A CRC–MYB-mediated local chromatin loop at the MAB4 locus determines auxin-mediated nectary size in Arabidopsis thaliana

Abstract The nectaries of flowers in angiosperms are typically located at the base of the stamens and secrete nectar, composed primarily of sugars and various secondary metabolites, either actively or passively. Although nectaries develop in specific locations and perform specialized functions, the regulatory mechanisms governing their formation are unclear. Through a pseudotime trajectory analysis based on single-nucleus RNA-seq data and newly performed spatial transcriptomics, we uncover a spatiotemporal regulatory network governing nectary development. We establish CRABS CLAW (CRC) as a master regulator that integrates temporal transcriptional regulation with spatial auxin transport, orchestrating nectary development through phytohormone signaling, sugar transport and terpene biosynthesis pathways. CRC interacts to MYB21, MYB24 and MYB57, with the CRC–MYB57 complex binding the 5′ and 3′ regulatory regions of the MACCHI-BOU 4 (MAB4) locus, facilitating the formation of a chromatin loop that enhances MAB4 expression. This loop is necessary for the development of properly sized nectaries. MAB4 reinforces PIN-FORMED 1 (PIN1)-mediated auxin transport to establish auxin maxima at the nectary tip and regulates PIN6 to maintain auxin gradients. These findings reveal how CRC integrates transcriptional regulation and auxin transport to coordinate nectary development, linking metabolic output with organogenesis.