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The datasets (PSGFS_compiled_data_2022.xlsx, PSGFS_compiled_data_2023 and PSGFS_compiled_data_2024.xlsx) were collected by undergraduate students during the time they participated in the Plant Science for Global Food Security (PSGFS) program in summers 2022, 2023 and 2024 at the International Rice Research Institute (IRRI; Los Baños, Philippines). The PSGFS program is an initiative funded by the National Science Foundation (Grant: NSF IRES #2106718) and led by Diane Wang and Gary Burniske of Purdue University and Amelia Henry and Anilyn Maningas of IRRI. Purdue University PhD student, To-Chia Ting, assisted in compiling these datasets.  The explanation of each worksheet in a excel file could be found in the associated word files (PSGFS_README_2022.doc, PSGFS_README_2023.doc and PSGFS_README_2024.doc). PDF files of the presentations given by the students are also provided and compressed in the Student_presentation_2022.zip, Student_presentation_2023.zip and Student_presentation_2024.zip file. File names of the presentations are composed of worksheet names and students’ last names. 

PSGFS_compiled_data_2022.xlsx contains datasets collected by eight undergraduate students during the time they participated in the Plant Science for Global Food Security (PSGFS) program in Summer 2022 at the International Rice Research Institute (IRRI; Los Baños, Philippines). The PSFGS program is an initiative funded by the National Science Foundation (Grant: NSF IRES #2106718) and led by Diane Wang and Gary Burniske of Purdue University and Amelia Henry and Anilyn Maningas of IRRI. Purdue University PhD student, To-Chia Ting, assisted in compiling these datasets. </p>  </p> The explanation of each worksheet in PSGFS_compiled_data_2022.xlsx could be found at the README.doc. PDF files of the presentations given by the eight students are also provided and compressed in the Student_presentation_PDFs.zip file. File names of the presentations are composed of worksheet names and students’ last names. </p> Grants: NSF IRES, grant number: 2106718 

Nitrogen (N) and Water (W) - two resources critical for crop productivity – are becoming increasingly limited in soils globally. To address this issue, we aim to uncover the gene regulatory networks (GRNs) that regulate nitrogen use efficiency (NUE) - as a function of water availability - in Oryza sativa, a staple for 3.5 billion people. In this study, we infer and validate GRNs that correlate with rice NUE phenotypes affected by N-by-W availability in the field. We did this by exploiting RNA-seq and crop phenotype data from 19 rice varieties grown in a 2x2 N-by-W matrix in the field. First, to identify gene-to-NUE field phenotypes, we analyzed these datasets using weighted gene co-expression network analysis (WGCNA). This identified two network modules ("skyblue" & "grey60") highly correlated with NUE grain yield (NUEg). Next, we focused on 90 TFs contained in these two NUEg modules and predicted their genome-wide targets using the N-and/or-W response datasets using a random forest network inference approach (GENIE3). Next, to validate the GENIE3 TF→target gene predictions, we performed Precision/Recall Analysis (AUPR) using nine datasets for three TFs validated in planta . This analysis sets a precision threshold of 0.31, used to "prune" the GENIE3 network for high-confidence TF→target gene edges, comprising 88 TFs and 5,716 N-and/or-W response genes. Next, we ranked these 88 TFs based on their significant influence on NUEg target genes responsive to N and/or W signaling. This resulted in a list of 18 prioritized TFs that regulate 551 NUEg target genes responsive to N and/or W signals. We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. Our results show that OsbZIP23 and Oshox22, known regulators of drought tolerance, also coordinate W-responses with NUEg. This validated network can aid in developing/breeding rice with improved yield on marginal, low N-input, drought-prone soils. 

Abstract Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic and antagonistic effects on key plant traits, such as root architecture and stomatal aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N metabolism affect drought responses, and vice versa. Specifically, perturbing key N signaling genes may lead to changes in drought-responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help to develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.