Global gene regulatory networks and abiotic stress

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Drought is a major threat to food security as it results in marked yield reductions in crops such as Asian rice (Oryza sativa), the staple food of 30% of the global population. However, diverse rice cultivars display markedly different responses to drought, thereby suggesting that a comparison of the mechanisms by which different cultivars respond to drought may offer insight into critical molecular factors required for drought response. Control of such responses is mediated through gene regulatory networks (GRNs), defined by the dynamic interactions of protein transcription factors (TFs) and the regulatory regions of their target genes. Physiologically, guard cells are key regulators of the rate at which plants lose water to the atmosphere and it has been suggested that regulation of these cells may be an important determinant of drought sensitivity of diverse cultivars. Thus understanding cell type specific GRNs is a promising avenue for improving crop resistance to environmental stress.***I hypothesize that natural variation in the drought tolerance of rice cultivars is determined by genomic changes that manifest as variation in TF activity and in chromatin accessibility; studies in other species suggest that guard cell GRNs are not adequately represented in studies of whole leaves and as such I hypothesize that this may also be the case for rice. My long term goal is to define GRNs and identify transcriptional modules that regulate stomatal function in response to drought.***Specific Aims:***1) Characterize drought-responsive GRNs in diverse rice cultivars. I will integrate my transcriptome and chromatin accessibility data with publicly available rice genome sequences to identify regulatory modules associated with divergent drought response phenotypes. ***2) Characterize guard cell GRNs in response to drought. I will use high throughput and low input sequencing technologies to investigate the GRNs of isolated guard cells in response to drought.***3) Functionally characterize TFs identified in Objectives 1 and 2 and from the literature. I will use genome-editing techniques (CRISPR-cas9) to examine the roles of candidate TFs identified in Aims 1 and 2 in the drought response.***The proposed studies address the fundamental biological question of how gene regulatory networks determine an organism's capacity to respond to environment stressors. The roles of the identified candidates will be functionally assessed providing possible candidates for crop improvement. The approaches used in these studies will generate biological insight and analytical capabilities that can be applied to other crop plants and other environmental stresses. The outlined studies are feasible as I have the demonstrated expertise and collaborations necessary to complete them. The project offers unique training opportunities for HQP in systems biology using advanced experimental and computational methods. **