Gene regulatory networks governing rice yield and grain quality under high-day and high-night temperature stress

The yield and quality of rice face significant threats from rising global temperatures. This study compared the effects between the stage-specific high day temperature (HDT) and high night temperature (HNT) initiated either during the flowering (S1) or early seed development (S2) with 10 (S1-10, S2-10) and 20 days (S1-20, S2-20) of stress durations. We found that HDT severely reduced yield, while HNT significantly degraded grain quality. Global transcriptome profiling revealed dynamic gene regulatory networks with altered metabolic priorities depending on the duration and timing of heat stress, showing co-expression modules involved in cell wall organization, protein folding, and carbohydrate metabolism. We also uncovered both ubiquitous and seed-specific heat-responsive genes conserved across land plants and earlier plant species. Further, we pinpointed key transcription factors, including OPAQUE3 proteins with specific alleles reducing chalkiness and increasing grain number under HNT stress. Our results provide genomic, transcriptomic, and varietal targets to be prioritized in climate-smart breeding programs that meet diverse consumer demands.