Intercellular signaling mediated by small peptides is critical to coordinate organ formation in animals, but whether extracellular polypeptides play similar roles in plants is unknown. Here we describe a role in Arabidopsis leaf development for two members of the CLAVATA 3/ ESR ‐ RELATED peptide family, CLE 5 and CLE 6, which lie adjacent to each other on chromosome 2. Uniquely among the CLE genes, CLE 5 and CLE 6 are expressed specifically at the base of developing leaves and floral organs, adjacent to the boundary with the shoot apical meristem. During vegetative development CLE 5 and CLE 6 transcription is regulated by the leaf patterning transcription factors BLADE ‐ ON ‐ PETIOLE 1 ( BOP 1) and ASYMMETRIC LEAVES 2 ( AS 2), as well as by the WUSCHEL ‐ RELATED HOMEOBOX ( WOX ) transcription factors WOX 1 and PRESSED FLOWER ( PRS ). Moreover, CLE 5 and CLE 6 transcript levels are differentially regulated in various genetic backgrounds by the phytohormone auxin. Analysis of loss‐of‐function mutations generated by genome engineering reveals that CLE 5 and CLE 6 independently and together have subtle effects on rosette leaf shape. Our study indicates that the CLE 5 and CLE 6 peptides function downstream of leaf patterning factors and phytohormones to modulate the final leaf morphology.

The shoot apical meristem produces all of the leaves, stems and flowers of a flowering plant from a reservoir of stem cells at its growing tip. In Arabidopsis, the small polypeptide signaling molecule CLAVATA3 (CLV3), a member of the CLV3/EMBRYO SURROUNDING REGION-RELATED (CLE) gene family, is a key component of a negative feedback loop that maintains stem cell activity in shoot and floral meristems throughout development. Because in some plant species multiple CLE genes are involved in regulating shoot apical meristem activity, we tested the hypothesis that CLE genes other than CLV3 might function in stem cell homeostasis in Arabidopsis. We identified three Arabidopsis CLE genes expressed in the post-embryonic shoot apical meristem, generated loss-of-function alleles using genome editing, and analyzed the meristem phenotypes of the resulting mutant plants. We found that null mutations in CLE16, CLE17 or CLE27 affected neither vegetative nor reproductive shoot meristem activity under normal growth conditions, although CLE27 appears to slightly prolong vegetative growth. Our results indicate that the CLE16, CLE17 and CLE27 genes have largely redundant roles in the Arabidopsis shoot apical meristem and/or regulate meristem activity only under specific environmental conditions.