing to analyze the transcriptional responses to ABA across these species, and innovative bioinformatics techniques were used to pinpoint biological pathways with significant divergence. Additionally, we utilized DAP-seq to map the gene regulatory networks associated with ABAresponsive transcription factors, revealing that variations in the regulation of growth hormone biosynthesis play a critical role in the distinct ABA effects on root growth among the species. This research sets a new standard for comparative physiology by integrating comparative genomics and transcriptomics to uncover pathway divergences.

  PublisherDOI

• Maize genetic diversity identifies moisture-dependent root-branch signaling pathways

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-27 · 2 citations

  preprintOpen accessSenior author

  Abstract Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by root tips leading to the patterning of new root branches towards available water, a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis in crops plants. Here, we develop an assay to measure hydropatterning in maize and reveal substantial differences between tropical/subtropical and temperate maize breeding germplasm that likely resulted from divergent selection. Genetic dissection of hydropatterning confirmed the regulatory role of auxin and revealed that the gaseous hormone ethylene acts to locally inhibit root branching from air-exposed tissues. These findings demonstrate the crop relevance of hydropatterning and establish its genetic basis.

  PublisherOA PDFDOI

Recent grants

• Collaborative Research: Salt-stress regulation of spatiotemporal gene expression patterns in the Arabidopsis root

  NSF · $506k · 2012–2016

• Signaling in cell expansion and morphogenesis

  NIH · $1.4M · 2017–2023

• Signaling in cell expansion and morphogenesis

  NIH · $467k · 2017–2021

Frequent coauthors

• Alexandra J. Dickinson

  University of California, San Diego

  62 shared

• Lina Duan

  Stanford University

  59 shared

• Philip N. Benfey

  Duke University

  51 shared

• Therese LaRue

  Carnegie Institution for Science

  41 shared

• Rui Wu

  Xiamen University

  36 shared

• Heike Lindner

  University of Bern

  35 shared

• Moisés Expósito‐Alonso

  Carnegie Institution for Science

  32 shared

• Muh‐Ching Yee

  Stanford University

  31 shared

Labs

• Dinneny labPI

Education

• Ph.D., Plant Biology

  Stanford University

  2009

• B.S., Botany

  University of California, Davis

  2003

Awards & honors

• HHMI Investigator (2024)
• Chan Zuckerberg Biohub Investigator
• AAAS Fellow
• HHMI-Simons Faculty Scholar
• National Research Foundation of Singapore fellow