A regulatory module tunes OsYABBY4 expression to modify vascular bundle development and tillering in rice

The arrangement of vascular tissue in monocots is characterized by an array of scattered bundles, which determines rice architecture and grain yield. To enhance cereal productivity, it is therefore crucial to outline the genetic mechanisms that govern vascular bundle development. In this study, we use a genome-wide association study (GWAS) to explore the genetic basis that regulates vascular bundles in rice. We find a link between vascular bundles and cis-element variations in the OsYABBY4 promoter. We show that the cis-element variations modulate the binding affinity of an activator-repressor module to control OsYABBY4 expression. Our findings outline a regulatory module that intricately connects cis- and trans-factors to regulate vascular bundle quantity and tillering in rice, providing a target for cis-element editing to engineer rice architecture.