2. Maintenance of Shoot Apical Meristems (SAM) and the Leaf Initiation Gene Network

The stem cells of plant meristems generate new organs and tissues throughout the life of the plant. The above-ground organs in plants are formed through SAM, whereas below-ground organs are created by root apical meristems (RAM). Beside these two apical meristems, various other types of meristems exist in plants, such as lateral meristems (e.g., axillary in the node of the leaves and flowers), intercalary meristems (at the base of the monocots leaf blade), and transient stem-like meristemoids (the precursor for guard cells) [6,7]. The SAM is a dome-shaped structure that comprises a reservoir of stem cells, provides cells that form the branches, leaves, and flowers of the plant, and also retains its own identity. The SAM is organized into several distinct cell layers and various zones [8] (Figure 1). The development and maintenance of SAM are crucial for determining the spatiotemporal arrangement (e.g., clockwise, anticlockwise, spiral and whorled) of aerial organs around the stem. The process of arranging different organs spatially is known as phyllotaxis, which is species and stage-dependent [9,10,11].

Figure 1. Schematic representation of Shoot Apical Meristems (SAM) maintenance by the various interacting genes. (A) The pluripotent stage and a specific number of cells in the SAM are controlled by the (WUS/CLV3) negative-feedback loop. CLAVATA3 (CLV3) is a ligand attached to CLV1 and CLV2 for the restriction of WUS. However, WUS activates CLV3 and works as a stem cell-promoting protein. STM activated the biosynthesis of CK through LONELY GUY (LOG). The STM and KNOX related genes also keep the stem cells undifferentiated by suppressing the expression of AS1 and gibberellic acid (GA) biosynthesis. STM also restricts the expression of the CUC gene due to negative regulators in a specific area. (B) The HAM and WUS-CLV3 loop. The regulatory loop requires CLV3, WUS, and HAM; the CLV3 negatively regulates the WUS expression, and the WUS protein moves from the organizing center to the active central zone (stem cells) to activate CLV3 expression. HAM1/2 is an interacting partner of WUS, and together with WUS protein suppresses the expression of CLV3 in the rib meristems. The expression zone of the CLV3 gene (blue), WUS gene (pink), HAM proteins (green) and the dot marks the WUS protein. (C) Regulatory networks that control leaf initiation. The cells in the SAM are arranged into layers L1, L2, and L3 and further into a distinct group of either tunica or corpus. According to the expression of genes, the SAM architecture is organized with the central zone (CZ), peripheral zone (PZ), organizing zone (OZ), and rib zone (RZ). During leaf initiation, auxin maxima repress the expression of the KNOX1 domains (gene) indeterminate meristem domains. KNOX1 maintains a high level of CK and low levels of GA in the meristem. In the ARP domain that has leaf identity, the leaf primordium separates from SAM by expression of boundary specific genes CUC and BOP regulates the petiole specification and polarity (positive and negative regulations are indicated by pointed and T-shaped arrows).

In Arabidopsis thaliana, the SAM possesses three cell layers (L1–L3). An external two-cell layer forms tunica, where the L1 overlies L2. This layer divides by anticlinal cell division and grows in a two-dimensional fashion [12]. An inner layer (L3) divides both periclinal and anticlinal cell divisions in a mostly random fashion, which is commonly called corpus. These three histogenic layers are responsible for producing different parts; the L1 layer divides and forms the entire shoot epidermis while the L2 layer produces the photosynthesizing cells of the sub-epidermis. The L3 layer forms the internal tissue, pericycle, and other corpus cells [13].

The SAM layers are further subdivided into three functional domains or zones according to the function and division rate (Figure 1). The three zones include the central zone (CZ), peripheral zone (PZ), and rib zone (RZ), which is present below the CZ. The CZ is mainly responsible for the maintenance of SAM. The CZ contains both tunica and corpus cells in which the stem cells are present, and below the CZ is the organizing center (OC) [14]. The tunica and corpus cells of the CZ are symplasmically interconnected through the plasmodesmata [15,16]. Any alteration in the intercellular signals through the plasmodesmata affects normal growth and development [17].