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Drought and flooding responses of tomato root cell types
Extreme precipitation patterns – droughts and flooding – are increasing with climate change. Plant development is a plastic process affected by environmental cues, and different plants respond to these water stresses differently. In order to maintain or improve agricultural yield it is critical to understand how crop species regulate or modify their development in order to acclimate to unfavorable environments. Here we describe how different tomato root cell types respond to drought and flooding.
We have developed a marker line resource to study cell type-specific gene expression in cultivated tomato Solanum lycopersicum cv. M82 and in the wild drought-tolerant species S. pennellii. This resource utilizes eleven different cell and tissue type-specific promoters and two different transgenic tags; a nuclear-envelope tag for Isolation of Nuclei Tagged in specific Cell-Types (INTACT) and a polysome tag for Translating Ribosome Affinity Purification (TRAP). We have used these techniques to isolate nuclei and polysomes in cell type-specific fashion and to subsequently profile three different levels of regulation of gene expression: 1) the nuclear chromatin accessibility, 2) the nuclear transcriptome and 3) the ribosomal transcriptome (“translatome”).
Firstly, we generated a gene expression atlas of plate-grown tomato roots to elucidate the cell type-specific gene expression patterns in a strictly controlled environment. For example, we identified candidate genes and candidate regulatory mechanisms for the identity and development of exodermis, a cell type that functions as a barrier to protect the root, but previously transcriptionally uncharacterized.
Secondly, we elucidated how tomato roots develop in response to drought and flooding. We characterized root phenotypic changes in S. lycopersicum cv. M82 and S. pennellii in response to long-term drought and waterlogging. Observed changes include increased suberization of the exodermis in S. lycopersicum in response to drought, protecting the root against water loss. Interestingly, the drought-tolerant S. pennellii has a constitutively suberized exodermis. In response to waterlogging, S. lycopersicum forms more adventitious hypocotyl-derived roots that have increased number of cortex layers interspersed with larger intercellular area, increasing the porosity and potentially allowing diffusion of air to the root. We profiled the gene expression patterns of cortex and exodermis from these roots to understand how these changes to cell type development in flooding and drought are regulated.
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