<i>CaHY5</i> functions as a central hub integrating waterlogging signaling with auxin-mediated adventitious root formation in pepper

Abstract HY5 is a key transcription factor integrating light and stress signals. However, its role in waterlogging adaptation remains unclear. This study unveils CaHY5 as a central hub integrating waterlogging signaling with auxin-mediated adventitious root formation in pepper. Wild-type and Cahy5 mutant pepper plants were subjected to waterlogging treatment. Subsequent statistical analysis of the number and temporal dynamics of adventitious root formation, combined with transcriptome data analysis, confirmed that CaHY5 acts as a negative regulator of waterlogging-induced adventitious root formation. Mechanistically, CaHY5 modulates auxin accumulation in the hypocotyl by directly repressing the expression of auxin transporters CaPIN1, while simultaneously suppressing auxin signaling by promoting the expression of CaIAA17. This dual regulatory action collectively attenuates the auxin response and inhibits adventitious root formation. In addition, CaHY5 can directly bind to the promoter regions of CaWOX5, CaLBD16, and CaSBRL, and inhibit their transcriptional activity, thereby suppressing adventitious root formation. However, the expression of CaHY5 is down-regulated under waterlogging stress, thereby alleviating its inhibitory effect on adventitious root formation. Our findings thus reveal a novel mechanism of waterlogging adaptation and identify CaHY5 as a key regulator coordinating root plasticity under waterlogging stress.