The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis

Increased seed number per silique in Brassica juncea by deleting cis-regulatory region affecting BjCLV1 expression in carpel margin meristem

Mustard yield per plant is severely restricted by the seed number per silique. The seed number per silique in the Brassica juncea trilocular mutant J163-4 is significantly greater than that in normal bilocular plants. However, how the trilocular silique of J163-4 is formed remains unclear. Here, we studied the gene structure and function of mc2 in B. juncea and Arabidopsis using comparative morphology and molecular genetic experiments. We found that mc2 is a CLV1 ortholog, BjA7.CLV1. The deletion of cis-regulatory region in mc2 promoter, which affects Mc2 expression in carpel margin meristem (CMM), led to trilocular silique formation. The BjCLV1 sequence with its complete promoter containing the cis-regulatory region can restore the Bjclv1 and clv1 mutant phenotypes in B. juncea and Arabidopsis, respectively. Additionally, this cis-regulatory region had a collinear segment in the promoter of CLV1 homologous gene in most Brassicaceae species. Our results are consistent with the report that BjCLV1 represents a conserved pleiotropic role in shoot meristem and CMM development, which contains a cis-regulatory sequence specifically expressed BjCLV1 in CMM in its promoter, and this cis-regulatory region is conserved in Brassicaceae species. These results offer a reliable approach for fine-tuning the traits of seed yield in Brassicaceae crops.

Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways

Stem cell homeostasis in plant shoot meristems requires tight coordination between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)-receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.

Identification of the unique molecular framework of heterophylly in the amphibious plant Callitriche palustris L

Heterophylly is the development of different leaf forms in a single plant depending on the environmental conditions. It is often observed in amphibious aquatic plants that can grow under both aerial and submerged conditions. Although heterophylly is well recognized in aquatic plants, the associated developmental mechanisms and the molecular basis remain unclear. To clarify these underlying developmental and molecular mechanisms, we analyzed heterophyllous leaf formation in an aquatic plant, Callitriche palustris. Morphological analyses revealed extensive cell elongation and the rearrangement of cortical microtubules in the elongated submerged leaves of C. palustris. Our observations also suggested that gibberellin, ethylene, and abscisic acid all regulate the formation of submerged leaves. However, the perturbation of one or more of the hormones was insufficient to induce the formation of submerged leaves under aerial conditions. Finally, we analyzed gene expression changes during aerial and submerged leaf development and narrowed down the candidate genes controlling heterophylly via transcriptomic comparisons, including a comparison with a closely related terrestrial species. We discovered that the molecular mechanism regulating heterophylly in C. palustris is associated with hormonal changes and diverse transcription factor gene expression profiles, suggesting differences from the corresponding mechanisms in previously investigated amphibious plants.

The sequenced genomes of nonflowering land plants reveal the innovative evolutionary history of peptide signaling

An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question-how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in nonangiosperms. These discoveries provoke questions regarding coevolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective, we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.

Genetics of Shoot Meristem and Shoot Regeneration

Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

CLAVATA3, a plant peptide controlling stem cell fate in the meristem

CLAVATA3 (CLV3) is a peptide signal initially identified in the analysis of clv mutants in the model plant Arabidopsis thaliana, as a regulator of meristem homeostasis and floral organ numbers. CLV3 homologs are widely conserved in land plants, collectively called CLV3/ESR-related (CLE) genes. A 12-amino acid CLE peptide with hydroxyproline residues was identified in Zinnia elegans cell culture system, in which cells secrete a CLE peptide called tracheary element differentiation factor (TDIF) into the culture medium. Mature CLV3 peptide is also a post-translationally modified short peptide containing additional triarabinosylation on a hydroxyproline residue. Genetic studies have revealed the involvement of leucin-rich repeat receptor-like kinases (LRR-RLKs) in CLV3 signaling, including CLV1/BAM-CIK, CLV2-CRN and RPK2, although the mechanisms of signal transduction and integration via crosstalk is still largely unknown. Recent studies on bryophyte model species provided a clue to understand evolution and ancestral function of CLV signaling in land plants. Fundamental understanding on CLV signaling provided an opportunity to optimize the crop yield traits using a novel breeding technology with CRISPR/Cas genome editing.

Expression of KNUCKLES in the Stem Cell Domain Is Required for Its Function in the Control of Floral Meristem Activity in Arabidopsis

In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.

Conserved and differentiated functions of CIK receptor kinases in modulating stem cell signaling in Arabidopsis

The shoot apical meristem (SAM) and root apical meristem (RAM) act as pools of stem cells that give rise to aboveground and underground tissues and organs in higher plants, respectively. The CLAVATA3 (CLV3)-WUSCHEL (WUS) negative-feedback loop acts as a core pathway controlling SAM homeostasis, while CLV3/EMBRYO SURROUNDING REGION (ESR) 40 (CLE40) and WUSCHEL-RELATED HOMEOBOX5 (WOX5), homologs of CLV3 and WUS, direct columella stem cell fate. Moreover, CLV3 INSENSITIVE KINASES (CIKs) have been shown to be essential for maintaining SAM homeostasis, whereas whether they regulate the distal root meristem remains to be elucidated. Here, we report that CIKs are indispensable for transducing the CLE40 signal to maintain homeostasis of the distal root meristem. We found that the cik mutant roots displayed disrupted quiescent center and delayed columella stem cell (CSC) differentiation. Biochemical assays demonstrated that CIKs interact with ARABIDOPSIS CRINKLY4 (ACR4) in a ligand-independent manner and can be phosphorylated by ACR4 in vitro. In addition, the phosphorylation of CIKs can be rapidly induced by CLE40, which partially depends on ACR4. Although CIKs act as conserved and redundant regulators in the SAM and RAM, our results demonstrated that they exhibit differentiated functions in these meristems.

Identification of novel QTLs for grain fertility and associated traits to decipher poor grain filling of basal spikelets in dense panicle rice

High grain number is positively correlated with grain yield in rice, but it is compromised because of poor filling of basal spikelets in dense panicle bearing numerous spikelets. The phenomenon that turns the basal spikelets of compact panicle sterile in rice is largely unknown. In order to understand the factor(s) that possibly determines such spikelet sterility in compact panicle cultivars, QTLs and candidate genes were identified for spikelet fertility and associated traits like panicle compactness, and ethylene production that significantly influences the grain filling using recombinant inbred lines developed from a cross between indica rice cultivars, PDK Shriram (compact, high spikelet number) and Heera (lax, low spikelet number). Novel QTLs, qSFP1.1, qSFP3.1, and qSFP6.1 for spikelet fertility percentage; qIGS3.2 and qIGS4.1 for panicle compactness; and qETH1.2, qETH3.1, and qETH4.1 for ethylene production were consistently identified in both kharif seasons of 2017 and 2018. The comparative expression analysis of candidate genes like ERF3, AP2-like ethylene-responsive transcription factor, EREBP, GBSS1, E3 ubiquitin-protein ligase GW2, and LRR receptor-like serine/threonine-protein kinase ERL1 associated with identified QTLs revealed their role in poor grain filling of basal spikelets in a dense panicle. These candidate genes thus could be important for improving grain filling in compact-panicle rice cultivars through biotechnological interventions.

Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

BACKGROUND

As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported.

RESULTS

A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress.

CONCLUSIONS

In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

Sulfur Deprivation Modulates Salicylic Acid Responses via Nonexpressor of Pathogenesis-Related Gene 1 in Arabidopsis thaliana

Mineral nutrients are essential for plant growth and reproduction, yet only a few studies connect the nutritional status to plant innate immunity. The backbone of plant defense response is mainly controlled by two major hormones: salicylic acid (SA) and jasmonic acid (JA). This study investigated changes in the macronutrient concentration (deficiency/excess of nitrogen, phosphorus, potassium, magnesium, and sulfur) on the expression of PR1, a well-characterized marker in the SA-pathway, and PDF1.2 and LOX2 for the JA-pathway, analyzing plants carrying the promoter of each gene fused to GUS as a reporter. After histochemical GUS assays, we determined that PR1 gene was strongly activated in response to sulfur (S) deficiency. Using RT-PCR, we observed that the induction of PR1 depended on the function of Non-expressor of Pathogenesis-Related gene 1 (NPR1) and SA accumulation, as PR1 was not expressed in npr1-1 mutant and NahG plants under S-deprived conditions. Plants treated with different S-concentrations showed that total S-deprivation was required to induce SA-mediated defense responses. Additionally, bioassays revealed that S-deprived plants, induced resistance to the hemibiotrophic pathogen Pseudomonas syringae pv. DC3000 and increase susceptibility to the necrotrophic Botrytis cinerea. In conclusion, we observed a relationship between S and SA/JA-dependent defense mechanisms in Arabidopsis.

Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing

Artificial domestication and improvement of the majority of crops began approximately 10,000 years ago, in different parts of the world, to achieve high productivity, good quality, and widespread adaptability. It was initiated from a phenotype-based selection by local farmers and developed to current biotechnology-based breeding to feed over 7 billion people. For most cereal crops, yield relates to grain production, which could be enhanced by increasing grain number and weight. Grain number is typically determined during inflorescence development. Many mutants and genes for inflorescence development have already been characterized in cereal crops. Therefore, optimization of such genes could fine-tune yield-related traits, such as grain number. With the rapidly advancing genome-editing technologies and understanding of yield-related traits, knowledge-driven breeding by design is becoming a reality. This review introduces knowledge about inflorescence yield-related traits in cereal crops, focusing on rice, maize, and wheat. Next, emerging genome-editing technologies and recent studies that apply this technology to engineer crop yield improvement by targeting inflorescence development are reviewed. These approaches promise to usher in a new era of breeding practice.

Verbena officinalis Verbenaceae (Lamiales): a new plant model system for phyllotaxis research

Phyllotactic diversity and developmental transitions between phyllotactic patterns are not fully understood. The plants studied so far, such as Magnolia, Torreya or Abies, are not suitable for experimental work, and the most popular model plant, Arabidopsis thaliana, does not show sufficient phyllotactic variability. It has been found that in common verbena (Verbena officinalis L.), a perennial, cosmopolitan plant, phyllotaxis differs not only between growth phases in primary transitions but also along the indeterminate inflorescence axis in a series of multiple secondary transitions. The latter are no longer associated with the change in lateral organ identity, and the sequence of phyllotactic patterns is puzzling from a theoretical point of view. Data from the experiments in silico, confronted with empirical observations, suggest that secondary transitions might be triggered by the cumulative effect of fluctuations in the continuously decreasing bract primordia size. The most important finding is that the changes in the primary vascular system, associated with phyllotactic transitions, precede those taking place at the apical meristem. This raises the question of the role of the vascular system in determining primordia initiation sites, and possibly challenges the autonomy of the apex. The results of this study highlight the complex relationships between various systems that have to coordinate their growth and differentiation in the developing plant shoot. Common verbena emerges from this research as a plant that may become a new model suitable for further studies on the causes of phyllotactic transitions.

Phyllotaxis: from classical knowledge to molecular genetics

Plant organs are repetitively generated at the shoot apical meristem (SAM) in recognizable patterns. This phenomenon, known as phyllotaxis, has long fascinated scientists from different disciplines. While we have an enriched body of knowledge on phyllotactic patterns, parameters, and transitions, only in the past 20 years, however, have we started to identify genes and elucidate genetic pathways that involved in phyllotaxis. In this review, I first summarize the classical knowledge of phyllotaxis from a morphological perspective. I then discuss recent advances in the regulation of phyllotaxis, from a molecular genetics perspective. I show that the morphological beauty of phyllotaxis we appreciate is the manifestation of many regulators, in addition to the critical role of auxin as a patterning signal, exerting their respective effects in a coordinated fashion either directly or indirectly in the SAM.

Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops

Flowering plants develop new organs throughout their life cycle. The vegetative shoot apical meristem (SAM) generates leaf whorls, branches and stems, whereas the reproductive SAM, called the inflorescence meristem (IM), forms florets arranged on a stem or an axis. In cereal crops, the inflorescence producing grains from fertilized florets makes the major yield contribution, which is determined by the numbers and structures of branches, spikelets and florets within the inflorescence. The developmental progression largely depends on the activity of IM. The proper regulations of IM size, specification and termination are outcomes of complex interactions between promoting and restricting factors/signals. Here, we focus on recent advances in molecular mechanisms underlying potential pathways of IM identification, maintenance and differentiation in cereal crops, including rice (Oryza sativa), maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare), highlighting the researches that have facilitated grain yield by, for example, modifying the number of inflorescence branches. Combinatorial functions of key regulators and crosstalk in IM determinacy and specification are summarized. This review delivers the knowledge to crop breeding applications aiming to the improvements in yield performance and productivity.

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.

Improving architectural traits of maize inflorescences

The domestication and improvement of maize resulted in radical changes in shoot architecture relative to its wild progenitor teosinte. In particular, critical modifications involved a reduction of branching and an increase in inflorescence size to meet the needs for human consumption and modern agricultural practices. Maize is a major contributor to global agricultural production by providing large and inexpensive quantities of food, animal feed, and ethanol. Maize is also a classic system for studying the genetic regulation of inflorescence formation and its enlarged female inflorescences directly influence seed production and yield. Studies on the molecular and genetic networks regulating meristem proliferation and maintenance, including receptor-ligand interactions, transcription factor regulation, and hormonal control, provide important insights into maize inflorescence development and reveal potential avenues for the targeted modification of specific architectural traits. In this review, we summarize recent findings on the molecular mechanisms controlling inflorescence formation and discuss how this knowledge can be applied to improve maize productivity in the face of present and future environmental challenges.

Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes

Several yield-related traits selected during crop domestication and improvement^1,2 are associated with increases in meristem size³, which is controlled by CLE peptide signals in the CLAVATA-WUSCHEL pathway^4-13. Here, we engineered quantitative variation for yield-related traits in maize by making weak promoter alleles of CLE genes, and a null allele of a newly identified partially redundant compensating CLE gene, using CRISPR-Cas9 genome editing. These strategies increased multiple maize grain-yield-related traits, supporting the enormous potential for genomic editing in crop enhancement.

Receptor-like Kinases in Root Development: Current Progress and Future Directions

Cell-to-cell and cell-to-environment communications are critical to the growth and development of plants. Cell surface-localized receptor-like kinases (RLKs) are mainly involved in sensing various extracellular signals to initiate their corresponding cellular responses. As important vegetative organs for higher plants to adapt to a terrestrial living situation, roots play a critical role for the survival of plants. It has been demonstrated that RLKs control many biological processes during root growth and development. In this review, we summarize several key regulatory processes during Arabidopsis root development in which RLKs play critical roles. We also put forward a number of relevant questions that are required to be explored in future studies.

Zygotic Embryogenesis in Flowering Plants

In the context of plant regeneration, in vitro systems to produce embryos are frequently used. In many of these protocols, nonzygotic embryos are initiated that will produce shoot-like structures but may lack a primary root. By increasing the auxin-to-cytokinin ratio in the growth medium, roots are then regenerated in a second step. Therefore, in vitro systems might not or only partially execute a similar developmental program as employed during zygotic embryogenesis. There are, however, in vitro systems that can remarkably mimic zygotic embryogenesis such as Brassica microspore-derived embryos. In this case, the patterning process of these haploid embryos closely follows zygotic embryogenesis and all fundamental tissue types are generated in a rather similar manner. In this review, we discuss the most fundamental molecular events during early zygotic embryogenesis and hope that this brief summary can serve as a reference for studying and developing in vitro embryogenesis systems in the context of doubled haploid production.

Kinase Function of Brassinosteroid Receptor Specified by Two Allosterically Regulated Subdomains

Plants acquire the ability to adapt to the environment using transmembrane receptor-like kinases (RLKs) to sense the challenges from their surroundings and respond appropriately. RLKs perceive a variety of ligands through their variable extracellular domains (ECDs) that activate the highly conserved intracellular kinase domains (KDs) to control distinct biological functions through a well-developed downstream signaling cascade. A new study has emerged that brassinosteroid-insensitive 1 (BRI1) family and excess microsporocytes 1 (EMS1) but not GASSHO1 (GSO1) and other RLKs control distinct biological functions through the same signaling pathway, raising a question how the signaling pathway represented by BRI1 is specified. Here, we confirm that BRI1-KD is not functionally replaceable by GSO1-KD since the chimeric BRI1-GSO1 cannot rescue bri1 mutants. We then identify two subdomains S1 and S2. BRI1 with its S1 and S2 substituted by that of GSO1 cannot rescue bri1 mutants. Conversely, chimeric BRI1-GSO1 with its S1 and S2 substituted by that of BRI1 can rescue bri1 mutants, suggesting that S1 and S2 are the sufficient requirements to specify the signaling function of BRI1. Consequently, all the other subdomains in the KD of BRI1 are functionally replaceable by that of GSO1 although the in vitro kinase activities vary after replacements, suggesting their functional robustness and mutational plasticity with diverse kinase activity. Interestingly, S1 contains αC-β4 loop as an allosteric hotspot and S2 includes kinase activation loop, proposedly regulating kinase activities. Further analysis reveals that this specific function requires β4 and β5 in addition to αC-β4 loop in S1. We, therefore, suggest that BRI1 specifies its kinase function through an allosteric regulation of these two subdomains to control its distinct biological functions, providing a new insight into the kinase evolution.

Plant stem-cell organization and differentiation at single-cell resolution

Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.

Improving the Identification and Coverage of Plant Transmembrane Proteins in Medicago Using Bottom-Up Proteomics

Plant transmembrane proteins (TMPs) are essential for normal cellular homeostasis, nutrient exchange, and responses to environmental cues. Commonly used bottom-up proteomic approaches fail to identify a broad coverage of peptide fragments derived from TMPs. Here, we used mass spectrometry (MS) to compare the effectiveness of two solubilization and protein cleavage methods to identify shoot-derived TMPs from the legume Medicago. We compared a urea solubilization, trypsin Lys-C (UR-TLC) cleavage method to a formic acid solubilization, cyanogen bromide and trypsin Lys-C (FA-CTLC) cleavage method. We assessed the effectiveness of these methods by (i) comparing total protein identifications, (ii) determining how many TMPs were identified, and (iii) defining how many peptides incorporate all, or part, of transmembrane domains (TMD) sequences. The results show that the FA-CTLC method identified nine-fold more TMDs, and enriched more hydrophobic TMPs than the UR-TLC method. FA-CTLC identified more TMPs, particularly transporters, whereas UR-TLC preferentially identified TMPs with one TMD, particularly signaling proteins. The results suggest that combining plant membrane purification techniques with both the FA-CTLC and UR-TLC methods will achieve a more complete identification and coverage of TMPs.

Plant stem-cell organization and differentiation at single-cell resolution

Plants possess the remarkable ability to grow and produce new organs throughout their lifespan, owing to the activities of persistent populations of pluripotent stem cells within their meristematic tips. Here we isolated individual cells from the microscopic shoot apical meristem (SAM) of maize and provide single-cell transcriptomic analysis of a plant shoot meristem. This study enabled an unbiased analysis of the developmental genetic organization of the maize shoot apex and uncovered evolutionarily divergent and conserved signatures of SAM homeostasis. The fine-scale resolution of single-cell analysis was used to reconstruct the process of shoot cell differentiation, whereby stem cells acquire diverse and distinct cell fates over developmental time in wild-type and mutant maize seedlings.

Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.

The role of CLV1, CLV2 and HPAT homologues in the nitrogen-regulation of root development

Plants use a variety of signals to control root development, including in modifying root development in response to nutrient stress. For example, in response to nitrogen (N) stress, plants dramatically modulate root development, including the formation of N-fixing nodules in legumes. Recently, specific CLE peptides and/or receptors important for their perception, including CLV1 and CLV2, have been found to play roles in root development, including in response to N supply. In the legume Medicago truncatula, this response also appears to be influenced by RDN1, a member of the hydroxyproline-O-arabinosyltransferase (HPAT) family which can modify specific CLE peptides. However, it is not known if this signalling pathway plays a central role in root development across species, and in particular root responses to N. In this study, we systematically examined the role of the CLV signalling pathway genes in root development of the legume pea (Pisum sativum) and non-legume tomato (Solanum lycopersicum) using a mutant-based approach. This included a detailed examination of root development in response to N in tomato mutants disrupted in CLV1- or CLV2-like genes or HPAT family member FIN. We found no evidence for a role of these genes in pea seedling root development. Furthermore, the CLV1-like FAB gene did not influence tomato root development, including the root response to N supply. In contrast, both CLV2 and the HPAT gene FIN appear to positively influence root size in tomato but do not mediate root responses to N. These results suggest the function of these genes may vary somewhat in different species, including the N regulation of root architecture.

A basic/helix-loop-helix transcription factor controls leaf shape by regulating auxin signaling in apple

Climate-driven phenological change across local spatial gradients leads to leaf shape variation. At higher elevations, leaves of broadleaf species tend to become narrower, but the underlying molecular mechanism is largely unknown. In this study, a series of morphometric analyses and biochemical assays, combined with functional identification in apple, were performed. We show that the decrease in apple leaf width with increasing altitude is controlled by a basic/helix-loop-helix transcription factor (bHLH TF), MdbHLH3. The MdbHLH3-overexpressing lines have a lower transcript abundance of MdPIN1 encoding an auxin efflux carrier but a higher transcript abundance of MdGH3-2 encoding a putative auxin amido conjugate synthase, resulting in a lower free auxin concentration; feeding the transgenic leaves with exogenous auxin partially restores leaf width. MdbHLH3 transcriptionally suppresses and activates MdPIN1 and MdGH3-2, respectively, by specifically binding to their promoters. This alters auxin homeostasis and transport, consequently leading to changes in leaf shape. These findings suggest that the bHLH TF MdbHLH3 directly modulates auxin signaling in controlling leaf shape in response to local spatial gradients in apple.

CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments

The ability to thrive in diverse environments requires that species maintain development and reproduction despite dynamic conditions. Many developmental processes are stabilized through robust signaling pathways that cooperatively ensure proper development.¹ During reproduction, plants like Arabidopsis thaliana continuously generate flowers on growing indeterminate inflorescences.² Flower primordia initiation and outgrowth depends on the hormone auxin and is robust across diverse environments.^3-6 Here, we show that reproductive development under different thermal conditions requires the integration of multiple pathways regulating auxin-dependent flower production. In colder/ambient temperatures, the receptor complex CLAVATA2/CORYNE (CLV2/CRN) is necessary for continuous flower outgrowth during inflorescence development. CLV2/CRN signaling is independent of CLAVATA1 (CLV1)-related receptor signaling but involves the CLAVATA3 INSENSITIVE RECEPTOR KINASE (CIK) family co-receptors, with higher order cik mutant combinations phenocopying clv2/crn flower outgrowth defects. Developing crn inflorescences display reduced auxin signaling, and restoration of auxin biosynthesis is sufficient to restore flower outgrowth in colder and ambient temperatures. In contrast, at higher temperatures, both clv2/crn signaling and heat-induced auxin biosynthesis via YUCCA family genes are synergistically required to maintain flower development. Our work reveals a novel mechanism integrating peptide hormone and auxin signaling in the regulation of flower development across diverse thermal environments.

Connections in the cambium, receptors in the ring

In plants, pluripotent cells in meristems divide to provide cells for the formation of postembryonic tissues. The cambium is the meristem from which the vascular tissue is derived and is the main driver for secondary (radial) growth in dicots. Xylem and phloem are specified on opposing sides of the cambium, and tightly regulated cell divisions ensure their spatial separation. Peptide ligands, phytohormones, and their receptors are central to maintaining this patterning and regulating proliferation. Here, we describe recent advances in our understanding of how these signals are integrated to control vascular development and secondary growth.

Emerging mechanisms to fine-tune receptor kinase signaling specificity

Organisms need to constantly inform their cellular machinery about the biochemical and physical status of their surroundings to adapt and thrive. While some external signals are also sensed intracellularly, a considerable share of external information is registered already at the plasma membrane (PM). Receptor kinases (RKs) are crucial for plant cells to integrate such cues from the environment, from microbes, or from other cells to coordinate their physiological response and their development. Early studies on RK signaling depicted the path from external signal to internal response in a linear fashion, but recent findings show that these cellular information highways are highly interconnected and pass signals through molecular intersections. In this review, we first discuss how individual RKs simultaneously contribute to the transduction and deconvolution of a multitude of signals by controlled assembly into diverse RK complexes, exemplified by FERONIA signaling versatility. We then elaborate on how cells can exert highly localized control over the assembly, interaction and composition of such complexes in order to attain essential cellular output specificity.

Recent Advances in Arabidopsis CLE Peptide Signaling

Like communities of people, communities of cells must continuously communicate to thrive. Polypeptide signaling molecules that act as mobile ligands are widely used by eukaryotic organisms to transmit information between cells to coordinate developmental processes and responses to environmental cues. In plants, the CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) genes encode a large family of extracellular signaling peptides that stimulate receptor-mediated signal transduction cascades to modulate diverse developmental and physiological processes. This review highlights the emerging roles of Arabidopsisthaliana CLE peptide signaling pathways in shoot stem cell homeostasis and root xylem development, as well as in root protophloem cell differentiation, vascular cambium activity, and stomatal formation and closure.

Comprehensive study and multipurpose role of the CLV3/ESR-related (CLE) genes family in plant growth and development

The CLAVATA3/endosperm surrounding region-related (CLE) is one of the most important signaling peptides families in plants. These peptides signaling are common in the cell to cell communication and control various physiological and developmental processes, that is cell differentiation and proliferation, self-incompatibility, and the defense response. The CLE signaling systems are conserved across the plant kingdom but have a diverse mode of action in various developmental processes in different species. In this review, we concise various methods of peptides identification, structure, and molecular identity of the CLE family, the developmental role of CLE genes/peptides in plants, environmental stimuli, and CLE family and some other novel progress in CLE genes/peptides in various crops, and so forth. According to previous literature, about 1,628 CLE genes were identified in land plants, which deeply explained the tale of plant development. Nevertheless, some important queries need to be addressed to get clear insights into the CLE gene family in other organisms and their role in various physiological and developmental processes. Furthermore, we summarized the power of the CLE family around the environment as well as bifunctional activity and the crystal structure recognition mechanism of CLE peptides by their receptors and CLE clusters functions. We strongly believed that the discovery of the CLE family in other organisms would provide a significant breakthrough for future revolutionary and functional studies.

Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition

Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition.

The manifold actions of signaling peptides on subcellular dynamics of a receptor specify stomatal cell fate

Receptor endocytosis is important for signal activation, transduction, and deactivation. However, how a receptor interprets conflicting signals to adjust cellular output is not clearly understood. Using genetic, cell biological, and pharmacological approaches, we report here that ERECTA-LIKE1 (ERL1), the major receptor restricting plant stomatal differentiation, undergoes dynamic subcellular behaviors in response to different EPIDERMAL PATTERNING FACTOR (EPF) peptides. Activation of ERL1 by EPF1 induces rapid ERL1 internalization via multivesicular bodies/late endosomes to vacuolar degradation, whereas ERL1 constitutively internalizes in the absence of EPF1. The co-receptor, TOO MANY MOUTHS is essential for ERL1 internalization induced by EPF1 but not by EPFL6. The peptide antagonist, Stomagen, triggers retention of ERL1 in the endoplasmic reticulum, likely coupled with reduced endocytosis. In contrast, the dominant-negative ERL1 remained dysfunctional in ligand-induced subcellular trafficking. Our study elucidates that multiple related yet unique peptides specify cell fate by deploying the differential subcellular dynamics of a single receptor.

Receptor-like protein kinase-mediated signaling in controlling root meristem homeostasis

Generation of the root greatly benefits higher plants living on land. Continuous root growth and development are achieved by the root apical meristem, which acts as a reservoir of stem cells. The stem cells, on the one hand, constantly renew themselves through cell division. On the other hand, they differentiate into functional cells to form diverse tissues of the root. The balance between the maintenance and consumption of the root apical meristem is governed by cell-to-cell communications. Receptor-like protein kinases (RLKs), a group of signaling molecules localized on the cell surface, have been implicated in sensing multiple endogenous and environmental signals for plant development and stress adaptation. Over the past two decades, various RLKs and their ligands have been revealed to participate in regulating root meristem homeostasis. In this review, we focus on the recent studies about RLK-mediated signaling in regulating the maintenance and consumption of the root apical meristem.

Morphological and proteomic analysis of young spikes reveals new insights into the formation of multiple-pistil wheat

A new multiple-pistil wheat mutant germplasm with more than one pistil in a floret was obtained from natural mutagenesis. This mutant can develop 2-3 grains in a glume after pollination and has a significant grain number advantage compared with normal wheat. However, the basis of the formation of multiple-pistil wheat has thus far not been well established. In this study, we first performed a continuous phenotypic observation of the floral meristem (FM) in multiple-pistil wheat. The results indicated that the secondary pistils are derived from extra stem cells that fail to terminate normally between the carpel primordium and the lodicule primordium. To further probe the potential molecular basis for the formation of secondary pistils, comparative proteomic analyses were conducted. A total of 334 differentially abundant proteins (DAPs) were identified using isobaric tags for relative and absolute quantification (iTRAQ), among which 131 proteins were highly abundant and 203 proteins were less abundant in the young spikes of multiple-pistil wheat. The DAPs, located primarily in the cell, were involved in the translation and the metabolisms of carbohydrate, nucleotide, and amino acid. Differential expression analysis showed that TaHUA2, TaRF2a, TaCHR12 and TaHEN2 may play vital roles in the regulation of wheat flower organ number. In general, the DAPs support the phenotypic analysis results at the molecular level. In combination, these results reveal new insights into the formation of multiple-pistil wheat and provide possible targets for further research on the regulation of floral organ number in wheat.

Tomato SD1, encoding a kinase-interacting protein, is a major locus controlling stem development

Stems serve as key determinants of plant development by connecting and supporting parts of the plant body, transporting nutrients important for long-distance communication that affect crop yield, and producing new organs. Nonetheless, studies on the regulation of stem development in crops are rather limited. Here, we found a significant correlation (P<0.001) between stem diameter (SD) and fruit size in tomato (Solanum lycopersicum). We performed a genome-wide association study and identified a novel quantitative trait locus (QTL), SDR9 (stem diameter regulator on CHROMOSOME 9), that co-localized with a gene encoding a kinase-interacting family protein (KIP), which is the most likely candidate gene related to SD (hereafter referred to as SD1). Overexpression of SD1 in thin-stem accessions resulted in increased SD. In contrast, suppressed expression of SD1 in thick-stem accessions using RNA interference exhibited the opposite effect. Further microscopic analyses showed that SD1 affected the stem diameter by controlling the size and number of secondary phloem cells. An 11-bp indel in the promoter region of SD1 that disrupts a gibberellin-responsive cis-element was linked to SD. Expression analysis revealed that SD1 was mainly expressed at the cambium of the stem and positively regulates stem development. Evolutionary analysis revealed that the thick-stem allele of SD1 was selected during the recent process of tomato improvement. Our results provide novel genetic and molecular insight into natural variation of SD in tomato and may accelerate the breeding of high yield tomato.

TDIF peptides regulate root growth by affecting auxin homeostasis and PINs expression in Arabidopsis thaliana

TDIF and TDIF-like peptides in excess simultaneously facilitate primary root elongation and lateral root formation through regulating auxin distribution and transport. Tracheary element differentiation inhibitory factor (TDIF) plays key roles in mediating cell-cell communication and stem cell maintenance during vascular development. Recently, TDIF has also been linked to lateral root (LR) organogenesis through Brassinosteroid Insensitive 2 (BIN2) action. In this work, by comparing the in vitro and in vivo activities of AtCLE41-encoded TDIF and one poplar-derived TDIF-like peptide in Arabidopsis thaliana, we demonstrated that both TDIFs promoted primary root (PR) growth and stimulated LR formation. Without affecting auxin biosynthesis and catabolism, TDIFs suppressed the auxin maxima at PR apex but intensified the auxin accumulation at LR initiation sites along the longitudinal axis of PR. TDIF did not alter root sensitivity to exogenous auxin and mutants with varied endogenous auxin levels responded to TDIF peptides in a wild-type manner but to a lesser extent. Intriguingly, TDIF specifically upregulated the transcript abundance of PINs and multiple pin mutants displayed insensitivity to TDIF, demonstrating that PIN-mediated polar auxin transport (PAT) is indispensably required for the TDIF-induced root phenotypes. Taken together, our results revealed that TDIF might target PAT via mobilizing auxin efflux carriers to dynamically regulate the auxin signaling output and hence facilitate PR growth and LR formation.

Evolution of CLE peptide signalling

CLEs are small non-cell autonomous signalling peptides that regulate cell division rate and orientation in a variety of developmental contexts. Recent years have generated a huge amount of research on CLE function across land plants, characterising their role across the whole plant; they control stem cell division in the shoot, root and cambial meristems, balance developmental investment into symbiosis, regulate leaf development, pattern stomata and control axillary branching. They have even been co-opted by parasitic nematodes to mediate infection. This review synthesises these recent findings and embeds them in an evolutionary context, outlining the likely evolution of the CLE signalling pathway. I use this framework to infer common mechanistic themes and pose key future questions for the field.

Overexpression of NtSnRK2.2 enhances salt tolerance in Nicotiana tabacum by regulating carbohydrate metabolism and lateral root development

SnRK2 is a plant-specific protein kinase family implicated in environmental stress tolerance. Individual SnRK2 genes have acquired distinct regulatory properties in response to various environmental stresses. In this study, NtSnRK2.2, a SnRK2 subclass II member in Nicotiana tabacum L., was cloned and characterised. Sequence alignment analysis showed that SnRK2.2 exhibits widespread sequence differences across Nicotiana species. The tissue expression pattern of NtSnRK2.2 showed a root-predominant expression. To investigate its biological function, NtSnRK2.2 was overexpressed in tobacco, which subsequently resulted in increased soluble sugars and more lateral roots under a normal condition. A salt-stress tolerance assay showed that NtSnRK2.2-overexpressing plants exhibited enhanced salt tolerance, which was further confirmed based on its better root architecture and increase in soluble sugars, thereby implying that NtSnRK2.2 is a multifunctional regulatory factor in plants. Together, our results indicated the possible role played by NtSnRK2.2 in maintaining metabolic homeostasis via the regulation of carbohydrate metabolism in response to environmental stress.

A functionally informed evolutionary framework for the study of LRR-RLKs during stem cell maintenance

Plants maintain populations of stem cells to generate new organs throughout the course of their lives. The pathways that regulate plant stem cell maintenance have garnered great interest over the past decades, as variation in these pathways contributes plant morphological diversity and can be harnessed for crop improvement. In order to facilitate cross-species comparisons of gene function and better understand how these stem cell regulatory pathways evolved, we undertook a functionally informed phylogenetic analysis of leucine-rich receptor-like kinases (LRR-RLK) and related proteins across diverse land plant model systems. Based on our phylogenetic analysis and on functional data, we propose a naming scheme for these stem cell signaling genes. We discovered evidence for frequent loss of protein domains in angiosperms but not in bryophytes. In addition, several clades of stem cell signaling genes are closely related to genes that function in immunity, although these distinct developmental and immune functions likely separated or after the divergence of lycophytes and angiosperms. Overall, the phylogenetic framework and evolutionary hypotheses we provide here will empower future research on cross-species comparisons of stem cell signaling pathways.

Origin and Diversity of Plant Receptor-Like Kinases

Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the diversity of the RLK gene family. We thus focus on the motifs and domains found in association with kinase domains to illustrate their origin, organization, and evolutionary dynamics. We discuss when these different domain associations first occurred and how they evolved, based on a literature review complemented by some of our unpublished results.

Regulation of Shoot Apical Meristem and Axillary Meristem Development in Plants

Plants retain the ability to produce new organs throughout their life cycles. Continuous aboveground organogenesis is achieved by meristems, which are mainly organized, established, and maintained in the shoot apex and leaf axils. This paper will focus on reviewing the recent progress in understanding the regulation of shoot apical meristem and axillary meristem development. We discuss the genetics of plant meristems, the role of plant hormones and environmental factors in meristem development, and the impact of epigenetic factors on meristem organization and function.

Crystal structure of DRIK1, a stress-responsive receptor-like pseudokinase, reveals the molecular basis for the absence of ATP binding

BACKGROUND

Plants reprogram metabolism and development to rapidly adapt to biotic and abiotic stress. Protein kinases play a significant role in this process by phosphorylating protein substrates that activate or inactivate signaling cascades that regulate cellular and metabolic adaptations. Despite their importance in plant biology, a notably small fraction of the plant kinomes has been studied to date.

RESULTS

In this report, we describe ZmDRIK1, a stress-responsive receptor-like pseudokinase whose expression is downregulated under water restriction. We show the structural features and molecular basis of the absence of ATP binding exhibited by ZmDRIK1. The ZmDRIK1 kinase domain lacks conserved amino acids that are essential for phosphorylation activity. The crystal structure of the ZmDRIK1 kinase domain revealed the presence of a spine formed by the side chain of the triad Leu²⁴⁰, Tyr³⁶³, and Leu³⁷⁵ that occludes the ATP binding pocket. Although ZmDRIK1 is unable to bind nucleotides, it does bind the small molecule ENMD-2076 which, in a cocrystal structure, revealed the potential to serve as a ZmDRIK1 inhibitor.

CONCLUSION

ZmDRIK1 is a novel receptor-like pseudokinase responsive to biotic and abiotic stress. The absence of ATP binding and consequently, the absence of phosphorylation activity, was proven by the crystal structure of the apo form of the protein kinase domain. The expression profiling of the gene encoding ZmDRIK1 suggests this kinase may play a role in downregulating the expression of stress responsive genes that are not necessary under normal conditions. Under biotic and abiotic stress, ZmDRIK1 is down-regulated to release the expression of these stress-responsive genes.

Gene regulatory network controlling carpel number variation in cucumber

The WUSCHEL-CLAVATA3 pathway genes play an essential role in shoot apical meristem maintenance and floral organ development, and under intense selection during crop domestication. The carpel number is an important fruit trait that affects fruit shape, size and internal quality in cucumber, but the molecular mechanism remains elusive. Here, we found that CsCLV3 expression was negatively correlated with carpel number in cucumber cultivars. CsCLV3-RNAi led to increased number of petals and carpels, whereas overexpression of CsWUS resulted in more sepals, petals and carpels, suggesting that CsCLV3 and CsWUS function as a negative and a positive regulator for carpel number variation, respectively. Biochemical analyses indicated that CsWUS directly bound to the promoter of CsCLV3 and activated its expression. Overexpression of CsFUL1^A , a FRUITFULL-like MADS-box gene, resulted in more petals and carpels. CsFUL1^A can directly bind to the CsWUS promoter to stimulate its expression. Furthermore, we found that auxin participated in carpel number variation in cucumber through interaction of CsARF14 with CsWUS. Therefore, we have identified a gene regulatory pathway involving CsCLV3, CsWUS, CsFUL1^A and CsARF14 in determining carpel number variation in an important vegetable crop - cucumber.

The Role of Plasmodesmata-Associated Receptor in Plant Development and Environmental Response

Over the last decade, plasmodesmata (PD) symplasmic nano-channels were reported to be involved in various cell biology activities to prop up within plant growth and development as well as environmental stresses. Indeed, this is highly influenced by their native structure, which is lined with the plasma membrane (PM), conferring a suitable biological landscape for numerous plant receptors that correspond to signaling pathways. However, there are more than six hundred members of Arabidopsis thaliana membrane-localized receptors and over one thousand receptors in rice have been identified, many of which are likely to respond to the external stimuli. This review focuses on the class of plasmodesmal-receptor like proteins (PD-RLPs)/plasmodesmal-receptor-like kinases (PD-RLKs) found in planta. We summarize and discuss the current knowledge regarding RLPs/RLKs that reside at PD-PM channels in response to plant growth, development, and stress adaptation.

Transcriptional circuits in control of shoot stem cell homeostasis

Plant shoot apical meristems (SAMs) play essential roles in plant growth and development. Located at the growing tip of a plant stem, these dome-like structures contain stem cells, which serve to perpetuate themselves in an undifferentiated state while continually adding new cells that differentiate and eventually form all above-ground tissues. In a SAM, the pool of stem cells is dynamically maintained through a balance between cell division (self-renewal) and differentiation (loss of stem-cell identity). In the model plant Arabidopsis thaliana, a negative feedback loop between WUSCHEL (WUS) and the CLAVATA3 (CLV3) plays important roles in maintaining the stem cell population. In this review, we highlight recent findings mainly from studies in Arabidopsis, and summarize the research progress on understanding how multiple transcriptional circuits integrate and function at different cell layers to control the WUS-CLV3 loop and stem cell homeostasis.

Integrating the dynamics of yield traits in rice in response to environmental changes

Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.