Integrated Phenomic and Transcriptomic Network Analysis Reveals Key Regulators of Drought Tolerance in OsC2H2-Edited Rice

Abstract

Drought poses a major threat to rice ( Oryza sativa ) production, causing severe yield losses and jeopardizing yield stability. C2H2 Jumonji domain–containing zinc-finger proteins play diverse roles in plant growth, development, and abiotic-stress responses through regulation of gene expression and chromatin-associated processes. However, the role of many rice JMJ proteins in drought responses remains unclear. In this study, we generated CRISPR/Cas9-mediated OsC2H2 -edited rice plants and investigated drought-associated physiological and molecular responses using integrated phenotyping and transcriptome analyses. Drought stress was imposed by controlled water limitation, followed by re-watering to evaluate drought tolerance and recovery. The edited lines exhibited higher survival rates, maintained higher soil moisture levels, and showed reduced irrigation demand compared with the wild type. RNA-seq revealed pronounced late-stage drought-responsive expression patterns, and integration of transcriptome and image-derived phenotypic data using weighted gene co-expression network analysis identified drought-associated modules linked to morphology-related traits and hub genes including LEA3 , Rab21 , OAT , and bZIP12 . These findings provide insight into drought-responsive networks associated with OsC2H2 disruption and identify candidate genes for future studies of drought adaptation in rice.