Summary Leaf shape is a vital economic and developmental trait in leafy vegetable Chinese cabbage ( Brassica rapa L. subsp. pekinensis ), which varies from smooth to deeply lobed, whereas the molecular basis remains unclear. Here, we detected an incompletely dominant major quantitative trait locus (QTL) qBrrLLA10 for the lobed-leaf trait in B. rapa , and identified BrrRCO , encoding a HD-Zip transcription factor, as the casual gene underlying lobed leaf formation in B. rapa. Genotyping analysis showed that abundant variations in promoter of BrrRCO is responsible for leaf lobe variation, and the expression levels and promoter activity were significantly affected by the promoter variations between two parents. BrrRCO was a nucleus-specific protein and possess highest expression level at the bases of each lobe. Ectopic overexpression of BrrRCO in Arabidopsis led to deeply lobed leaves have never been seen in wild type, and leaf lobe development was blocked when BrrRCO expression was down-regulated through virus-induced gene silencing assays. Taken together, our findings revealed that BrrRCO positively regulate leaf lobe formation in Chinese cabbage, and the cis-regulatory element modifications result in functional variation of BrrRC O, providing a novel insight into the leaf shape improvement in Chinese cabbage and other Brassica species. Highlight BrrRCO is essential for leaf lobe formation by repressing local growth of leaf margin cells in B. rapa , and cis-regulatory modifications cause the different allele effects.

BrrRCO, encoding a homeobox protein, is involved in leaf lobe development inBrassica rapa