Understanding Gene Expression Responses to the Environment in Tomato Roots at the Cell Type and Tissue-Specific Level

Roots mediate plant interactions with the environment by physically anchoring plants into the soil, taking up water and nutrients, and responding dynamically to environmental stimuli through changes in gene expression. During this century, rising atmospheric CO₂ concentrations and increasingly extreme precipitation conditions will significantly affect plant development and physiology, thus challenging agricultural production. Critical to understanding and improving whole plant responses to these environmental stimuli is understanding root responses at the molecular level. Using domesticated tomato (Solanum lycopersicum, cv M82) and a wild Solanum species (S. pennellii) as models, we are investigating the effects of environmental changes including drought, flooding and elevated atmospheric CO₂ on the root transcriptome from the cell type-specific to the tissue level. In order to investigate the effects of water stresses on cell type-specific transcription and translation, a library of promoters that drive cell type-specific expression in tomato roots has been generated and optimized vectors have been designed for use in the INTACT (Isolation of Nuclei TAgged in specific Cell Types) and TRAP (Translating Ribosome Affinity Purification) protocols. To understand root responses to elevated atmospheric CO₂, RNAseq libraries were prepared from whole roots and shoots of domesticated and wild tomato seedlings grown at ambient and elevated CO₂, and differential expression was analyzed in each tissue and species in response to elevated CO₂. This presentation will discuss development of molecular tools and methodologies for cell type-specific analysis, and present differential expression results for tissue level effects of elevated atmospheric CO₂.