The phytochrome-interacting factor PIL13 enhances water use efficiency under fluctuating light and drought resilience in rice and soybean.

In natural environments, fluctuating light (FL) conditions significantly influence plant growth by modulating the balance between photosynthesis and water loss through stomata, quantified as the intrinsic water use efficiency under fluctuating light (iWUE). This effect is particularly pronounced under drought stress (FL-DS). To elucidate the genetic basis of stomatal responses to FL-DS, we analyzed iWUE variations across 206 rice accessions and identified OsPIL13, a phytochrome-interacting factor, as a key gene associated with iWUE through genome-wide association studies. Functional validation revealed that overexpressing OsPIL13 in rice (WYG7) and its homolog in soybean (DN50) enhanced iWUE by 13% and 15%, respectively, under FL-DS, demonstrating its conserved role across species. Conversely, knockout of OsPIL13 or mutation of a causal SNP in its promoter reduced iWUE by at least 10%. Mechanistically, OsPIL13 regulates stomatal responses by repressing OsSAL1, a chloroplast retrograde signal regulator, and activating OsNHX1, a vacuolar sodium/proton antiporter. These findings highlight the potential of PIL13 in improving crop resilience to FL-DS, particularly in maize-soybean intercropping systems.