A clear example of interspecific variation is the number of root cortical layers in plants. The genetic mechanisms underlying this variability are poorly understood, partly because of the lack of a convenient model. Here, we demonstrate that , unlike, has two cortical layers that are patterned during late embryogenesis. We show that a miR165/6-dependent distribution of the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) transcription factor PHABULOSA (PHB) controls this pattern. Our findings reveal that interspecies variation in miRNA distribution can determine differences in anatomy in plants.

The Arabidopsis root is a dynamic system where the interaction between different plant hormones controls root meristem activity and, thus, organ growth. In the root, a characteristic graded distribution of the hormone auxin provides positional information, coordinating the proliferating and differentiating cell status. The hormone cytokinin shapes this gradient by positioning an auxin minimum in the last meristematic cells. This auxin minimum triggers a cell developmental switch necessary to start the differentiation program, thus, regulating the root meristem size. To position the auxin minimum, cytokinin promotes the expression of the IAA-amido synthase group II gene GH3.17, which conjugates auxin with amino acids, in the most external layer of the root, the lateral root cap tissue. Since additional GH3 genes are expressed in the root, we questioned whether cytokinin to position the auxin minimum also operates via different GH3 genes. Here, we show that cytokinin regulates meristem size by activating the expression of GH3.5 and GH3.6 genes, in addition to GH3.17. Thus, cytokinin activity provides a robust control of auxin activity in the entire organ necessary to regulate root growth.

Summary In both animals and plants, development involves anatomical modifications. In the root of Arabidopsis thaliana , maturation of the ground tissue (GT)—a tissue comprising all cells between epidermal and vascular ones—is a paradigmatic example of these modifications, as it generates an additional tissue layer, the middle cortex (MC). 1 , 2 , 3 , 4 In early post-embryonic phases, the Arabidopsis root GT is composed of one layer of endodermis and one of cortex. A second cortex layer, the MC, is generated by asymmetric cell divisions in about 80% of Arabidopsis primary roots, in a time window spanning from 7 to 14 days post-germination (dpg). The cell cycle regulator CYCLIN D6;1 (CYCD6;1) plays a central role in this process, as its accumulation in the endodermis triggers the formation of MC. 5 The phytohormone gibberellin (GA) is a key regulator of the timing of MC formation, as alterations in its signaling and homeostasis result in precocious endodermal asymmetric cell divisions. 3 , 6 , 7 However, little is known on how GAs are regulated during GT maturation. Here, we show that the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) transcription factor PHABULOSA (PHB) is a master regulator of MC formation, controlling the accumulation of CYCD6;1 in the endodermis in a cell non-autonomous manner. We show that PHB activates the GA catabolic gene GIBBERELLIN 2 OXIDASE 2 ( GA2ox2 ) in the vascular tissue, thus regulating the stability of the DELLA protein GIBBERELLIN INSENSITIVE (GAI)—a GA signaling repressor—in the root and, hence, CYCD6;1 expression in the endodermis.

In both animal and plants, establishment of body axes is fundamental for proper organ development. Plant roots show two main developmental axes: the proximo-distal axis, which spans from the hypocotyl-root junction to the root tip, and the radial axis, which traverses from the vascular tissue to the epidermis.Root axes are determined in the root meristem. The root meristem occupies the tip of the root and contains self-renewing stem cells, which continuously produce new root cells. An intricate network of signalling pathways regulates meristem function and patterning to ensure proper root development and growth. In the last decade, microRNAs (miRNAs), 20-21 nucleotide-long molecules with morphogenetic activity, emerged as central regulators of root cell patterning. Their activity intersects with master regulators of meristematic activity, including phytohormones. In this review we discuss the latest findings about miRNAs activity and their interaction with other molecular networks in the formation of root meristem axes. Furthermore, we describe how these small molecules allow root growth to adapt to changes in the environment, while maintaining a correct patterning.

Highlights d PHB regulates cell non-autonomously the timing of MC formation d A time-dependent rise of PHB expression controls the CYCD6;1 switch in the GT d PHB regulates GAI stability modulating GA levels d PHB regulates root GA levels activating GA2ox2 expression in the vasculature