Protein-independent regulation by transgene-derived small interfering RNAs rewires endogenous regulatory networks to enhance plant growth, architecture, and drought performance

Abstract

Plants produce diverse small interfering RNA (siRNA) molecules that modulate development, environmental responses, and immunity. Although transgene-derived siRNAs are traditionally viewed as mediators of gene silencing, whether they can actively regulate endogenous host pathways remains largely unexplored. Previously obtained Arabidopsis, wheat, and soybean plants expressing the sunflower gene encoding the transcription factor HaHB4 exhibited water deficit tolerance. Here, we show that expressing inverted-repeat constructs that generate HaHB4-derived siRNAs without producing the HaHB4 protein bypasses transgenic growth penalties and instead enhances vegetative vigor and reproductive performance. In Arabidopsis, these DCL-dependent siRNA-producing lines exhibited enhanced root growth, increased stem and pith areas, increased cauline branching, and higher seed yield under both optimal and water-limiting conditions. Transcriptomic analysis revealed convergent repression of biotic stress-related genes, accompanied by increased bacterial susceptibility and reduced sensitivity to salicylic acid-mediated growth inhibition, suggesting an altered balance between immunity and growth. Functional characterization of candidate endogenous HD-Zip I targets further showed that athb20 and athb53 mutants recapitulated the increased stem expansion and cauline branching of the RNAi lines, respectively, pointing to endogenous HD-Zip I genes as candidate mediators of these traits. Remarkably, these effects were observed in newly obtained transgenic soybean plants, where expression of HaHB4-derived siRNAs enhanced vegetative vigor under controlled growth conditions. Overall, these findings show that transgene-derived siRNAs act independently of protein function to rewire endogenous regulatory networks, providing a potential strategy to optimize crop architecture and yield.