Quantification of the L1 layer cell size in MorphoGraphX47,48 revealed that cells of csld5 were much larger than those of WT (Fig. 2a). The reduced meristem size in the xxt2 single mutant was consistent with the dominant activity of XXT2 in xyloglucan synthesis43. The color of the boxes correlates with the function of each gene in cell wall synthesis, as shown in (a). Mutants of each gene were selected based on their mRNA expression patterns. The homozygous T-DNA insertion lines in the Col-0 background for each of these 29 GT genes, with insertion sites preferentially in an exon if available, were isolated, and the T-DNA insertions were confirmed by genotyping with gene-specific primers. A framework that describes inflorescence development in terms of shifting meristem identities has emerged and garnered empirical support in a number of model systems. Thus, newly uncovered signaling molecules including CLE peptides may have key functions in the response to variable environmental states and may be involved in stem cell maintenance, and further molecular analysis to provide a new framework for understanding what happens after perception by an LRR receptor complex is required. In addition, recent reports have demonstrated a tight connection between nitrogen nutrition status, ROS, and hypoxic state in the regulation of stem cell homeostasis (Araya et al. 2014; Kong et al. 2018; Landrein et al. 2018; Shen et al. 2013; Weits et al. 2019; Zeng et al. 2017). CLV3 and CLE40 belong to the same evolutionary clade as the CLV3 orthologs in rice, maize, barley, and tomato, implying that these combined regulatory circuits arose from two CLE peptides; the regulatory circuit comprising the CLV3 and CLE40 signaling modules may thus be a common system to maintain SAM homeostasis among plant species (Goad et al. 2017; Suzuki et al. 2019). Integrating Auxin Metabolism and Transport at the Shoot Meristem: A Challenge for the Future Expanding the regulatory network for meristem size in plants. Stem cell regulation by arabidopsis WOX genes. WOX genes expression during the formation of new lateral roots from secondary structures in populus nigra (L.) taproot. This suggests that KpWUS is also involved during plantlet initiation, increasing meristem activity as a response to leaf. The CLV/WUS feedback system prevents the over-proliferation of stem cells preserving the SAM size (Yadav et al., 2011). The single mutant bop1 and double mutant bop1 and bop2 both exhibited leaf growth on the petiole with a reduced petiole region (Ha et al., 2003; Hepworth et al., 2005). All PHB, PHV, and REV genes have complementary sequences with miR165 and miR166 (Rhoades et al., 2002; Tang et al., 2003). The YABs playing a vital role in polarity maintenance and leaf development. Adaxial polarity genes encompass AS1, AS2, and the Class III Homeodomain-leucine Zipper (HD-ZIPIII) family genes. 2 shows the reconstructed expression of representative genes whether our modifications are applied or not. Subsequently, we studied the performance of these modifications by calculating the area under the receiver operating characteristic (AUROC) for predicting the expression of each reference gene when this gene was removed from the spatial map during the data integration step. Cluster 4 represents the floral meristem, containing specific markers such as APETALA3 (AP3)49, REPRODUCTIVE MERISTEM 34 (REM34)50 (Supplementary Fig. 3). Cluster 8 is enriched for vascular xylem parenchyma genes, for example, CYTOCHROME P450, FAMILY 708 (CYP708A3)45 (Supplementary Fig. 3), and shows signatures of cell expansion and cellulose biosynthesis. For example, the top 20 marker genes of cluster 1 have a high specific expression on the ATHB8-domain, meaning that they are specific to this domain. Alignment between PIN1 polarity and microtubule orientation in the shoot apical meristem reveals a tight coupling between morphogenesis and auxin transport. Signals derived from YABBY gene activities in organ primordia regulate growth and partitioning of Arabidopsis shoot apical meristems. CaJOINTLESS is a MADS-box gene involved in suppression of vegetative growth in all shoot meristems in pepper. These results show that the expression of five HD-ZIP III-target genes (PSK5, ATH1, ZPR1, AMP1 and POL) is significantly increased in zpr2-3 insertion mutants. Twenty-four hours of hypoxia, but not oestradiol treatment (50 μM), was sufficient to repress pTAA1-driven GUS expression in the wild-type background, probably via stabilization of the endogenous ZPR2 protein (2 out of 3 plants). At the growth condition used, the rosette of four-week-old zpr2-3 plants was smaller than that of the wild type. The higher expression of these mRNAs in the SAM, compared to the leaf samples, was repressed by hyperoxia. Meristems are protected within a specialized microenvironment from undergoing differentiation through a variety of regulatory systems, and are located in the apical regions of shoots and roots, and as lateral meristems such as vascular cambium, where they comprise a small number of cells with undifferentiated and dividing states. STM has previously been shown to be essential for embryonic SAM formation and continued SAM maintenance throughout the plant life-cycle, with loss-of-function mutants either failing to develop a SAM during embryogenesis, or developing defective SAMs that exhibit stem cell depletion caused by inappropriate organogenesis from the central zone of stem cells18,19. Indeed, co-localization of VENUS-GA2ox4 signal with SVP-GFP was observed in the floral primordia of wild-type plants carrying both transgenes (Figure 9I–K and Figure 9—figure supplement 1M and N). Meristem diameter was large primarily in Euphorbiaceae andRanunculaceae, whereas it was small in Hypericum and almost all speciesfrom the commelinid clade (Fig. 5). In addition, we also examined path coefficients andcovariations in an identical model using residualized values of the variables, i.e. withphylogenetic effect removed by the approach of Diniz-Filho et al. (1998) The path models were fitted using thefunction sem from the package sem (Fox etal., 2016). Wethen searched for the best model in terms of good fit of the data assessed by theχ2 test. We assumed genome size to bean exogenous variable (i.e. not affected by any of the variables in the data set), whereasall other variables were assumed to be endogenous (i.e. affected by some variables andpotentially affecting some other variables). To take into account potential correlations between plant traits, we used path analysis(Grace, 2006). An extensive list of genes involved in flower organ morphogenesis with their inferred functions, mutant phenotypes and mRNA expression patterns is given in Table S1 (139KB, xls) . Several of these have also been identified as important regulators of leaf development, substantiating the proposal of Goethe that all plant organs are elaborations or modifications of a core leaf-like developmental program (for review of common pathways see Sablowski, 2009). Before meiosis the Ar cells divide and generate the primary parietal layer (1°P) and the primary sporogenous layer (1°Sp). However, the number of cauline leaves was significantly higher in soc1-2 ga2ox4–3 compared to soc1-2 (17% more cauline leaves than soc1-2), suggesting that increased expression of GA2ox4 delayed flower formation in soc1-2 during later developmental stages (Figure 6G). Although ga2ox4 mutation resulted in slightly earlier flowering than wild-type plants (6% fewer rosette leaves), it did not significantly affect the late-flowering phenotype of soc1-2 (4% fewer rosette leaves than soc1-2) (Figure 6F). We also examined the effect of genes in the photoperiodic flowering pathway on the mRNA level of GA2ox4. The synergistic effect of ga20ox2 on soc1 is not simply caused by the general growth defect of GA deficiency, because mutation in another GA biosynthesis enzyme gene, GA3ox1, had only a minor effect on soc1 flowering time (Figure 6E–G). 1 Regulation of plant hormones on leaf senescence Moreover, gene expression regulation is temporally and spatially coordinated via crosstalk between chromatin remodeling complexes (CRCs) and the transcription machinery (Deem et al., 2012). Histone modifications, nucleosome remodeling and DNA methylation have been shown to regulate chromatin structure and gene expression (Henikoff and Shilatifard, 2011). Gene regulatory mechanisms in eukaryotic cells (such as transcription, DNA repair and replication) act upon chromatin structure as a substrate. However, cells have evolved in response to this impediment through chromatin remodeling (Groth et al., 2007). Vascular tissue that delivers water, hormones and mineral nutrients from the root to the shoot. Our analysis so far showed that CHH methylation is generally higher in the SAM than in the leaf. This suggests that CHH methylation near genes reflects CHH methylation in MITEs near genes. MITEs preferentially occur near genes14,18,19,20,21,22,23 (Supplementary Fig. 4a) and their presence or absence closely parallels the level of CHH methylation around genes (Supplementary Fig. 4b–e). Mutating two cytokinin receptors, AHK2 and AHK3, caused significant reduction in the secondary growth of vascular tissues (Hejatko et al, 2009). When the cytokinin level was significantly reduced in the quadruple mutant of IPTs (ipt ), secondary growth did not occur (Matsumoto-Kitano et al, 2008). These CLEs were found to enhance cytokinin signalling through the repression of A-ARRs, and thereby suppress the protoxylem cell fate. Recently, exogenous application of CLE peptides was reported to inhibit protoxylem formation in Arabidopsis roots through a CLV2-dependent pathway (Kondo et al, 2011). Taken together, cytokinin signalling restricts the auxin signalling maximum to the xylem axis by regulating the bisymmetric localization of PINs. The shoot apical meristem contains multipotent stem cells and produces primordia that develop into all the above ground organs of a plant. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. The plasticity of stem cells allows plants to adapt their shape in response to developmental, physical, and environmental cues (Wierzba and Tax 2013; Xu et al. 2018, 2019; Yu et al. 2019a). Therefore, the Arabidopsis HAM genes may function as conserved interacting cofactors with both WUS and WOX5 proteins in shoot or root meristems. Interestingly, the expression of the WUS from the WOX5 promoter completely restores stem cells in the wox5 root meristem. Leaf senescence is regulated by a variety of genes, and age-dependent leaf senescence is an important research focus, mainly focusing on annual and perennial plant leaf senescence. During leaf senescence, the expression profile of a large number of genes is changed, which forms a complex genetic regulatory network with other signal regulatory pathways in transcriptional regulation (Lim et al., 2007). Genetically redundant WOX3 transcription factors regulate this rim domain, and high-order mutations of Wox3 genes in maize result in a significant reduction in leaf width and disruption of leaf growth and patterning. KNOX1 expression is indispensable for the development of lobules in plants with compound leaves. Both KNOX1 and RCO curtail local cell growth by extending the growth potential of leaf primordium cells, promoting anisotropic cell expansion, and giving rise to compound leaves (Wang et al., 2022c). The soybean genome sequence and annotated gene set available at Phytozome () were used for the mapping and annotation. Briefly, poly(A) containing mRNA molecules were purified from 3 µg total RNA for each sample. The expression level of transcripts in reads per kb per million (RPKM) for each library. A Venn diagram showing the overlap of identified transcripts based on Glyma1 annotation for the leaf and SAM library. Thus, the repression of GA mediated by KNOX proteins may be overcome during floral induction. Thaliana, and individual family members exhibit distinct expression patterns (Han and Zhu, 2011; Mitchum et al., 2006; Plackett et al., 2012). The earliest known gene to respond directly to FT/FD at the SAM is SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) that encodes a MADS-domain type transcription factor (Lee et al., 2000; Samach et al., 2000). The authors declare that all other data supporting the findings of this study are available within the manuscript and its Supplementary files or are available from the corresponding author upon request. TRAP-seq data have been deposited in the NCBI Short Read Archive with accession number SRP145572. Scanning electron microscopy was performed to observe the fine structure of leaf axils using a Hitachi S-3000N variable pressure scanning electron microscope after standard tissue preparation. For immunolocalization, shoot apices were fixed in fresh FAA solution (3.7% formaldehyde, 50% ethanol, and 5% acetic acid) under vacuum and embedded in Steedman’s wax composed of polyethylene glycol 400 distearate and 1-hexadecanol (Sigma-Aldrich). Co-expression networks were displayed using Cytoscape74. DMRs were identified using the same strategy as Stroud et al. (2013)17. Windows with at least four cytosines that were each covered by at least four reads in at least one sample were used. About 50 SAMs were sampled in 50 μl of Buffer AP1 of the DNeasy Plant Mini Kit (Qiagen), heated at 65 °C for 10 min with gentle mixing. Total DNA was extracted from mature leaf blades of 25-day-old N8 seedlings using a DNeasy Plant Mini Kit (Qiagen). These insights and our present findings emphasize the importance of epigenetic regulation via smRNAs for reproduction in eukaryotes. GA signalling is required in the early xylem domain For TSA/IAA cotreatments, shoot apical meristems were dissected from about 4 cm high stem and cultured in vitro in Apex Growth Medium (AGM) overnight45. This idea is supported by our findings that following local suppression of auxin signaling, stem cell fate was able to expand into the peripheral zone. Auxin and cytokinin signaling are directly coupled also in other stem cell systems and balancing their outputs is key to maintaining functional plant stem cell niches15,43. D, Light microscope images of roots of wild-type, ritf1-3 and ritf1-2 roots stained with NBT 24 h after treatment with 5 nM RGF1. B, Confocal images of wild-type, ritf1-1 (CRISPR mutant) and ritf1-2 (Salk line) roots stained with PI. Dots indicate each data point. Left, PI-stained roots; right, GFP signals. Soon after auxin accumulates, the microtubule arrays disorganise to become fully isotropic. Importantly, KTN directly interacts with RHO INTERACTING CRIB CONTAINING PROTEIN 1 (RIC1), which in turn interacts with RHO in PLANTS 6 (ROP6), thus potentially linking KTN function to cellular signalling . First of all, the direction of microtubule movements driven by motor proteins on artificial substrates in vitro is sensitive to stress, although the effects of this property in the living cell remains to be established . ML platforms must be flexible and robust, with the ability to distinguish multiple disease symptoms on a single leaf or within the same plant canopy. Similarly, deep convolutional neural networks were used to detect 10 different diseases in rice and differentiate them from the healthy plants on a dataset of 500 images. Such autonomous systems, alongside test images, add much more information to the project, such as phenotype score, metrics, parameters, generating up to terabytes of data per day. Although ground-based imaging platforms has the same limitation as drones due to limited battery capacity, but they provide more detailed and accurate images at the individual plant to individual branches, even down to the single leaf level. We discuss these issues in the context of leaf initiation, the balance between morphogenesis and differentiation, and patterning of the leaf margin. We also detected HvLEAFY (2HG )71 and 59 transposon-related genes specifically expressed in the FMc.Auxin maximously inhibits CUC2 at the tip of the tooth and promotes the growth of the tooth (Barkoulas et al., 2007; Wang et al., 2021a).Termination of stem cell activity during flower development is achieved by a temporal feedback loop involving both stem cell maintenance genes and flower patterning genes.The split-ubiquitin membrane yeast two-hybrid system was used to test the interaction between CSLD5 and CSLD3.For meristem maintenance, and therefore continuous root growth, the rate of cell differentiation must equal the rate of generation of new cells.Since H2B-GFP only function as a reporter, there is no feedback regulation from the H2B-GFP reporter to the other components in the system described in Eqs.Together, the results indicate that the binding of SEP3 to the MIR319a locus acts to dampen elevated MIR319a levels (as observed in the jaw-D/SEP3HE4.1k double mutant), while SEP3 positively regulates TCP4 expression to restrict petal size. Due to their sessile lifestyle, plants exhibit a variety of morphological and physiological leaf traits that have allowed adaptation to different natural habitats. A plant that forms two seed leaves during embryogenesis and has three or more pores in its pollen. We concentrate on clarifying the precise mutual regulation between shoot apical meristem (SAM) and AM-related factors. Percentage of duplicate genes at different evolutionary groups of plant taxa (A) and in different subfamilies (B). Scatter plots of 27 TFome tsCUT&Tag data from SAM-related homeobox genes. Supplementary Data 6 SCOOP stimulates root growth by interacting with MIK2, leading to the formation of a co-receptor complex with BAK1. Additionally, the peptides OsPEP1 and RALF34 have promoting effects on lateral root development in rice and in Arabidopsis, respectively. TDIF positively regulates lateral root development by promoting the phosphorylation of ARF receptors. CLE has an inhibitory effect on root nodules, while CEP promotes the formation of plant root nodules. In root regulation, both CLE and CEP can be transported from the roots to the stem, acting on mir2111. This figure was composed partially from information in Clark (2001b), Blazquez et al. (2006), Hord et al. (2006), Shani et al. (2006) and Feng and Dickinson (2007). Not all the genes involved in each module are depicted, just some of the most representative ones, which help us to understand how they are interconnected. AP2 is also implicated in the upregulation of the B genes, AP3 and Pl(Zhao et al., 2007). AP2 mRNA is found throughout the flower meristem (Figures 10 and 12; Jofuku et al., 1994). In contrast to the MADS-box ABCs, the expression pattern of AP2 does not correlate with the site where it exerts its function in floral organ identity. The Charophycean green algae, the closest relative of the extant land plants 63,64, provides an evolutionary example of the transition from unicellular to multicellularity.Dashed arrows indicate cell-to-cell movement.During these first 4 years, the affected palms are taken care of as normal palms, meaning a waste of labor, resources and plantation area, on top of the reduced oil yields (Jaligot et al., 2011).C, Expression profiles of selected MADS-box transcription factor genes along the developing spike.Dicot plants are decapitated and their wound sites are injected or rubbed with a solution of Agrobacterium.These data suggest that cell division rate decreased in response to short-term osmotic stress, which is in line with the high sensitivity of the cell cycle duration to other environmental changes (Grif et al., 2002).This includes genes that control organ identity, organ number, organ boundaries, and symmetry. We next used a modest z-score-based criterion, which allows retrieving genes enriched in two or a few domains. For example, the CLV3 domain CZ cells of the SAM are enriched in transcripts with high cell specificity (quantified by z values, see Methods), suggesting a dramatic translatome change during CZ to PZ transition. Although many genes were commonly expressed and translated in different domains, the abundance of their ribosome-bound transcripts could be highly variable among domains (Supplementary Fig. 6). We observed that 14,152 genes (42.5%) were translated in all domains. Chromatin remodeling in plant development. The putative SWI/SNF complex subunit BRAHMA activates flower homeotic genes in Arabidopsis thaliana. Pickle acts throughout the plant to repress expression of embryonic traits and may play a role in gibberellin-dependent responses. Roles and activities of chromatin remodeling ATPases in plants. Arabidopsis SWC4 binds DNA and recruits the SWR1 complex to modulate histone H2A.Z deposition at key regulatory genes. Here we discuss how multiple networks converge to specify and maintain the root stem cell niche. Recently, locally produced auxin was added to the list of important mobile factors in the stem cell niche. All aerial tissues, including the germ line, arise from the shoot meristem, and all root tissues arise from the root meristem. Nevertheless, a significant difference in cell area was observed between Col-0 and ga2ox4–3 SAMs after exposure to 5 LDs, with the cells of ga2ox4–3 being slightly larger than those of Col-0 (Figure 4—figure supplement 6D). Indeed, treatment of 2wSD-grown plants with exogenous GA caused expansion of the VENUS-GA2ox4 signal into the RZ, but it was still not detected in the CZ of the SAM (Figure 4I and Figure 4—figure supplement 3I). The VENUS-GA2ox4 transgene complemented the early-flowering phenotype of ga2ox4–3 (Figure 4—figure supplement 4), suggesting that the dynamic expression pattern of VENUS-GA2ox4 is necessary and sufficient for the role of GA2ox4 in flowering (Figure 4 and Figure 4—figure supplement 4). After transfer of plants from 3wSDs to LDs, the relatively high level of GA2ox4 mRNA under SDs was downregulated after 3–5 days in LDs, and upregulated again after 7 days in LDs (Figure 4—figure supplement 1J). Plants grown under SDs for different time periods were transferred to LDs, and in those plants that were still in the vegetative phase (2wSD, 3wSD, 4wSD, and 5wSD) the VENUS-GA20ox2 signal was upregulated after exposure to 3LDs (Figure 2—figure supplement 3B). Taken together, these facts suggest that a mutual repression between DL and B class genes is conserved in grasses, although this is not yet clear whether it is direct or not.Consistent with previous reports49, CSLD5 decorated the cell plates together with CESA3, and this co-localization on the cell plate was also evident between CSLD5 and CESA1 or CESA6.The activity of the resulting fusion protein could be induced by dexamethasone (DEX) treatment, which allowed the translocation of BDL-D-GR from the cytoplasm to the nucleus, its native cellular compartment21.The meristem is devoid of intercellular spaces and composed of cells that are small, rich in cytoplasm and with numerous small vacuoles (e.g. Astragalus sinicus in Figs. 2, 3) and Łotocka et al. (1997) and Newcomb (1981).PIN1 has been shown to be basally localized in vascular cells11,13,36,37.A tissue in plants consisting of pluripotent cells. Briefly, the protoplast suspension was subjected to a 10× Chromium Controller (10× Genomics) to form single‐cell droplets. Then, the samples were incubated at 25°C for 2 h at 50 rpm/min, and the mixture (Figure S24b) was filtered by a 40‐μm nylon strainer and centrifuged at 1000 rpm/min for 2 min. Each EMS mutant was backcrossed with B73 (recurrent parent) to generate the BC2F2 population. Indeed, changes in the cell division rate, should they occur, must rely on specific unknown mechanisms to regulate cell cycle progression of different cell types and in different locations. As discussed earlier (Baskin, 2000), whether the cell division rate is constant or varies along the RAM has direct implications for the mechanisms of cell cycle control. These studies have served to demonstrate that the relative elemental growth rate in the RAM and elongation zone are spatially separated (van der Weele et al., 2003). C Differential expression analysis based on RNA-seq of V6-stage internodes from wild type and wox13a mutant. WOX13A regulates the expression of Gn1 and affects maize architecture. “Treatment” refers to the co-transformation of the pM999 vector containing the TF effector and the p0800 vector containing the 2-kb promoter region of the target gene. CVt2, a functional target gene, is regulated by multiple TFs. We cloned 2-kb Vt2 and Hb20 promoter regions upstream of the LUC reporter gene and used Knox6 and Hb20 as effectors. KN1 is often used as a marker for the meristem corpus, which is mostly absent in the L1 layer and downregulated at sites of organ initiation14. Accuracy improved linearly with increasing reference cell number, but plateaued at ~2,500 cells (Supplementary Fig. 9). We then explored the impact of cell number and gene selection on the accuracy of imputation. This provides insights into how plant domestication, primarily driven by developmental changes, may involve crosstalk between cell wall and meristem biology. The effect of ectopic activity of CSLD5 in Arabidopsis SAM, and of OsCSLD4 in inflorescence meristem development in rice, demonstrates a cross-species conserved role of the L1 layer in guiding shoot meristem growth. In contrast, csld5, xxt2, gaut9, gaut10, gals2, and gals3 plants exhibited smaller meristems compared to WT. One interesting question to be addressed in the future is whether WOX activity is also linked to PIN7 expression and auxin patterns from the one-cell embryo stage.The phenomenon was likely due to the difference in genetic background between the A188 and B73 lines.The transcript encoding bHLH identified in this study likely represents a novel floral repressor.Dissecting the molecular signatures of apical cell-type shoot meristems from two ancient land plant lineages.Among the 10 paralogs of AGO genes in the Arabidopsis genome, AGO10/ZWILLE (ZLL) is indispensable and has an overlapping function with AGO1 for shoot meristem maintenance over different developmental stages (Du et al. 2020; Tucker et al. 2008).These include the use of alternative explants and propagation techniques, the introduction of specific embryo maturation treatments and the detection of the mantled abnormality in an early stage.To study the function of key meristem genes and to reveal the genetic means modulating induced plantlet formation in K.Subsequently, the zygote undergoes asymmetric cell division, resulting in apical cells that give rise to the embryo proper and later mature into the complete embryo, while basal cells develop into the suspensor (Chen et al. 2017). All-in-One Control AGO proteins belong to the RNA-binding protein class and play a pivotal role in small RNA-mediated gene silencing (Baumberger and Baulcombe, 2005). In addition, leaf polarity establishment is under the regulation of ARGONAUTE (AGO) proteins and long non-coding RNAs (lncRNAs). The recessive wide leaf mutant wl1(wide leaf 1), a novel DROUGHT AND SALT TOLERANCE(DST) allele, has also been found in rice. The conserved function of WOX1 is regulating the development of medio-lateral axes of leaves. BRs, in turn, facilitate the demethylation of cell wall pectin, resulting in isotropic in-plane cell wall loosening. As we delve deeper into this review, we will examine Meristems operational ethos, service provision, and the correlated risk factors to assess whether this broker represents a formidable opportunity or a potential trap for investors. Meristem Securities has carved a significant niche within Nigeria's financial services landscape, presenting itself as a comprehensive provider for individual investors and corporations alike. This research was funded by a seal of excellence grant from the Autonomous Province of Bozen/Bolzano (umor-D to S.J.U.). We are grateful to Miltos Tsiantis for support through generation of materials and helpful discussions. The AP2 paralogs TARGET OF EAT1–3 (TOE1–3), SCHNARCHZAPFEN (SNZ), and SCHLAFMUETZE (SMZ) were identified as key repressors of floral transition20,21. All floral homeotic proteins, with the exception of AP2 whose classification as a homeotic factor is under debate16, encode members of the MADS-domain TF family. According to the “floral quartet model”, floral homeotic proteins form organ-specific tetrameric protein complexes, and the higher-order interactions are mediated by the redundantly acting SEPALLATA (SEP) proteins (including SEP1, SEP2, SEP3, and SEP4)14. Over the past three decades, key TFs controlling floral transition and flower formation have been identified in Arabidopsis thaliana1,2,3. Differential expression of genes during… Baron, C.S., van Oudenaarden, A. Unravelling cellular relationships during development and regeneration using genetic lineage tracing. We discuss how these approaches are used to understand cell fate during embryogenesis, cell differentiation and tissue regeneration. Finally, single-cell mRNA-sequencing datasets that capture different cell states within a developmental or differentiation trajectory can be used to recapitulate lineages. E–G Time series of new organs growing out of a non-dissected pin-like meristem 2 days after transferring to NPA-free medium at T0, T4, T8, and T24 hours. Boundary cells that were originally shrinking during the first 2 h (T0 vs. T2) reversed this trend in the next 2 h (T2 vs. T4), revealing an elastic behavior (cells type 1 in Fig. 5G, H). Cell types 1 (shrinking cell), 2 (adjacent to shrinking cell), and 3 (non-adjacent organ cells) are identified in T0–T2 and T2–T4. This confirms that a subpopulation of late boundary cells shrinks, consistent with predicted water efflux simulations, independent of dissection. The volumetric analysis revealed that organ cells grow by more than 20% (Fig. 5C, D). E eFP browser view of expression changes in the shoot apex for selected genes. In this study, we provide a domain-specific gene expression map covering key SAM and leaf domains, allowing direct comparison among shoot domains. RNA profiling of mutant and over-expression seedlings with leaf polarity defects has been used to identify regulators of leaf development17,18,19, but these are profiles of heterogeneous tissues. In other fossils of Early Devonian lycophytes, non-gravitropic thin root-like structures in position of leaves originated from shoot-like positively gravitropic axes (Matsunaga and Tomescu, 2016). Indirectly, this further supports that such root traits must have convergently evolved independently in the other major vascular plant lineage, the euphyllophytes (Hetherington and Dolan, 2018b). Therefore, true roots likely evolved independently in these two major vascular plant branches. It is currently unclear how homorhizoic and allorhizoic roots relate to each and whether the evolution of a primary root in the seed plant lineage can be seen as a third root-evolution event (3) (see Liu and Xu, 2018). CLV3 is localized to the extracellular space, where it activates the Arabidopsis CLAVATA stem cell signaling pathway. Arabidopsis WIH1 and WIH2 genes act in the transition from somatic to reproductive cell fate. WUSCHEL is a primary target for transcriptional regulation by splayed in dynamic control of stem cell fate in Arabidopsis. In this way, Refahi et al.32 combined the information on spatiotemporal expression patterns of 28 regulatory genes into 3D reconstructed Arabidopsis flower meristems, ranging from initiation to stages 4, 5 of flower development. Here we discuss the current knowledge about the molecular regulation of stem cell maintenance in the shoot apical meristem and recent attempts to delineate the molecular signatures of “stemness” in flowering plants. The four types of meristematic cells include the shoot apical meristem, root apical meristem, intercalary meristem, and floral meristem. They either use the growing tips of plant shoots or roots—sites containing meristematic cells—for the culturing process. The regulation of cell differentiation at meristems is crucial to developmental patterning in plants. Together these data demonstrate that meristem activation and radicle elongation are not required for seed germination, but also that completion of germination is not required for meristem activation. However, abi mutations did not reduce the GA requirement for the induction of the mitotic cell cycle in the radicle meristem (Fig. 2B,D,F). Collectively, these data confirm that the induction of division in the radicle meristem during germination requires GA, and is not blocked by ABA. Premature activation of the radicle meristem was seen in the strong abi3-5 mutant in viviparous embryos, and has been reported for the shoot meristem in another strong abi3 mutant24. The direct regeneration mechanism has many advantages over the indirect mechanism as it is simpler and quicker to perform; however, it leads to the formation of chimeric T0 mutants that require segregation in the T1 generation to obtain non-chimeric offspring. All of the sections referring to specific in planta transformation techniques de facto refer to this compendium to limit the number of in-text references. On the whole, we manually curated, annotated, and reviewed 323 references (research articles, thesis, patents, etc.) tackling the topic of in planta transformation using this classification scheme (Table S1). Subsequently, we describe several in planta experimental approaches with a focus on recent advances and finally discuss the future avenues and possibilities in this field of research. Besides, the expression level of OsMADS13 is increased and more widely detectable in the gynoecium of fon4-2 mutant (Xu et al., 2017). The number of carpelloid structures in the fon4-1 osmads13-3 double mutant is greatly increased in comparison with the single mutants, and the expression domain of OSH1 is wider. Reiteration of carpels and prolonged expression of OSH1 have been observed in osmads13 mutants (Dreni et al., 2007; Yamaki et al., 2011). Mutation in the ovule identity specification gene OsMADS13 also results in partial loss of FMD. Besides the above three regulators, OsMADS13, the D function gene of rice (Dreni et al., 2007), also plays a role in carpel establishment, although limited to its adaxial side, as we described above (Figure 2B). In contrast, the large SAM ZmLAX2-ALT lines ND246 and Co255 displayed transcript accumulation in the P0 and older leaf primordia, as well as on the flank of the SAM opposite the P0 (Fig. 5c,d). In four large SAM ZmLAX2-COM lines, transcript accumulation was detected in the P0 and in older leaf primordia (Fig. 5a). Leaves are designated according to plastochron number, which specifies the relative time elapsed since initiation from the SAM, such that the newly initiated leaf is termed P1 and the next incipient primordium is designated P0 (ref. 32). (e) Arrow denotes procambial expression in minor vein prior to xylem and phloem differentiation. (a,b) In situ hybridization of 14-day-old maize seedlings (inbred B73) reveals ZmLAX2 transcript localization in the vascular traces of leaf primordia. As such, we investigated the TFs expressed in MMC and MDC for identifying the causal regulators of SAM development. Several TFs (including KNOXI, WUS and NAC) regulating the SAM development have been identified in previous studies (Aida and Tasaka, 2006; Laufs et al., 1998; Satterlee et al., 2020; Shani et al., 2006). The development of maize SAM is controlled by a complex transcription regulatory network. Asterisks — vascular endodermis layer, large arrows — founder cells of provascular meristem. The meristem is devoid of intercellular spaces and composed of cells that are small, rich in cytoplasm and with numerous small vacuoles (e.g. Astragalus sinicus in Figs. 2, 3) and Łotocka et al. (1997) and Newcomb (1981). At the same time, the competent cells of the root are activated by transmissible rhizobial morphogens, the Nod factors, and re-enter the cell cycle. The protein encoded by this gene requires co-factors to set the spatial limits of expression of the floral organ identity genes AP3, Pl, and AG. EMF genes are required for vegetative growth, but they seem to regulate flowering time and inflorescence development too (Sung et al., 1992; Aubert et al., 2001 ; Yoshida et al., 2001). Mutual repression of the IM and FMI genes seem to underlie the co-existence, identity and boundaries of both types of meristem in the SAM in the transition to flowering (Chen et al., 1997; Liljegren et al., 1999; Ratcliffe et al., 1999). Later in development, LFY and AP1 repress the expression of TFL1 and flowering genes SOC1 and AGL24, among others, thus maintaining the FMI. The gene CUP-SHAPED COTYLEDON2 (CUC2) is expressed in the slow-dividing cells that expand in a latitudinal direction (Reddy et al., 2004) to define the second boundary between the floral primordium proper and the IM (Breuil-Broyer et al., 2004). Although the exact mechanism is not yet understood, during electrotherapy, a continuous electric current is applied to the exposed plant tissues, and as a result, their nucleoprotein is degraded and leads to the elimination of their virulence activity (Gonzalez et al. 2006; Sabry et al. 2009). Since then, cryotherapy has been used to eradicate viruses in several plant species (Wang et al. 2022b). Ultimately, Şekerz et al. (2015) successfully eliminated PPV from infected apricots using the Brison cryotherapy method; however, the majority of the samples did not survive the treatment, requiring protocol optimization for these sensitive materials. Brison et al. (1997) concluded that the size of excised shoot tip is not a key for virus eradication in cryotherapy. KNOX, WOX, and ZF-HD subfamilies partially overlap in binding-site specificity Fifty top-scoring networks were generated and a consensus network was produced via influence scores with a threshold of 30%. Sequencing was performed on the Illumina Next Seq 500 System by the Biosciences Genomics Research Hub within the School of Biosciences, Cardiff University. DNA from IP and NoAB chromatin samples was recovered using a Qiagen MinElute DNA Purification Kit alongside an input sample consisting of fragmented chromatin that was not immunoprecipitated. Two biological replicates were performed for each sample type (as per ENCODE guidelines). All plant research was conducted within the Plant Growth Technology Hub in the Cardiff School of Biosciences in compliance with international and UK guidelines. Herein, the leaves, roots, stems, tassels and ears were collected at flowering period. Cytoscape software was used to plot the regulation networks for the TFs and their target genes (Shannon et al., 2003). Cells were clustered using the FindClusters function according to their gene expression levels and visualised using the t‐SNE algorithm and the UMAP analysis (Becht et al., 2019; Butler et al., 2018). We applied the principal component analysis to reduce the dimensionality of the top variable genes. Genetic interactions among floral homeotic genes of Arabidopsis. Superman, a regulator of floral homeotic genes in Arabidopsis. For example, the use of these atlases to examine epigenetic factor expression patterns and their downstream targets within the context of their different functions at distinct floral stages will be of significant interest. Shang et al. (2021) examined the range of KNU repressive transcriptional activities in the floral meristem to elucidate floral termination control within a limited temporal context (between floral stages 6 to 8). AHL18 encodes a known regulator of lateral root development, while PLATZ10 encodes a transcription factor that belongs to a family of plant-specific zinc-dependent DNA-binding proteins (Nagano et al., 2001; Širl et al., 2020). Overall, this study reveals transcription factor interactions mediating the repression of B- and C-class floral homeotic genes. Indeed, in root explant experiments for reprogramming to floral fate, AP1 activation was detected only after 24 hours of LFY induction, with gradual accumulation of LFY protein over 5 days. Future work aimed at examining the roles of the different SWI/SNF classes in greater detail will address the current gaps in our knowledge on how the chromatin environment determines floral meristem identity. HD-ZIP III proteins function in promoting “adaxial” fates in lateral organs and “central” fates in the meristem (Engstrom et al., 2004). PLT genes are direct targets of TPL. CZ, central meristem zone; PZ, peripheral meristem zone; RZ, rib meristem zone; OC, organizer center. More recently, live-imaging technology has enabled high-resolution spatio-temporal analysis of gene expression patterns, which is useful to analyze the spatial parameters of hormonal and transcriptional regulatory modules (Sijacic and Liu 2010). In SAM, the intracellular auxin concentration is regulated by PIN1 (Vernoux et al. 2000), which is sensed by the nuclear receptor TRANSPORT INHIBITOR RESPONSE1 (TIR1). Besides auxin, CLAVATA3/ESR-RELATED 40 regulates WOX5 expression through the receptor kinases CRINKLY4 (ACR4) (Stahl et al. 2009). Besides auxin efflux facilitators (PINs)-dependent polar auxin transport (Grieneisen et al. 2007), WOX5 also coordinates local auxin production in the QC of the root (Tian et al. 2014). Apparently, all meristem control points involve the action of phytohormones. Any factors impairing nitrogen fixation efficiency increase senescence processes in the nodule (see e.g., Vance et al. 1980), including the loss of meristem function as in the case of nodules induced by defective rhizobia (see e.g., Hirsch et al. 1983). Third, it is possible that the authors were examining senescent nodules which had slowed or already lost their meristematic activity. The internal organization of a plant module raises essentially the same problems in the genetic control of pattern formation as does animal development, and they are solved in analogous ways. Each module (shown in different shades of green) consists of a stem, a leaf, and a bud containing a potential growth center, or meristem. They have evolved their multicellular organization independently but using the same initial tool kit—the set of genes inherited from their common unicellular eucaryotic ancestor. C, 3H-IAA transport in abcb19 and abcb21 mutant backgrounds from the root-shoot transition zone to 1.8–2.6 mm from the root tips (upper panels) or to the root tips (lower panels) after 1 h GA treatment (in 6-days old plants). The number of individual plants, cross-sections or clones analysed is displayed as n in figures or figure legends. In addition, STM prevents expression of ASYMMETRIC LEAVES1 (AS1), a repressor of the meristem genes BP/KNAT1 and KNAT2. WUS is required to maintain the stem cells undifferentiated and for CLAVATA3 (CLV3) expression therein (Mayer et al., 1998; Schoof et al., 2000). In the leaf primordium, adaxial and abaxial cell fates are marked by expression of HD-ZIP III and KANADI family genes, respectively. Within the Genisteae tribe, genera other than lupines, produce cylindrical nodules. These may represent cytosolic complexes of host cell enzymes, supplying some substances (proteins?) necessary for symbiosome functioning (divisions?). The most characteristic component of infected cell ultrastructure is the symbiosome. The formation of such folds may be the preliminary stage of the development of protein-containing vacuoles. Note a distinct NVT, which is the result of the origin of bacteroid-containing tissue from a sub-rhizodermal cell. PATTERNING REQUIRES SIGNALING: A FOCUS ON CHEMICAL SIGNALS Following the leaf detachment, plantlet leaf primordia (L1 and L2) emerged from the EBs after approximately 9 days (Figure 2A). At the leaf margin where plantlets are speculated to form, EB consists of a globular protuberance located in the abaxial side of the leaf crenulation (Figure 1N). Pinnata leaves, we initially examined the leaf crenulations during leaf development. (G) Magnified transversal section of the T24 with inset showing 2 cells with H1.3 positive nuclei at the boundary.In addition to TDR/PXY, two LRR-RLKs were shown to regulate vascular stem cell activities (Agusti et al, 2011b).The leaf primordia of plants start from SAM, which is an embryonal cell population with a “tunica-corpus” structure.It was observed that shoots developed from 0.3 to 0.5 mm meristems were able to retrieve ACLSV, as the values are slightly more than negative control.Embedded samples were cut with a vibratome into 200 µm sections for confocal analysis.This study reveals interesting links among dynamic cellular changes, the flowering regulatory network and GA signaling in the SAM during the floral transition. Similar approaches can be used to analyze the roles of other phytohormones such as auxin and cytokinin and to image the machinery that controls the behavior of the stem cells. We describe at unprecedented resolution the changes in shape and cellular composition that occur at the shoot meristem during floral transition induced by the environmental cue of day length. GA20ox2 was expressed in the meristem transiently after exposure to 3–5 LDs during the transition, whereas GA2ox4 was repressed at this stage, but strongly induced in floral primordia at 7 LDs (Figure 9—figure supplement 2). Previous studies showed that GA is critical for cell division and elongation in root meristems (Achard et al., 2009; Ubeda-Tomás et al., 2009; Ubeda-Tomás et al., 2008). Although KNOX proteins have a general role in reducing GA levels in meristems (Bolduc and Hake, 2009; Hay et al., 2002; Jasinski et al., 2005; Sakamoto et al., 2001a; Sakamoto et al., 2001b), they are unlikely to have a regulatory function in modulating GA levels in the SAM specifically during floral transition. BRM acts in the PLT pathway to regulate the expression of PIN genes, which in turn influence auxin distribution in the QC region to ensure RAM maintenance. Chromatin remodelers in shoot and root apical meristem establishment and maintenance. The subsequent establishment of the leaf, stem and flower meristems occurs in the postembryonic phase. WOX5 is necessary for the maintenance of CSCs as in wox5 mutant roots, cells in the CSC position acquire starch granules like differentiated CCs (Sarkar et al., 2007). In this review we will focus on the function and regulation of known TFs important for stem cell regulation in the RAM (summarized in Table 1). Ep, epidermis; c, cortex; en, endodermis; LRC, lateral root cap; CC, columella cells. Arabidopsis meristematic zone organization and regulation of WOX5 expression in the QC. Stem cells for the lateral root cap (LRC)/epidermis and the columella are positioned distal to the QC. The evolution of vivipary in flowering plants. Functional analysis of all AGAMOUS subfamily members in rice reveals their roles in reproductive organ identity determination and meristem determinacy. Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis. Three IDD genes (mentioned above) are direct targets of RA1 (Eveland et al., 2014). We propose that phyllotaxis is intimately connected to meristem identity. However, how this concentration gradient of HAM is defined in the developing meristem and continually maintained in the established SAMs remains to be elucidated. As many regulators have multiple roles in diverse aspects of inflorescence development, more precise insight into their role in a given process/trait of interest, for example by cell-type-specific loss-of-function mutants, is important. For example, identification of direct targets of transcriptional regulators by chromatin immunoprecipitation and defining the underlying cis motifs will allow precise “rewiring” of specific regulatory interactions by CRISPR/Cas9 mutagenesis of noncoding DNA. That CRISPR/Cas9 approaches that target domestication genes can lead to rapid increase in fruit size and number in wild relatives was also recently shown in tomato (Zsögön et al. 2018). In addition, genes that contribute to the architecture of the inflorescence, such as AGL79/VEG1, CUC3, FZP, and TAW1, are potentially linked to yield enhancement (Crowell et al. 2016; Li et al. 2016; He et al. 2017; Zheng et al. 2017; Fujishiro et al. 2018; Gao et al. 2018; Ta et al. 2018). During floral meristem identity specification, these events may initially correspond to stages 0–2 of flower development wherein LFY and AP1 activity have been observed (Smyth et al., 1990; Ó’Maoiléidigh et al., 2014). Additionally, LFY’s ability to reprogram root identity to floral meristem identity was also demonstrated to be dependent on its pioneer function (Jin et al., 2021). In this study, the authors highlighted the importance of the spatial context of gene expression dynamics in uncovering the molecular networks behind cellular differentiation during development (Neumann et al., 2022). Moreover, gene expression could be correlated with growth patterns through pairwise comparisons of genes with partially overlapping expression patterns. Caggiano et al demonstrated that wounding disrupts the adjacent expression domains of dorsoventral specificity factors REVOLUTA (REV) and KANADI1 (KAN) in the SAM, and the boundary of auxin signaling that separates them.Single-gene mutations within these SAM genetic networks can alter the morphology of both the shoot meristem and the plant9,10, revealing that SAM structure and function are intimately linked.High PAR and high temperature widely downregulated genes involved in photosynthesis, including photosystem I/II components, thylakoid protein and light harvest complex proteins with strong folds (≤60-fold).(Chromatin immunoprecipitation followed by next-generation sequencing).The choices between alternative modules and their organization into a whole plant depend on external cues and long-range hormonal signals that play a much smaller part in the control of animal development.The former transfer strategy aims at introducing naked DNA into a plant genome through chemical or physical means (e.g. biolistics, electroporation, and polyethylene glycol), whereas the latter involves the introduction of DNA using biological vectors (e.g. Agrobacterium spp., Ochrobactrum haywardense, or viral vectors) .In this review, we mainly discuss how the plant phytohormones, such as auxin and cytokinin, coordinate with the key transcription factors to regulate plant stem cell initiation and maintenance in root and shoot apical meristems.The first examples of genes regulated by the ABC genes were two MADS-box genes, AGL1 and AGL5 (renamed the SHATTERPROOF genes (SPH1 and 2, respectively). Of the 86 genes in the MC dataset, 81 were expressed in a sufficient number of cells and at differing levels to be regarded as informative. Heat maps show selected examples of imputed differentially expressed genes using a one-sided MAST, with Padj m, Imputed expression of candidate genes specifically expressed in the founder cells or n, in TSM primordium. K, By data integration and imputed gene expression, we can virtually dissect the IM (dark blue), Fo (cyan) and P cells (purple). B, In inflorescence meristems (IM), spikelet founder cells (white arrows and dotted line) also show HvKN1 mRNA depletion, but this is restored once the primordia are organized (magenta arrow). Thus in Arabidopsis, FMI is regulated by a large and partly redundant GRN that serves to ensure the robustness and stability of meristem determinacy and prevent reversion to vegetative growth.We also delved into the mechanisms employed by stem cells to withstand and respond to abiotic stressors.Genes selected using PERSIST, which identifies representative gene sets for distinct cell populations46, outperformed hand-selected or randomly selected genes, and 20 genes were sufficient for reliable cell similarity determination.Based on sequence differences in conserved domains, it can be divided into two subgroup including classI (promoting cell proliferation and plant growth) and class II (inhibiting cell proliferation) (Liu and Gao, 2016; Yang et al., 2019).Amongst the different protocols using direct de novo shoot organogenesis, the plumular meristem strategy was proposed as a time-efficient direct regeneration-based transformation approach with high transformation rates for chickpea 22, 146 and pigeon pea 147, 148.Forward and reverse genetic studies on maize meristem mutants have driven forward our fundamental understanding of meristem maintenance and differentiation mechanisms.Therefore, GAs might not be the main driver of cell division activities of vascular cambium under an unstressed condition, but might be under the mechanical stress.Thaliana, point mutations in the miR319 target sites of TCP4 reduce interactions with miR319, resulting in higher levels of miR396, lower accumulation level of GRFs, and smaller leaf formation (Rodriguez et al., 2010). RNA-directed DNA methylation: an epigenetic pathway of increasing complexity We calculated the methylation differences between WT and the osdrm2 mutant28 for SAM and leaf DMRs. To assess the contribution of the RdDM pathways to CHH hypermethylation in the SAM, we analyzed whether SAM and leaf DMRs are hypomethylated in the osdrm2 mutant relative to wild type (WT). CHH methylation increased during the vegetative-to-reproductive transition in the SAM, but this increase was not coupled with changes in the mRNA expression level of RdDM pathway components between the vegetative and reproductive SAM (Fig. 4b). The AS2 genes encode plant-specific LATERAL ORGAN BOUNDARIES (LOB) domain proteins. Regulatory genes expressed in the abaxial domain of the leaf exert a suppressive effect on the genes expressed in the adaxial domain. The adaxial-abaxial axes play a role in defining medio-lateral axes polarity by controlling the differential distribution of auxin and its downstream signaling molecules in the leaves, facilitating flat leaf growth (Qi et al., 2014). During the development of compound leaves, KNOX1 expression is reestablished within the leaf primordium, thereby initiating the formation of distinct lobules (Hay and Tsiantis, 2006; Leiboff et al., 2021). Apart from ARP, the KNOX2 gene also promotes leaf development by counteracting KNOX1 (Furumizu et al., 2015). Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa). Genetic enhancer analysis reveals that FLORAL ORGAN NUMBER2 and OsMADS3 co-operatively regulate maintenance and determinacy of the flower meristem in rice. The YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa. Functional diversification of the two C-Class MADS Box genes OsMADS3 and OsMADS58 in Oryza sativa. Structural characterization, chromosomal localization and phylogenetic evaluation of two pairs of AGAMOUS-like MADS-box genes from maize. BLADE-ON-PETIOLE1 encodes a BTB/POZ domain protein required for leaf morphogenesis in Arabidopsis thaliana. Control of Arabidopsis leaf morphogenesis through regulation of the YABBY and KNOX families of transcription factors. Comparative analysis of the RTFL peptide family on the control of plant organogenesis. Internode stem diameter and length are inversely correlated in maize and other grasses47,48, such that internode width decreases markedly in upper (younger) nodes as internode length increases. Such a correlation in seedling SAM size and adult stem size is quite remarkable, considering there is an ∼800-fold increase in size between the average SAM radius and the average stem diameter for the 369 lines in our study. Significant correlations were likewise discovered between SAM size and stem diameter, which is an important factor in lodging resistance and damage from stem boring insects45,46. Our data agree with previous reports that correlate large SAM size with early flowering (decreased days to anthesis) phenotypes2, and our data expand this correlation to a markedly larger panel of inbred maize varieties. However, because 77% of SNPs from our genotyping matrix were generated by RNAseq analysis, we expect a bias towards the identification of genic polymorphisms by GWAS (Fig. 3b)26. Cell type-specific profiling approaches have been used to understand the floral meristem (FM) that develops into flowers3,19,20,21. The stem cell niche is maintained by the OC which provides stem cell-promoting cues7,8,9. Technologies to achieve this have been developed and have substantially expanded our understanding of cell identity and function in plants1,2,3,4,5,6. WUS expression is limited to the cells immediately below the stem cells, an expression domain regulated by the receptor-kinase signaling system that includes the CLAVATA1, 2 and 3 (CLV1, 2, 3) gene products (Mayer et al., 1998; Brandetal., 2000; Schoof et al., 2000). Flower development ends when mature organs are formed and all the flower meristem cells are used up (Takeda et al., 2004; Krizek and Fletcher, 2005). The cells originating from L2 also divide periclinally (outside the SAM) and contribute for example to the leaf mesophyll or stem ground tissue formation during organogenesis. Interestingly, half of these 30 genes were annotated as agamous-liked genes, and most of these agamous-liked genes showed higher expression in the shoot meristem and flower (Supplementary Fig. 13a). Interestingly, maize scRNA-seq data identified some tunica cells expressing ZmKN1 (ref. 31), and the rice orthologue of ZmKN1 (OsH1) is expressed in the L1 of FM, in some cells of the IM, but not in L1 cells of the vSAM47. We used our integrated datasets in BARVISTA to probe gene expression patterns in detail during early primordia initiation. Genes selected using PERSIST, which identifies representative gene sets for distinct cell populations46, outperformed hand-selected or randomly selected genes, and 20 genes were sufficient for reliable cell similarity determination. Validating with the same 81 anchor genes gave a mean CS of 0.84 ± 0.10, and validation with all 48,904 genes gave a still robust, although slightly lower CS of 0.73 ± 0.10 (Supplementary Table 8). We therefore analysed the overall expression pattern of APL in more detail. Next, we tested whether GA affects the production of different phloem cell types. Previous histological studies in hypocotyl21 and our lineage-tracing results in root (Fig. 1i) show that GA inhibits phloem production. Under GA-treated conditions, clone cell lineages show an unequal distribution (Fig. 1g,i), with a preference towards the xylem side, while lineages in the ga1 mutant background preferably span towards the phloem (Fig. 1h,i). This enabled us to monitor the cambium growth dynamics over time. In the Golden Promise genetic background, a two-row type of barley, only the CSM continues its development and will form a floret meristem (FM), which then generates gynoecium (GyP) and stamen primordia (StP). C, At W3.5, the inflorescence meristem (IM) at the top of the spike is determined to form lateral meristems specified as triple spikelet meristems (TSMs), which will then generate two lateral spikelet meristems (LSMs) and one central spikelet meristem (CSM). A, Scanning electron micrograph (SEM) of the vegetative shoot apical meristem (vSAM), highlighting leaf primordium (LP) formation (green). We detected the expression of an average of 4,527 genes per cell and 17,553 transcripts, mapping to 46,495 gene models, including low- and high-confidence models, of the reference genome assembly for barley cultivar Morex (Morex V3). The PAN gene mutation specifically alters floral organ number, yielding fertile plants with a pentamerous meristic pattern (Running and Meyerowitz, 1996). Increased auxin levels mark the initiation sites for organ primordia (including those of floral organs) and local application of auxin is sufficient to trigger leaf or flower formation in the shoot apex (Reinhardt et al., 2000; Tanaka et al., 2006). Some of these phenotypes are pleiotropic consequences of mutations in genes acting from earlier steps of plant and flower development. Plant morphogenesis is influenced both by the orientation and rate of cell division, as well as by cell expansion and differentiation (see section 2 for a description of floral organ initiation and morphogenesis). Next at the rhizoplane they colonize the emerging root hairs and penetrate their wall to become internalized by the host. Initial stages of the symbiosis involve complex processes of mutual recognition, root colonization and invasion which occur nearly simultaneously in the rhizosphere, at the rhizoplane and within the host root (Foucher and Kondorosi 2000). In this review, the anatomy of indeterminate legume root nodule is briefly summarized. A member of the knotted class of homeodomain proteins encoded by the STM gene of Arabidopsis. However, until now, the role of water has been considered non-limiting for morphogenesis in aboveground organs, with water playing essentially no role in the patterning per se. During development, multicellular tissues are patterned by biochemical and mechanical cues1,2,3,4,5,6,7. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. 2 modulates leaf rolling by trafficking and endosomal degradation of auxin biosynthetic enzyme OsYUC8 in rice. In total, QTL intervals recaptured 11 previously identified SAM-morphology candidate genes implicated by GWAS of maize inbred varieties (Supplementary Data Sheet 4) (Leiboff et al., 2015). Parabolic estimators of MxT line SAM shape and size identify meristem morphology QTL. Supplementary Data Sheet 4 details all significant QTL intervals as well as known GWAS candidate genes within those intervals. Shoot apical meristem contours were digitized with an Intuos Draw Tablet (Wacom Technology Corporation, Portland, OR, USA) and used for both linear model fitting with the lm() function and Fourier transform with the Momocs package for R. Near-median DIC images were processed by custom ImageJ macros to extract meristem contours and measures of SAM height and SAM radius (as reported in 10).