Afterward, ANT expression is confined to the cotyledons, together with AS1 that, in analogy to leaves, might downregulate the meristem genes KNAT1 and KNAT2 to allow differentiation (Byrne et al., 2000; Ori et al., 2000). CUC1 and CUC2 activities in turn are required to initiate STM expression and overexpression of CUC1 induces the formation of ectopic meristems, indicating CUCs as promoters of shoot meristem fate (Takada et al., 2001). This suggests that cotyledon initiation, albeit morphologically similar to postembryonic leaf initiation, uses a different genetic repertoire than the postembryonic shoot meristem. Interestingly, however, the earliest defects observed in wus mutants are in heart stage embryos, when the cells and the structure of the shoot meristem primordium are abnormal. Developmental Analysis of Arabidopsis Root Meristem The sense probe is the same as that used in Fig. A, c, e, mRNA in situ hybridization of GhSUT4 (a), GhCYCD2;1 (c), and GhZAT11 (e) in dormant and growth-transited cormels. G, k, Growth-transited buds show stronger cell division capacity than dormant buds. Enhanced PAS staining was observed in growth-transited buds. “Flow cytometry and sorting in arabidopsis,” in Arabidopsis protocols methods in molecular biology. Negative regulation of the Arabidopsis homeotic gene AGAMOUS by the APETALA2 product. The Arabidopsis FILAMENTOUS FLOWER gene is required for flower formation. A novel sensor to map auxin response and distribution at high spatio-temporal resolution. Genes directing flower development in Arabidopsis. In the populations, sibling plants of positive homozygous mutation at the target sites (zmereb14‐1 and zmereb14‐2) were used to investigate the trait phenotypes. The shoot apexes with the 2–3 most recently initiated leaf primordia were collected for preparing protoplasts (Figure S24a). Our results provide new information about shoot apex development and will be helpful for perfecting the mechanisms of shoot apex development. Previous studies have shown that the above‐ground organs of mature plants and ears were originated from SAM and AM, respectively (Sun et al., 2020; Zhang et al., 2021a). In the immature ears, ZmEREB14 maintained a stable expression level throughout the early development of ears and showed a slight upregulation at the stage of 3–5 cm ears, the decisive stage for silking (Figure S21l; Shen et al., 2023). These findings indicated that STM is required for whorl 4 and/or carpel development in FMs. Ectopic expression of STM results in the formation of ectopic carpels, carpelloid organs and the conversion of ovules to carpels (Scofield et al., 2007). STM binds and activates CUC1 expression, and CUC1 can directly activate STM expression to comprise a direct positive-feedback loop, which is attenuated by STM-induced miR164c (Hibara et al., 2003; Spinelli et al., 2011; Scofield et al., 2018). Supplementary Table 1 List of gene modules maintaining stage-independent expression variance between individual SAMs. Dots indicate individual plants and bars showing mean and SE. E) Comparison of log2 total-UMIs obtained from randomly selected half of the replicates in each uf meristem (denoted as replicate #1, x-axis) to the other half (replicate #2, y-axis). The four genotypes were sampled over time as marked by the x-axis (red line indicates no data was collected at this DAG for the respective genotype). D) Fractions of SAMs classified as at flowering meristem (FM) stage or later. Thus, these lycophyte roots formed as a novel type of organ, and this fossil further suggests that certain lycophyte roots may have co-opted positive gravitropism at a later evolutionary step. Hence, Hetherington and Dolan take this as evidence for step-wise acquisitions of key root traits during root evolution in the lycophyte linage. The earliest fossils with true roots have affinity to the lycophytes. Evolution of homorhizoic and allorhizoic roots are marked in red, other major root evolutionary events are indicated in green. Characterization and expression of a Pinus radiata putative ortholog to the Arabidopsis SHORT-ROOT gene. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. The interrelationships of land plants and the nature of the ancestral embryophyte. Intercellular movement of the putative transcription factor SHR in root patterning. Natural genetic variation in plant photosynthesis. A protracted and dynamic maturation schedule underlies Arabidopsis leaf development. Quantitative control of ASYMMETRIC LEAVES2 expression is critical for leaf axial patterning in Arabidopsis. A conserved molecular framework for compound leaf development. This is particularly striking at the inflorescence meristems, as the full knock-out mp mutant forms a naked, pin-like stem with very few or no flowers forming.The model parameters are adjusted such that L1, L2, and L3 cells are growing thanks to the water provided by cells underneath (Fig. 2D and Supplementary Table 1).Identifying genes specifically affecting organ and tissue coordination is expected to be difficult.After 2 d of washing the samplesin 0.1 m l-arginine, pH 8, SAMs were viewed with a Zeiss confocal LSM5 microscopeequipped with an argon laser (excitation 514 nm).Gene expression domains are indicated.Third, a recently developed perception sensor that is degraded in the presence of high auxin concentrations confirms the presence of auxin maxima at the sites of organ formation (Vernoux et al., 2011).The progression described above has been established by numerous researchers through sectioning or imaging methods using plants grown under various growth conditions, and by investigating the spatiotemporal expression of a handful of key genes in the different floral organs. Blue cells represent stem cells, green shadowed area represents the meristematic cell or meristematic zone. A traditional approach to studying meristems considers their morphology and focuses on their correlation to plant growth patterns. In fact, moss and fern gametophyte SAMs share key transcription factors (TFs) with angiosperm sporophyte SAMs 47,48, which suggests the existence of fundamental mechanisms involved in stem cell regulation across land plants. Consequently, similar classes of genes have been co-opted as central regulators in both types of meristems 18,19. The QC and OC are the signaling centers responsible for stem cell maintenance in both meristems and have been proposed to be functionally equivalent 17,18. Rudall, P. Lateral meristems and stem thickening growth in monocotyledons. Although monocotyledons lack a vascular cambium of the type found in dicotyledons and conifers, lateral meristems still play an important role in the establishment of their growth habits. Diversity of maize shoot apical meristem architecture and its relationship to plant morphology. In addition, the strong expression levels at the meristem periphery suggest high auxin sensitivity there. Interestingly, most of these genes were more strongly expressed at the periphery of the meristem where the organs are initiated. Altogether, the available data indicate that the formation of local auxin maxima mainly depends on the action of PIN exporters at the meristem surface. Conversely, at least in Arabidopsis, cytokinin responses are apparently repressed when cells leave the meristem and are incorporated in the young primordia, since young primordia express ARABIDOPSIS PHOSPHOTRANSFER PROTEIN6 (Bartrina et al., 2011). It also induces them to express the peptide ligand CLAVATA3 (CLV3), which via interaction with the receptor-like kinase CLV1, feeds back to inhibit WUS expression and maintain a stem cell pool of a constant size (Schoof et al., 2000). In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. Stem cells residing in plant meristems possess dual functions, controlling both self-renewal and organogenesis by precisely coordinating the balance between proliferation and differentiation. Given the enriched functions identified in the GO analysis, we next examined our ChIP and transcriptomics datasets to identify genes with known roles in meristem or lateral organ development, particularly those involved in the control of cellular differentiation and pluripotency or the regulation of plant hormone function. Furthermore, the highest level of expression of GA20ox2 in the PZ was observed in meristems of 2w- or 3w-old SD-grown plants transferred to 3LDs (Figure 2—figure supplement 3). Furthermore, after transfer of 2wSD-grown plants to LDs, the size of the meristem and the cell number in the SAM of ga2ox4–3 were indistinguishable from those of wild-type Col-0 (Figure 4—figure supplement 6A–C), consistent with GA2ox4 expression being reduced in Col-0 plants under these conditions. The proximal cells continue dividing within a division zone (DZ), until they reach a point in which division ceases and elongation begins. As discussed above, the evolution of roots was predated by shoots growing indeterminately. It is currently an unresolved issue if the allorhizoic seed plant root is homologous with the homorhizoic fern root. Similar to lycophytes, fern roots develop as adventitious outgrowths in relation to the longitudinal axis of the embryo, and form so called “homorhizoic” roots (Raven and Edwards, 2001). D Numbers of expressed genes in multiple domain groups. C Numbers and proportion of expressed genes in each domain. Previous work has defined transcriptional regulatory networks of abaxial- and adaxial-promoting protein and microRNA encoding genes10,11,12. To understand how cells work and how they interface with the environment, it is useful to acquire quantitative information on transcriptomes and translatomes (translating messenger RNAs (mRNAs)) at cellular and cell-type resolution. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. The developmental gene Knotted-1 is a member of a maize homeobox gene family. Architecture of floral branch systems in maize and related grasses. Bearded-ear encodes a MADS box transcription factor critical for maize floral development. Genetics of floral development in Petunia. To understand how cells work and how they interface with the environment, it is useful to acquire quantitative information on transcriptomes and translatomes (translating messenger RNAs (mRNAs)) at cellular and cell-type resolution.Age-dependent increases in intron retention (IR) splicing variants from Sen-NAC can fine-tune the molecular mechanisms of Populus leaf senescence (Wang et al., 2021b).Some plants, such as tobacco (Nicotiana tabacum), Arabidopsis thaliana, and rice (Oryza sativa), can be easily regenerated in vitro, whereas other plants, such as soybean (Glycine Max), wheat (Triticum aestivum), and maize (Zea mays), are more difficult to regenerate.However, when roots are examined based on their typical habitats, they can be useful when comparing groups of plants.QTL analyses of bi-parental populations have shown that differences in SAM morphology may involve loci not previously identified via single-gene mutations2,11. Kinematic approaches have also been used to assess cell proliferation kinetics outside the RAM, e.g. for lateral root development (Dowd et al., 2020) and leaves (Rymen et al., 2010). Thus, considering that after initiating the EdU treatment ~35–40% of cells become labeled, after ~3–4 h (an average G2 duration in Arabidopsis roots) they will start to divide and increase the percentage of EdU-labeled cells not derived from entry of new cells into S-phase. It is true that the use of nucleoside analogues such as EdU has not only simplified enormously the experimental procedures but also avoided potentially deleterious effects on root cells due to radiation from 3Hthymidine, particularly when long treatments are carried out. As a way to simplify the system, the RAM was considered the sum of single cell files, all of them with the same proliferation properties (López-Sáez et al., 1975; Green and Bauer, 1977; Baskin, 2000). Indeed, differences at the transcriptomic level in the RAM cells have been demonstrated by single-cell RNA-seq, allowing the identification of developmental trajectories of the various cell types in the RAM (Denyer et al., 2019; Jean-Baptiste et al., 2019; Shulse et al., 2019; Ryu et al., 2019; Zhang et al., 2019; Wendrich et al., 2020; Long et al., 2021). Additionally, traits such as yield, flower and fruit number, and stress resistance are influenced by SAM and Floral Meristem activity (Fletcher, 2018). In contrast, plant heightis an aggregate trait that can be achieved by varying these contributing attributes, andits relationships to the drivers of these attributes is consequently weaker. This is in accordance with, using alarge comparative set, the patterns identified in cell size/cell number variation inindividual species (e.g. Gonzalez etal., 2010). Much of cell biology today seems to involve networks of intra- and intercellular interactions. The Meristem program provides participants with opportunities to socialize through various activities such as group outings and events like movie nights or game nights. The Meristem program is available nationwide and has been helping young adults with ASD since 2008. The team at Meristem was incredibly helpful and they delivered the results I was looking for. The establishment and maintenance of stem cells in secondary niches involve the reacquisition of stem cell identity by a group of cells, followed by morphogenetic processes. Here, we showed that meristem genes were differentially expressed in the leaf crenulations of K. SHOOT MERISTEMLESS (STM), which mediates SAM functions, appears to be involved in Kalanchoë plantlet formation, suggesting that meristem genes may be essential for plantlet formation. The gene-cell matrices (named ‘filtered_gene_bc_matrices’ by 10× Genomics) were served as processed raw data for further analyses.Modern day ELISA is one of the most widely used serological test for the detection of plant viruses.Meristem identity and phyllotaxis are intimately linked.This review summarizes current knowledge on meristem structure, function, and evolution.SE computed based on binomial sampling.In ra mutants, auxin signaling is perturbed before any morphological phenotype can be observed (Eveland et al., 2014).It was seen that the maximum survival percentage of 24.32 and 35.29 were observed in the buds collected both from basal and distal portions respectively of the actively growing shoots (Table 2).GIF family genes form functional complexes with GRF transcription factors and participate in cell proliferation activities during leaf development (Kim and Kende., 2004; Lee et al., 2009; Debernardi et al., 2014; Lee and Kim., 2014). It remains unclear if this RAX1 binding represents primary regulation or secondary feedback, as CUC2 expression precedes that of RAX1. Consistent with this differential expression, only CUC1 and CUC2 transcripts are degraded by miR164. Among the RAX gene mutants, rax1 mutants have the strongest AM initiation defects, which are enhanced by rax2 and rax3 mutations. Rice MOC1 promotes tiller bud outgrowth , which is distinct from the functions of its orthologs in Arabidopsis and tomato. In rice, a co-activator of the cell cycle anaphase-promoting complex, TILLERING AND DWARF 1 (also named TILLER ENHANCER), targets MOC1 to the 26S proteasome for degradation in a cell cycle-dependent manner 34, 35. Model for the regulation of arabidopsis thaliana leaf margin development. Pinnata as a transitional form from sexual to asexual reproduction instigates the acquisition of meristematic competency to achieve the production of plantlets on the leaves. Pinnata recruited meristem pathways to facilitate the novel reproductive strategy such as the formation of EBs in the leaf crenulations. KpWUS AS lines showed downregulation in KpCLV1, KpCLV2 and KpCUC2, suggesting that KpWUS positively regulated the expression of these genes in the EBs of K. The D-lineage MADS-box gene OsMADS13 controls ovule identity in rice. Ovule development, a new model for lateral organ formation. The petunia MADS box gene FBP11 determines ovule identity. Colombo, L., Franken, J., Koetje, E., Van Went, J., Dons, H. J., Angenent, G. C., et al. (1995). At the late globular stage, four procambial cells divide periclinally, giving rise to the pericycle and vascular stem cells. At the early globular stage of Arabidopsis embryos, cells inside the protoderm divide into distinct layers, the ground tissue precursors and vascular stem cell initials (procambium) (Figure 3A; Mansfield and Briarty, 1991; Lau et al, 2010). These findings suggest the existence of conserved regulatory programs among different plant stem cell pools (reviewed by Sablowski, 2011). In RAM, daughter cells of stem cells are committed into specific cell fates depending on their position (B). To investigate the regulatory network of ZmEREB14 in SAM development, we compared the transcriptomes of the shoot apexes from wild‐type B73 and zmereb14‐1 mutant. To verify whether ZmEREB14 affected the axillary meristem (AM), we measured the AM size of these lines. In results, ZmEREB14 showed the highest expression in shoot tips and the lowest expression in tassels, respectively (Figure 4a). Extraction of RNA from the plant kalanchoe daigremontiana.In any case, it is a useful boundary to consider since it reflects a key functional difference in cell proliferation potential within the RAM.As mentioned above, plant phytochromes contain a C-terminal HKRD but surprisingly a recent report concluded that the PSM of phytochromes (including phyB) directly phosphorylates PIFs50.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.Single-molecule FISH (smFISH) and other high-resolution FISH experiments are also rarely used in plant studies13,14 due to the endogenous autofluorescence of many plant cells13.The main inflorescence meristems at the bolting stage were used to analyze the SAM size, gene expression patterns, and protein subcellular dynamics. Taken together, cytokinin signalling restricts the auxin signalling maximum to the xylem axis by regulating the bisymmetric localization of PINs. Furthermore, auxin signalling maximum is expanded throughout the vascular cylinder in the wol mutant. These suggest that cytokinin signalling might regulate the expression of PINs in Arabidopsis vascular tissues. Interestingly, the expression of these PINs is significantly downregulated in the wol mutant where the cytokinin signalling is reduced. As in animals, genes governing plant development can be identified through genetic screens and their functions tested by genetic manipulations. An axillary bud is a potential new meristem, capable of giving rise to a side branch; the environment—and long-range hormonal signals within the plant can control the development of the plant by regulating bud activation. Typically, the shoot generates a repetitive series of modules, each consisting of a segment of stem, a leaf, and an axillary bud. A great majority of secondary plant metabolites belong to the redox-active compounds which, depending on their intrinsic redox potential and environment, might exert opposite ROS/RNS scavenging or promoting actions. ROS initiate the development of resistance mechanisms such as the biosynthesis of secondary polyphenols with antioxidant and free radical scavenging properties. Thus, a 2 min sonication of Taxus cell cultures induced rapid and dose-dependent NO production, followed by induction of taxol biosynthesis . H Quantification of terminated seedlings grown on auxin plates from two independent experiments. E Auxin treated SAM; f TSA treated SAM; g TSA and auxin treated SAM. These results underlined the relevance of histone de-acetylation for the genome-wide functional output of WUS and prompted us to investigate whether this mechanism is relevant for controlling auxin responses in the SAM. Genes downstream this pathway are annotated as “responsive to auxin” and are also highly overrepresented among WUS targets (GO term enrichment taken from Supplementary Table 1). Pathway level control underlies WUSCHEL mediated gating of auxin signaling. D, Expression levels of BR biosynthetic genes and BRI1 in the Arabidopsis root. E, Decreased root growth by the inducible, tissue-specific expression of BAS1–GFP in the endodermis. Root meristems of the 6-day-old seedlings from two independent transgenic lines for each GFP–tagged enzyme are shown. Our finding that spatiotemporal regulation of hormone synthesis results in local hormone accumulation provides a paradigm for hormone-driven organ growth in the absence of long-distance hormone transport in plants. Brassinosteroid (BR) hormones are indispensable for root growth and control both cell division and cell elongation through the establishment of an increasing signalling gradient along the longitudinal root axis. Since we had found that stem cell specific expression of individual auxin signaling components was not sufficient to interfere with stem cell fate, we wanted to test whether reducing WUS function would sensitize stem cells to activation of the entire pathway. Neither of the 17 factors tested caused meristem phenotypes when expressed in stem cells (Fig. 3 and Table 1), highlighting the robustness of stem cell fate in the presence of WUS on the one hand and the activity of auxin signaling in these cells on the other hand. After 24 h induction of nanobody expression, WUS-linker-GFP signal was substantially reduced in stem cells of the epidermis and subepidermis (Fig. 4g–h) and after five days we observed shoot termination (Fig. 4i). Taken together, these experiments demonstrated that auxin signaling is locally gated to permit a low instructive output level, while at the same time protecting stem cells from the differentiation inducing effects of the phytohormone at high signaling levels. This experiment demonstrated that the loss of auxin signaling output clearly precedes an elevation of CLV3 expression and allowed us to rule out that the expression of BDL-D forced stem cells into differentiation independently from its role in auxin signaling. For each roi file containing one cell from the segmentation, the pixel values were changed to the cell ID, creating the 16-bit mask file. Briefly, the developed macro creates a new image file the same size as the original image with pixel values of zero, creating a black background. The count matrices were CPM normalized and rounded to zero decimal points, compressed using gzip with six compression levels and saved separately in two matrices for the MC and SC data. Multiple input files were prepared for visualization based on Seurat clustering results, containing cell IDs, UMAP coordinates, cluster IDs and cluster names for all calculated resolutions. The datasets were integrated using IntegrateData, scaled using ScaleData, and PCA was performed using RunPCA with VariableFeatures as PCA features and 50 dimensions. A mutation in either ZmFCP1 or FEA3 results in a marked enlargement of the IM, and both genes function in the same genetic pathway.During the lifecycle, once a certain number of fruits are produced, all meristem activity arrests coordinately (termed global proliferative arrest, or GPA) to promote subsequent fruit filling and plant death.When plants experience salt stress, exacerbating cell damage leads to the release of AtPEP3, which in turn induces downstream signaling responses.Reported DNA methylome data for egg cells16 and sperm cells31 of rice were re-analyzed with our methods and we confirmed that the TE bodies are CHH-hypermethylated in the egg cells (Fig. 5a).This makes water a patterning factor at the shoot apex acting in synergy with mechanical and biochemical cues.Meristem is dedicated to preparing young adults with autism and other neurodiversity for a life of greater independence and fulfillment.Auxin promotes cell proliferation and expansion (Leyser et al., 1996) and acts as a signal during cell proliferation to determine the shape and size of the final organ (Lincoln et al., 1990). Indeed, plants are rich in endogenous bioactive metabolites with potential cosmetic and pharmaceutical applications 7, 8, 9. Since time immemorial, the mankind has used different plants and their extracts to create cosmetics with the aim to establishing a state of eternal youth 6. The aim of this paper is to review the recent progress in plant cell technology for cosmetic application and to provide short overview on commercialized plant cell culture – derived active cosmetic ingredients available on the market. Coordinated presence of TFBSs from 11 TFs that act in flower morphogenesis can largely predict the floral domain-specific expression patterns (Fig. 5b).Recently developed high-throughput methods to profile gene expression at single-cell resolution have been successfully applied to plants.Kernel density plots were generated by comparing the average cytosine methylation rate within a 100-bp window between vegetative SAM and either mature leaf blades or reproductive SAM.Limited availability of P, N, and sometimes sulfur promotes SL production in, and exudation from, the roots, upregulates expression of SL biosynthetic genes, and inhibits branching in a number of species (Yoneyama et al., 2007, 2012; Drummond et al., 2015; Abuauf et al., 2018; Shindo et al., 2018).A fate map of the Arabidopsis embryonic shoot apical meristem.BLR was also found to be involved in repression of AG in the outer floral whorls, especially in later developing flowers and at higher temperatures75. Supplementary Data 6 Here we show that STM binds upstream of the TCP4 promoter, though not the promoters of the related genes TCP3 and TCP10, suggesting only regulation of TCP4 is direct. In support of this, AIL7, and to a lesser extent AIL6 and RAP2.6L, were highly connected hub nodes within the network, and showed connections to numerous other genes with functions including boundary formation, KNOX gene regulation, hormone function and chromatin regulation. Indeed, two additional genes (At1g49830, encoding a bHLH transcription factor, and the homeobox gene HB7) were identified that showed network connections to CUC1 and/or the LSH genes and may represent additional new components of this regulatory module. From a functional perspective, the STM-bound target genes identified here were in broad agreement with those found in maize and rice25,26. Specificity in the regulation of target genes could therefore rely on the composition of these heterodimeric complexes, which also facilitate nuclear import, with different KNOX and BELL partners interacting to recognise different cis-regulatory elements using nucleotides outside of the TGAC core34. The L1 (epidermal) cells were segmented in MorphoGraphX and shown as a heatmap. 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). The template of a whole SAM was used for all the simulations, and only a half of the SAM is displayed for visualization of cells in inner layers. M, n Simulated HAM1 mRNA expression patterns in SAMs from the wild type control (m) and the plant with ectopic activation of ATML1(n). In this model, the miR171 and HAM mRNA are essential for the apical-basal pattern of HAM gene expression. The axillary meristem is initiated from the boundary between the shoot apex and leaf primordia Among the genes detected in corpus subclusters, we found 46 MADS TF genes, 26 of which were differentially expressed between 0.24 and 74.7% of the 4,807 cells in the corpus (Fig. 4c,d and Supplementary Table 15). The TF encoded by HvHD-zip/HvHDZIV2/HvOCL2 (2HG ) was previously reported as an IM or spike tip marker, but our smRNA-FISH data showed that it is also expressed at the tips of other meristems within the inflorescence48 (Fig. 3f,g). HvLOG1 is expressed at the tips of the SAM, IM, TSM and FM (Fig. 3e and Supplementary Table 9) and could potentially generate a cytokinin source at meristem apices that promotes WOX9C expression. In the spike, almost 9% (268 of 3,023) of all tunica cells expressed HvKN1 (Fig. 3c,d), and also the cytokinin biosynthesis gene HvLOG1 (5HG ), as well as HvWOX9C.2 (3HG ) and HvWOX9C.1 (1HG ), which are WUSCHEL-LIKE HOMEOBOX genes related to rice OsWOX9C. We found that genes with substantial variations in expression across samples performed better than less variably expressed genes. Gene expression programs governing meristem and floral organ identity To reach that goal, we analysed roots during the early stages of secondary growth, when cell division and differentiation dynamics are easier to follow. To understand the role of GA on cambial growth dynamics, we analysed GA’s effect in Arabidopsis roots at a cellular resolution. Conversely, reduced gibberellin levels favour specification of phloem-side stem cell daughter as phloem. Occasionally, this broadening leads to direct specification of both daughters as xylem, and consequently, adjacent phloem-identity cell reverts to being stem cell. Nonetheless, the data suggest that the stem cell population housed in the diminutive, microscopic maize seedling SAM is predictive of several impactful adult agricultural traits, despite substantial intervening development and growth. Morphological evidence showing P1 and P0 leaf primordia arising from the periphery of all the samples examined in this study (Figs 1a,b and 2a–c) confirm that these SAMs are indeed vegetative shoot meristems and have not transformed into male inflorescences4. We also discuss the evidence connecting viral invasion of meristematic cells and the ability of plants to recover from acute infections. Embryonic shoot apical meristem formation in higher plants The peptide VISP1, acting as a selective autophagy receptor, plays an essential role in plant immunity . The antimicrobial peptide DmAMP1W from wheat curtails the proliferation of fungi, including fungi Rhizoctonia cerealis and Bipolaris sorokiniana, effectively combating wheat sharp eyespot and root rot diseases . The involvement of CLE peptides in leaf processes underscores their potential as long-distance signaling molecules. Salt stress triggers ion imbalance, osmotic shifts, oxidative stress, and secondary stresses in plants . The Small Paraquat resistance protein (SPQ), LcSPQ, equipped with an N-terminal signal peptide, has been found to enhance plant drought resistance upon overexpression ; however, its specific receptors and underlying mechanisms require additional study. Furthermore, S1Fa has been shown to bolster the tolerance of various other plants, including corn and Chinese cabbage, to a range of abiotic stresses. Researchers have discovered a number of small peptides that assist plants in resisting drought stress. We then used gene expression information from the scRNA-seq dataset to impute the missing expression values of almost all barley genes for all cells in the tissue sections. To validate the method, we compared imputed and experimentally determined gene expression values (Supplementary Fig. 6c) on a cell-by-cell basis for all 22,082 segmented cells, using expression data for the anchor genes to determine CS. Biologically relevant clusters representing ‘dividing cells’, ‘floret meristem’, ‘xylem’ and ‘L1 – epidermis’ were identified at cr0.3, indicating that these involve highly distinct gene expression patterns, separating them from other cell populations (Supplementary Fig. 5). In addition to auxin-mediated regulation, there are additional hypotheses explaining the Sussex experiment. In addition, redundant ARF suppressors are expressed in the abaxial domain to inhibit WOX expression (Guan et al. 2017). The abaxial domain also has lower auxin levels, as indicated by DII, than the middle domain. Recent advances in single-cell RNA sequencing (scRNA-seq) technology provide unprecedented opportunities to systematically identify the entire cellular and molecular differentiation trajectory of plant stem cells at the single-cell level. For both rice and Arabidopsis, root apical meristem (RAM) is formed during embryogenesis which generates the radicle or primary root after seed germination. Finally, we demonstrate the potential of the platform for functional genetic studies by using spatiotemporal modeling to identify a rice root meristematic mutant from a cell-specific gene cohort. We further identify characteristic processes, transcriptome profiles, and marker genes for these cell types and reveal conserved and divergent root developmental pathways between dicots and monocots. Thus, a similar genetic mechanism regulates stem cell maintenance in both the established meristem and the developing meristem during axillary bud formation. This difference is even higher in humans, where the number of germ-cell divisions is about 31 in females, while for a 20-year old male this number is already 150, and further increases by more than five times for a 50-year old male (Crow, 2000). For example, in female mice there are 25 germ-cell divisions compared to 62 divisions in males (Drost and Lee, 1995). In mammal females, there is a relatively small number of cell divisions preceding the production of the ovum, which does not increase with age, because all cell divisions are completed before the birth. Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation. NaCI reduces Indole-3-Acetic Acid levels in the roots of tomato plants independent of Stress-Induced Abscisic Acid. ARR12 promotes de novo shoot regeneration in Arabidopsis thaliana via activation of WUSCHEL expression. Cytokinin signaling as a positional cue for patterning the apical-basal axis of the growing Arabidopsis shoot meristem. Condensation of STM is critical for shoot meristem maintenance and salt tolerance in Arabidopsis. This includes understanding how phytochromes through the regulation of several classes of transcription factors regulate expression at the tissue and cellular levels. Such studies will also benefit from a better integration of cellular, developmental, and photo-biology. However, given that there is ample evidence for organ-specific phytochrome responses, focusing on other phenotypes such as leaf development will certainly yield interesting new insight. CSLD5 forms complexes with CESAs to guide cellulose-based wall construction. Using model species to answer these questions has been extremely informative, but one particular challenge remains, given increasing stresses on the world’s food supply, how to control precisely the growth of specific branches in cultivated crops and perennial species, with the goal of enabling greater sustainable food production. Sugars have been shown to promote axillary bud outgrowth as observed in rice, pea, Arabidopsis, and chrysanthemum, with increasing evidence for the role of trehalose 6-phosphate (T6P) in this process (Mason et al., 2014; Fichtner et al., 2017, 2020; Barbier et al., 2019; Liu et al., 2020; Wang et al., 2020). The nutrient regulation of BRC1 might also be mediated through hormone biosynthesis and signaling, including SLs, CK, and auxin. Short days and low temperatures suppressed branching in Populus by up-regulating the expression of BRC1 and TERMINAL FLOWER 1/CENTRORADIALIS 1 (TFL1/CEN1, Maurya et al., 2020). For example, CRISPR-Cas9 promoter editing of maize Arabidopsis CLV3-LIKE genes enhanced grain-yield-related traits (Liu et al., 2021). As transcriptional activators of CK signalling, type-B ARRs (ARR1, ARR2, ARR10, and ARR12) directly activate WUS expression following binding to its promoter (Zhang et al., 2017), while also suppressing YUC-mediated auxin accumulation to further promote WUS expression (Meng et al., 2017). The abundance of markers of histone 3 lysine 9 acetylation (H3K9ac) and histone 3 lysine 4 trimethylation (H3K4me3) at WUS sites increases, whereas the abundance of inhibitory markers histone 3 lysine 9 di-methylation (H3K9me2) decreases during shoot regeneration (Li et al., 2011). The expression of HAM1 mRNA in the mock-treated SAM was consistent with the previous observation6,7,9, with a concentration gradient from the epidermis to the deep cell layers. Therefore, we decided to apply a dexamethasone (Dex) inducible transient activation system (ATML1-GR) to examine the immediate effects of ATML1 activation on the expression of MIR171 and HAM. To further study the regulatory cascade in the SAM, we computationally predicted the patterns of miR171 and HAM gene expression when the ATML1 protein is ectopically activated in the SAM. Here, PHB activates CYCD6;1 resulting in a division, and thereby the formation of an additional cortex cell layer (Di Ruocco et al., 2018). The expanded PHB activity domain results in the formation of a cortex/endodermis mixed (CEM) cell. A correct patterning with one endodermis and one cortex cell layer also requires the restriction of PHABULOSA (PHB) to the stele by the action of the endodermally expressed miRNA165/6 (Miyashima et al., 2011). In the CEI, SHR directly activates transcription of the D-type cyclin CYCD6;1, which is required for its specific cell division (Sozzani et al., 2010). Here, SHR becomes nuclear localized and is prevented from further movement to neighboring outer cell layer by complexing with SCR. Cell morphology examination The pin1-7 loss-of-function mutant has a lower baseline level of PAT, and pin1 mutant roots did not show increased 3H-IAA transport upon GA treatment, similar to rga,gai and arf7,19 mutants (Fig. 4f and Extended Data Fig. 6b). As GA signalling is able to both enhance PAT and broaden PIN1 expression in the cambium, we postulated that PIN1 might be required for GA’s effect on PAT. Similarly, arf7,19 failed to respond to GA (Fig. 4f and Extended Data Fig. 6b), indicating that ARF7/19-mediated auxin signalling is required for GA-induced PAT as well as for xylem formation (Fig. 3f,g). Increased 3H-IAA signals were observed in the upper part of GA-treated WT roots 1 day after GA application (Fig. 4f). HZ prepared the manuscript figures. On the other hand, during flower development, FHY3 directly actives SEPALLATA1 (SEP1) and SEP2 expression, in parallel to the FHY3-CLV3 pathway, to repress WUS expression and to promote FM determinacy (Li et al., 2016; Figure 2). At later FM stages (stages 5–6), AG and auxin increase ARF3 expression, while AP2 represses ARF3 expression. Specifically, auxin induces the expression of ARF5/MP to repress ARR7/15 to fine tune CK activity and WUS expression (Zhao et al., 2010). DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development The regulatory loop between auxin and cytokinin controls vascular patterning in the Arabidopsis primary root. This suggests that AHP6 counteracts cytokinin signalling and thereby allows cells to differentiate into protoxylem identity (Mahonen et al, 2006a). AHP6 is specifically expressed in the protoxylem cells, and its loss-of-function mutation results in sporadic differentiation of protoxylem (Mahonen et al, 2006a). Long-Distance Signal Transduction Mediated by Small Peptides under Stress The highest ear on the maize plant was designated the ‘primary ear.’ The primary ear is clonally related to the node, internode and leaf on the opposite side of the stem, above its own point of insertion at maturity70. Notably, our data suggest that either known SAM master regulatory genes do not make major contributions to natural SAM morphometric variation, or else these contributions are not detectable in our experiment. At the same internode, increased SAM height leads to decreased stem diameter and increased SAM radius leads to decreased plant height. Previous research has shown that SAM size increases throughout vegetative development2,43,44, whereafter the SAM transforms into the male inflorescence meristem. Studies of natural variation in plants and animals have found that biologically significant changes are often linked to polymorphisms in non-genic regulatory regions that may contribute to the evolution of novel expression patterns39,40,41,42. Here, we adapted novoSpaRc34, a methodology for spatial reconstruction of single-cell RNA-seq data, to generate a 3D single-cell transcriptome atlas of a floral meristem by integrating single-nuclei RNA-seq and a 3D reconstructed flower meristem32. Therefore, tools to integrate scRNA-seq with expression data of defined, limited sets of 3D reference gene expression patterns need to be developed for spatial reconstruction of single-cell transcriptomes in plants. Here, we propose a method to reconstruct genome-wide gene expression patterns of individual cells in a 3D flower meristem by combining single-nuclei RNA-seq with microcopy-based 3D spatial reconstruction. Nevertheless, we believe that the inclusion of the soc1 mutant data helps to integrate the different themes of the manuscript, as requested by the reviewer.The stem cell niche is boxed, and colors inside of box are enhanced.CLV3 is the only component of this system that is specifically expressed in stem cells and hence serves as a faithful molecular marker.The size of the SAMs is determined by measuring the average of the radii of three successive primordia to the SAM center, and the results are displayed as box and whisker plots with individual data points.Kauff et al. (2000) found a dimorphic rhizodermis in Hydrocharitaceae and Pontederiaceae, but Seago et al. (1999a, 2000a) showed developmentally that only the outer layer is the epidermis.Stamen primordia giving rise to stamen filaments occur from stage 7, in accordance with the predicted and observed AHL18 spatiotemporal expression pattern (Figure 4). It is remarkable that, as land plants diversified, life cycle generation dominance twisted, and the sporophyte generation became dominant and increasingly specialized, whereas the gametophyte generation became reduced 36,37. In the SAM, a stem cell pool is located in the Central Zone (CZ, purple) above the organizing center (OC, yellow), which expresses the WUSCHEL transcription factor (TF) (yellow). Cells undergoing non-terminal differentiation appear to retain a stem cell potential . Weaker mutants are defective in arabinosyltransferases that extend arabinose chains, indicating that CLV3 must be fully arabinosylated to maintain meristem size. I have been using Meristem LLC's services for quite some time now, and I must say, I am thoroughly impressed. 👍 I'm extremely satisfied with Meristem LLC. 😀 I cannot express how satisfied I am with the services provided by Meristem LLC. Three blue dots indicate selected meristems and red dots exemplify their K nearest neighbors (see Methods for more details). For both g and h, the number of meristems assayed in each plate depicted above each distribution. A) Distribution of morphology-based scores during random sampling of plants sown together and scored at five consecutive days (10-14 Days after germination - DAG). Induced expression of these short-lived transition-state genes allowed us to determine their genetic hierarchies and to bypass the need for the main flowering pathways. These constitute functional modules that are complementarily integrated into SAM homeostasis, and each of their loss-of-function mutants shows broadly expanded WUS expression with a dramatically enlarged and disorganized SAM, as does the clv3 mutant. Taken together, these observations suggest that BIG acts synergistically and influences auxin transport by controlling PIN1 localization to distribute proper auxin maxima and to maintain SAM homeostasis (Zhang et al. 2020). Auxin is required for entry into mitosis and promotes cell division to cause cell proliferation by interacting with the signaling cascade of another canonical phytohormone, cytokinin (Shimotohno et al. 2021). Auxin-dependent organ initiation is mediated by AUXIN RESPONSE FACTOR 5/MONOPTEROUS (ARF5/MP) transcription factor, which directly represses the transcription of DORNRÖSCHEN (DRN) in the SAM by binding to a conserved auxin response element in the DRN promoter (Figure 1C). Mostly the apical meristems are often virus free but some viruses are known to actually invade the meristematic region of the growing tips, in that case it has also been possible to obtain virus free plants by combining meristem culture with thermotherapy. At the shoot apex, stem cells not only produce lateral organs, but also regulate organ patterning. After floral transition, the SAM generates floral primordia instead of leaf primordia in plants with a simple raceme, an indeterminate inflorescence, such as in Arabidopsis. These results suggest that, in contrast to Arabidopsis, class C genes are not a key regulator for carpel specification in rice. Furthermore, no known flower organs including carpels were specified in a double mutant of DL and SUPERWOMAN1 (a class B gene), which expresses only class C genes in whorls 3 and 4. Analysis of a complete loss-of-function mutant of OsMADS3 and OsMADS58 revealed that carpel-like organs expressing DL were formed in the absence of the two class C genes. Here, we have addressed this controversial issue by phenotypic characterization of floral homeotic gene mutants. In contrast, another group reported that carpels are specified by two class C genes, OsMADS3 and OsMADS58. According to widely accepted hypotheses, growth occurs when the cell walls yield to these forces and start to deform plastically. Growth is a physical process and the deformation of living tissues requires mechanical forces, which cause cells to grow at a certain rate and into a certain direction. So far, I have only considered the molecular regulation of meristem function. We show that in the majority of target loci, STM binds within 1 kb upstream of the TSS, with other loci showing STM binding at more distal enhancer sites, and we reveal enrichment of DNA motifs containing a TGAC and/or TGAT core in STM-bound target gene cis-regulatory elements. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Brightness and contrast were adjusted when necessary and to the same extent in the GFP and the VENUS channels. The current simplified model for auxin transduction is that Aux/IAAs dimerize with the Q-rich ARFs. TIR1 and the AFBs act directly as auxin receptors and their activation leads to auxin-dependent degradation of Aux/IAAs. The action of auxin does not only depend on the regulation of its synthesis or transport, but the competence to react to auxin seems also to be controlled in time and space. Their endodermis ensures a one-way mode of water transport into the plant, while the pericycle is usually where the lateral roots originate. The free-living gametophytes of bryophytes, lycophytes and monilophytes grow on moist environments, and anchorage is accomplished by a system of unicellular or undifferentiated multicellular rhizoids. Of the various plant organs, the roots have been the least studied, primarily because of the difficulty in obtaining materials, particularly from large woody species. Anatomy had been one of the foundations in our understanding of plant evolutionary trends and, although recent evo-devo concepts are mostly based on molecular genetics, classical structural information remains useful as ever. To elucidate these networks, multi-omics data at the single-cell level are needed. Defective AM initiation in maize inflorescences is a defining feature of the barren inflorescence (bif) mutant class, which include the recessive barren stalk1 (ba1) and bif2 mutants, and the semi-dominant Bif1 and Bif4 mutants, and is often a read-out of problems in auxin biology. KN1 directly binds and negatively regulates VANISHING TASSEL2 (VT2) (Bolduc et al. 2012) which is a co-ortholog of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1), involved in the tryptophan-dependent auxin biosynthesis pathway (Phillips et al. 2011; Zhao 2012). The early steps in maize inflorescence development include the patterning and specification of new AMs at the peripheral zone of the IM. The 2021 study featured a quantitative 3D reference atlas of the Arabidopsis ovule, laying out a framework for morphogenetic characterization of deep tissue structures (Vijayan et al., 2021).Each picture is combined from ~15 pictures with the phloem poles and thinnest cell walls aligned.Nowadays, the plant extracts are becoming the most popular active ingredients of cosmetics due to the ever‐increasing demand for natural compounds which in addition to esthetic looks can provide additional health benefits.One of these loci, with a particularly dramatic effect, corresponds to a gene called teosinte branched-1 (tb1).The full names of selected genes are given in Supplementary Data 3.Relationship between stem diameter and overall meristem size (area of thecross-section) based on species means.The stem cell can be defined as a cell that self-renews and generates differentiating cells (Heidstra and Sabatini, 2014; Slack, 2018). First, the homeodomain protein SHOOTMERISTEMLESS (STM), in combination with several members of the so-called CUP SHAPED COTYLEDON (CUC) family of transcription factors, defines meristematic identity, preventing cells from being recruited by the young organs (e.g., Aida et al. 1999). At the periphery of the meristem, the initial recruitment of the organ founder cells appears to be the result of two antagonistic processes. DR5 expression in young emerging primordia indicates activation of auxin induced-genes. To study the function of key meristem genes and to reveal the genetic means modulating induced plantlet formation in K. Other phenotypes of KpCUC2 AS plants also showed abundant root development and slower development of leaf primordia, L1 and L2 remained undeveloped (Figure 6O). To study the role of meristem genes in plantlet formation, we scored plantlet emergence in detached leaves of K. Several key meristem genes and closely-related genes were differentially expressed in the EBs after leaf detachment.