WUSCHEL-RELATED HOMEOBOX4 acts as a key regulator in early leaf development in rice

Spatially distributed cytokinins: Metabolism, signaling, and transport

Cytokinins are mobile phytohormones that regulate plant growth, development, and environmental adaptability. The major cytokinin species include isopentenyl adenine (iP), trans-zeatin (tZ), cis-zeatin (cZ), and dihydrozeatin (DZ). The spatial distributions of different cytokinin species in different organelles, cells, tissues, and organs are primarily shaped by biosynthesis via isopentenyltransferases (IPT), cytochrome P450 monooxygenase, and 5'-ribonucleotide phosphohydrolase and by conjugation or catabolism via glycosyltransferase or cytokinin oxidase/dehydrogenase. Cytokinins bind to histidine receptor kinases in the endoplasmic reticulum or plasma membrane and relay signals to response regulators in the nucleus via shuttle proteins known as histidine phosphotransfer proteins. The movements of cytokinins from sites of biosynthesis to sites of signal perception usually require long-distance, intercellular, and intracellular transport. In the past decade, ATP-binding cassette (ABC) transporters, purine permeases (PUP), AZA-GUANINE RESISTANT (AZG) transporters, equilibrative nucleoside transporters (ENT), and Sugars Will Eventually Be Exported transporters (SWEET) have been characterized as involved in cytokinin transport processes. This review begins by introducing the spatial distributions of various cytokinins and the subcellular localizations of the proteins involved in their metabolism and signaling. Highlights focus on an inventory of the characterized transporters involved in cytokinin compartmentalization, including long-distance, intercellular, and intracellular transport, and the regulation of the spatial distributions of cytokinins by environmental cues. Future directions for cytokinin research are also discussed.

Advancements in Rice Leaf Development Research

Rice leaf morphology is a pivotal component of the ideal plant architecture, significantly impacting rice yield. The process of leaf development unfolds through three distinct stages: the initiation of leaf primordia, the establishment and maintenance of polarity, and leaf expansion. Genes regulating leaf morphology encompass transcription factors, hormones, and miRNAs. An in-depth synthesis and categorization of genes associated with leaf development, particularly those successfully cloned, hold paramount importance in unraveling the complexity of rice leaf development. Furthermore, it provides valuable insights into the potential for molecular-level manipulation of rice leaf types. This comprehensive review consolidates the stages of rice leaf development, the genes involved, molecular regulatory pathways, and the influence of plant hormones. Its objective is to establish a foundational understanding of the creation of ideal rice leaf forms and their practical application in molecular breeding.

WOX2 functions redundantly with WOX1 and WOX4 to positively regulate seed germination in Arabidopsis

MAIN CONCLUSION

WOX family gene WOX2 is highly expressed during seed development, which functions redundantly with WOX1 and WOX4 to positively regulate seed germination. WOX (WUSCHEL-related homeobox) is a family of transcription factors in plants. They play essential roles in the regulation of plant growth and development, but their function in seed germination is not well understood. In this report, we show that WOX1, WOX2, and WOX4 are close homologues in Arabidopsis. WOX2 has a redundant function with WOX1 and WOX4, respectively, in seed germination. WOX2 is highly expressed during seed development, from the globular embryonic stage to mature dry seeds, and its expression is decreased after germination. Loss of function single mutant wox2, and double mutants wox1 wox2 and wox2 wox4-1 show decreased germination speed. WOX2 and WOX4 are essential for hypocotyl-radicle zone elongation during germination, potentially by promoting the expression of cell wall-related genes. We also found that WOX2 and WOX4 regulate germination through the gibberellin (GA) pathway. These results suggest that WOX2 and WOX4 integrate the GA pathway and downstream cell wall-related genes during germination.

A Comprehensive Identification and Expression Analysis of the WUSCHEL Homeobox-Containing Protein Family Reveals Their Special Role in Development and Abiotic Stress Response in Zea mays L

Maize is an important food and cash crop worldwide. The WUSCHEL (WUS)-related homeobox (WOX) transcription factor (TF) family plays a significant role in the development process and the response to abiotic stress of plants. However, few studies have been reported on the function of WOX genes in maize. This work, utilizing the latest maize B73 reference genome, results in the identification of 22 putative ZmWOX gene family members. Except for chromosome 5, the 22 ZmWOX genes were homogeneously distributed on the other nine chromosomes and showed three tandem duplication and 10 segmental duplication events. Based on phylogenetic characteristics, ZmWOXs are divided into three clades (e.g., WUS, intermediate, and ancient groups), and the majority of ZmWOXs in same group display similar gene and protein structures. Cross-species collinearity results indicated that some WOX genes might be evolutionarily conservative. The promoter region of ZmWOX family members is enriched in light, plant growth/hormone, and abiotic stress-responsive elements. Tissue-specific expression evaluation showed that ZmWOX genes might play a significant role in the occurrence of maize reproductive organs. Transcriptome data and RT-qPCR analysis further showed that six ZmWOX genes (e.g., ZmWOX1, 4, 6, 13, 16, and 18) were positively or negatively modulated by temperature, salt, and waterlogging stresses. Moreover, two ZmWOXs, ZmWOX1 and ZmWOX18, both were upregulated by abiotic stress. ZmWOX18 was localized in the nucleus and had transactivation activities, while ZmWOX1 was localized in both the cytoplasm and nucleus, without transactivation activity. Overall, this work offers new perspectives on the evolutionary relationships of ZmWOX genes and might provide a resource for further detecting the biological functions of ZmWOXs.

Hormonal control of medial-lateral growth and vein formation in the maize leaf

Parallel veins are characteristic of monocots, including grasses (Poaceae). Therefore, how parallel veins develop as the leaf grows in the medial-lateral (ML) dimension is a key question in grass leaf development. Using fluorescent protein reporters, we mapped auxin, cytokinin (CK), and gibberellic acid (GA) response patterns in maize (Zea mays) leaf primordia. We further defined the roles of these hormones in ML growth and vein formation through combinatorial genetic analyses and measurement of hormone concentrations. We discovered a novel pattern of auxin response in the adaxial protoderm that we hypothesize has important implications for the orderly formation of 3° veins early in leaf development. In addition, we found an auxin transport and response pattern in the margins that correlate with the transition from ML to proximal-distal growth. We present evidence that auxin efflux precedes CK response in procambial strand development. We also determined that GA plays an early role in the shoot apical meristem as well as a later role in the primordium to restrict ML growth. We propose an integrative model whereby auxin regulates ML growth and vein formation in the maize leaf through control of GA and CK.

Genetic basis controlling rice plant architecture and its modification for breeding

The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.

Identification of a Rice Leaf Width Gene Narrow Leaf 22 (NAL22) through Genome-Wide Association Study and Gene Editing Technology

Rice leaf width (RLW) is a crucial determinant of photosynthetic area. Despite the discovery of several genes controlling RLW, the underlying genetic architecture remains unclear. In order to better understand RLW, this study conducted a genome-wide association study (GWAS) on 351 accessions from the rice diversity population II (RDP-II). The results revealed 12 loci associated with leaf width (LALW). In LALW4, we identified one gene, Narrow Leaf 22 (NAL22), whose polymorphisms and expression levels were associated with RLW variation. Knocking out this gene in Zhonghua11, using CRISPR/Cas9 gene editing technology, resulted in a short and narrow leaf phenotype. However, seed width remained unchanged. Additionally, we discovered that the vein width and expression levels of genes associated with cell division were suppressed in nal22 mutants. Gibberellin (GA) was also found to negatively regulate NAL22 expression and impact RLW. In summary, we dissected the genetic architecture of RLW and identified a gene, NAL22, which provides new loci for further RLW studies and a target gene for leaf shape design in modern rice breeding.

Multi-model genome-wide association studies of leaf anatomical traits and vein architecture in rice

Introduction

The anatomy of rice leaves is closely related to photosynthesis and grain yield. Therefore, exploring insight into the quantitative trait loci (QTLs) and alleles related to rice flag leaf anatomical and vein traits is vital for rice improvement.

Methods

Here, we aimed to explore the genetic architecture of eight flag leaf traits using one single-locus model; mixed-linear model (MLM), and two multi-locus models; fixed and random model circulating probability unification (FarmCPU) and Bayesian information and linkage disequilibrium iteratively nested keyway (BLINK). We performed multi-model GWAS using 329 rice accessions of RDP1 with 700K single-nucleotide polymorphisms (SNPs) markers.

Results

The phenotypic correlation results indicated that rice flag leaf thickness was strongly correlated with leaf mesophyll cells layer (ML) and thickness of both major and minor veins. All three models were able to identify several significant loci associated with the traits. MLM identified three non-synonymous SNPs near NARROW LEAF 1 (NAL1) in association with ML and the distance between minor veins (IVD) traits.

Discussion

Several numbers of significant SNPs associated with known gene function in leaf development and yield traits were detected by multi-model GWAS performed in this study. Our findings indicate that flag leaf traits could be improved via molecular breeding and can be one of the targets in high-yield rice development.

A splice site mutation in the FvePHP gene is associated with leaf development and flowering time in woodland strawberry

Leaves and flowers are crucial for the growth and development of higher plants. In this study we identified a mutant with narrow leaflets and early flowering (nlef) in an ethyl methanesulfonate-mutagenized population of woodland strawberry (Fragaria vesca) and aimed to identify the candidate gene. Genetic analysis revealed that a single recessive gene, nlef, controlled the mutant phenotype. We found that FvH4_1g25470, which encodes a putative DNA polymerase α with a polymerase and histidinol phosphatase domain (PHP), might be the candidate gene, using bulked segregant analysis with whole-genome sequencing, molecular markers, and cloning analyses. A splice donor site mutation (C to T) at the 5' end of the second intron led to an erroneous splice event that reduced the expression level of the full-length transcript of FvePHP in mutant plants. FvePHP was localized in the nucleus and was highly expressed in leaves. Silencing of FvePHP using the virus-induced gene silencing method resulted in partial developmental defects in strawberry leaves. Overexpression of the FvePHP gene can largely restore the mutant phenotype. The expression levels of FveSEP1, FveSEP3, FveAP1, FveFUL, and FveFT were higher in the mutants than those in 'Yellow Wonder' plants, probably contributing to the early flowering phenotype in mutant plants. Our results indicate that mutation in FvePHP is associated with multiple developmental pathways. These results aid in understanding the role of DNA polymerase in strawberry development.

The APC/CTAD1-WIDE LEAF 1-NARROW LEAF 1 pathway controls leaf width in rice

Leaf morphology is one of the most important features of the ideal plant architecture. However, the genetic and molecular mechanisms controlling this feature in crops remain largely unknown. Here, we characterized the rice (Oryza sativa) wide leaf 1 (wl1) mutant, which has wider leaves than the wild-type due to more vascular bundles and greater distance between small vascular bundles. WL1 encodes a Cys-2/His-2-type zinc finger protein that interacts with Tillering and Dwarf 1 (TAD1), a co-activator of the anaphase-promoting complex/cyclosome (APC/C) (a multi-subunit E3 ligase). The APC/CTAD1 complex degrades WL1 via the ubiquitin-26S proteasome degradation pathway. Loss-of-function of TAD1 resulted in plants with narrow leaves due to reduced vascular bundle numbers and distance between the small vascular bundles. Interestingly, we found that WL1 negatively regulated the expression of a narrow leaf gene, NARROW LEAF 1 (NAL1), by recruiting the co-repressor TOPLESS-RELATED PROTEIN and directly binding to the NAL1 regulatory region to inhibit its expression by reducing the chromatin histone acetylation. Furthermore, biochemical and genetic analyses revealed that TAD1, WL1, and NAL1 operated in a common pathway to control the leaf width. Our study establishes an important framework for understanding the APC/CTAD1-WL1-NAL1 pathway-mediated control of leaf width in rice, and provides insights for improving crop plant architecture.

Characterization of WOX genes revealed drought tolerance, callus induction, and tissue regeneration in Gossypium hirsutum

Cotton is an important natural fiber crop; its seeds are the main oil source. Abiotic stresses cause a significant decline in its production. The WUSCHEL-related Homeobox (WOX) genes have been involved in plant growth, development, and stress responses. However, the functions of WOX genes are less known in cotton. This study identified 39, 40, 21, and 20 WOX genes in Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum, and Gossypium raimondii, respectively. All the WOX genes in four cotton species could be classified into three clades, which is consistent with previous research. The gene structure and conserved domain of all WOX genes were analyzed. The expressions of WOX genes in germinating hypocotyls and callus were characterized, and it was found that most genes were up-regulated. One candidate gene Gh_ A01G127500 was selected to perform the virus-induced gene silencing (VIGS) experiment, and it was found that the growth of the silenced plant (pCLCrVA: GhWOX4_A01) was significantly inhibited compared with the wild type. In the silenced plant, there is an increase in antioxidant activities and a decrease in oxidant activities compared with the control plant. In physiological analysis, the relative electrolyte leakage level and the excised leaf water loss of the infected plant were increased. Still, both the relative leaf water content and the chlorophyll content were decreased. This study proved that WOX genes play important roles in drought stress and callus induction, but more work must be performed to address the molecular functions of WOX genes.

Translational repression of FZP mediated by CU-rich element/OsPTB interactions modulates panicle development in rice

Panicle development is an important determinant of the grain number in rice. A thorough characterization of the molecular mechanism underlying panicle development will lead to improved breeding of high-yielding rice varieties. Frizzy Panicle (FZP), a critical gene for panicle development, is regulated by OsBZR1 and OsARFs at the transcriptional stage. However, the translational modulation of FZP has not been reported. We reveal that the CU-rich elements (CUREs) in the 3' UTR of the FZP mRNA are crucial for efficient FZP translation. The knockout of CUREs in the FZP 3' UTR or the over-expression of the FZP 3' UTR fragment containing CUREs resulted in an increase in FZP mRNA translation efficiency. Moreover, the number of secondary branches (NSB) and the grain number per panicle (GNP) decreased in the transformed rice plants. The CUREs in the 3' UTR of FZP mRNA were verified as the targets of the polypyrimidine tract-binding proteins OsPTB1 and OsPTB2 in rice. Both OsPTB1 and OsPTB2 were highly expressed in young panicles. The knockout of OsPTB1/2 resulted in an increase in the FZP translational efficiency and a decrease in the NSB and GNP. Furthermore, the over-expression of OsPTB1/2 decreased the translation of the reporter gene fused to FZP 3' UTR in vivo and in vitro. These results suggest that OsPTB1/2 can mediate FZP translational repression by interacting with CUREs in the 3' UTR of FZP mRNA, leading to changes in the NSB and GNP. Accordingly, in addition to transcriptional regulation, FZP expression is also fine-tuned at the translational stage during rice panicle development.

OsQHB Improves Salt Tolerance by Scavenging Reactive Oxygen Species in Rice

Soil salinity is a major environmental stress that restricts the growth and yield of crops. Mining the key genes involved in the balance of rice salt tolerance and yield will be extremely important for us to cultivate salt-tolerance rice varieties. In this study, we report a WUSCHEL-related homeobox (WOX) gene, quiescent-center-specific homeobox (OsQHB), positively regulates yield-related traits and negatively regulates salt tolerance in rice. Mutation in OsQHB led to a decrease in plant height, tiller number, panicle length, grain length and grain width, and an increase in salt tolerance. Transcriptome and qPCR analysis showed that reactive oxygen species (ROS) scavenging-related genes were regulated by OsQHB. Moreover, the osqhb mutants have higher ROS-scavenging enzymes activities and lower accumulation of ROS and malondialdehyde (MDA) under salt stress. Thus, our findings provide new insights into the role of rice WOX gene family in rice development and salt tolerance, and suggest that OsQHB is a valuable target for improving rice production in environments characterized by salt stress.

Vascular function of the T3/modern clade WUSCHEL-Related HOMEOBOX transcription factor genes predate apical meristem-maintenance function

BACKGROUND

Plants have the lifelong ability to generate new organs due to the persistent functioning of stem cells. In seed plants, groups of stem cells are housed in the shoot apical meristem (SAM), root apical meristem (RAM), and vascular cambium (VC). In ferns, a single shoot stem cell, the apical cell, is located in the SAM, whereas each root initiates from a single shoot-derived root initial. WUSCHEL-RELATED HOMEOBOX (WOX) family transcription factors play important roles to maintain stem-cell identity. WOX genes are grouped phylogenetically into three clades. The T3WOX/modern clade has expanded greatly in angiosperms, with members functioning in multiple meristems and complex developmental programs. The model fern Ceratopteris richardii has only one well-supported T3WOX/modern WOX gene, CrWUL. Its orthologs in Arabidopsis, AtWUS, AtWOX5, and AtWOX4, function in the SAM, RAM, and VC, respectively. Identifying the function of CrWUL will provide insights on the progenitor function and the diversification of the modern WOX genes in seed plants.

RESULTS

To investigate the role of CrWUL in the fern, we examined the expression and function of CrWUL and found it expresses during early root development and in vasculature but not in the SAM. Knockdown of CrWUL by RNAi produced plants with fewer roots and fewer phloem cells. When expressed in Arabidopsis cambium, CrWUL was able to complement AtWOX4 function in an atwox4 mutant, suggesting that the WOX function in VC is conserved between ferns and angiosperms. Additionally, the proposed progenitor of T3WOX genes from Selaginella kraussiana is expressed in the vasculature but not in the shoot apical meristem. In contrast to the sporophyte, the expression of CrWUL in the gametophyte exhibits a more general expression pattern and when knocked down, offered little discernable phenotypes.

CONCLUSIONS

The results presented here support the occurrence of co-option of the T3WOX/modern clade gene from the gametophyte to function in vasculature and root development in the sporophyte. The function in vasculature is likely to have existed in the progenitor of lycophyte T3WOX/modern clade genes and this function predates its SAM function found in many seed plants.

The LONELY GUY gene family: from mosses to wheat, the key to the formation of active cytokinins in plants

LONELY GUY (LOG) was first identified in a screen of rice mutants with defects in meristem maintenance. In plants, LOG codes for cytokinin riboside 5'-monophosphate phosphoribohydrolase, which converts inactive cytokinin nucleotides directly to the active free bases. Many enzymes with the PGGxGTxxE motif have been misannotated as lysine decarboxylases; conversely not all enzymes containing this motif are cytokinin-specific LOGs. As LOG mutants clearly impact yield in rice, we investigated the LOG gene family in bread wheat. By interrogating the wheat (Triticum aestivum) genome database, we show that wheat has multiple LOGs. The close alignment of TaLOG1, TaLOG2 and TaLOG6 with the X-ray structures of two functional Arabidopsis thaliana LOGs allows us to infer that the wheat LOGs 1-11 are functional LOGs. Using RNA-seq data sets, we assessed TaLOG expression across 70 tissue types, their responses to various stressors, the pattern of cis-regulatory elements (CREs) and intron/exon patterns. TaLOG gene family members are expressed variously across tissue types. When the TaLOG CREs are compared with those of the cytokinin dehydrogenases (CKX) and glucosyltransferases (CGT), there is close alignment of CREs between TaLOGs and TaCKXs reflecting the key role of CKX in maintaining cytokinin homeostasis. However, we suggest that the main homeostatic mechanism controlling cytokinin levels in response to biotic and abiotic challenge resides in the CGTs, rather than LOG or CKX. However, LOG transgenics and identified mutants in rice variously impact yield, providing interesting avenues for investigation in wheat.

D-type cyclin OsCYCD3;1 is involved in the maintenance of meristem activity to regulate branch formation in rice

D-type cyclins (CYCDs) are involved in a wide range of biological processes, as one of the major regulators of cell cycle activity. In Arabidopsis (Arabidopsis thaliana), three members of CYCD3 subgroup genes play important roles in plant development such as leaf development and branch formation. In rice (Oryza sativa), there is only one gene (OsCYCD3;1) belonging to the CYCD3 subgroup; its function is unknown. In this study, in order to elucidate the function of OsCYCD3;1, we generated knockout mutants of the gene and conducted developmental analysis. The knockout mutants showed a significantly reduced number of branches compared with a wild type, suggesting that OsCYCD3;1 promotes branch formation. Histological analysis showed that the activities of the axillary meristem and the shoot apical meristem (SAM) were compromised in these mutant plants. Our results suggest that OsCYCD3;1 promotes branch formation, probably by regulating cell division to maintain the activities of the axillary meristem and the SAM.

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

Ecological divergence in a species provides a valuable opportunity to study the early stages of speciation. We focused on Metrosideros polymorpha, a unique example of the incipient radiation of woody species, to examine how an ecological divergence continues in the face of gene flow. We analyzed the whole genomes of 70 plants collected throughout the island of Hawaii, which is the youngest island with the highest altitude in the archipelago and encompasses a wide range of environments. The continuous M. polymorpha forest stands on the island of Hawaii were differentiated into three genetic clusters, each of which grows in a distinctive environment and includes substantial genetic and phenotypic diversity. The three genetic clusters showed signatures of selection in genomic regions encompassing genes relevant to environmental adaptations, including genes associated with light utilization, oxidative stress, and leaf senescence, which are likely associated with the ecological differentiation of the species. Our demographic modeling suggested that the glaberrima cluster in wet environments maintained a relatively large population size and two clusters split: polymorpha in the subalpine zone and incana in dry and hot conditions. This ecological divergence possibly began before the species colonized the island of Hawaii. Interestingly, the three clusters recovered genetic connectivity coincidentally with a recent population bottleneck, in line with the weak reproductive isolation observed in the species. This study highlights that the degree of genetic differentiation between ecologically-diverged populations can vary depending on the strength of natural selection in the very early phases of speciation.

Knowledge about how genetic barriers are formed between populations in distinct environments is valuable to understand the processes of speciation and conserve biodiversity. Metrosideros polymorpha, an endemic woody species in the Hawaiian Islands, is a good system to study developing genetic barriers in a species, because it colonized the diverse environments and diversified the morphology for a relatively short period of time. We analyzed the genomes of 70 M. polymorpha plants from a broad range of environments on the island of Hawaii to infer the current and past genetic barriers among them. Currently, M. polymorpha plants growing in different environments have substantially different genomes, especially at the genomic regions with genes putatively controlling physiology to fit in distinct environment. However, in its history, they had hybridized with one another, possibly because plants formerly growing in different environments came into close contact due to the climate changes. It is suggested that genetic barriers can easily strengthen or weaken depending on environments splitting the ecology of a species before reproductive isolation becomes complete.

RLB (RICE LATERAL BRANCH) recruits PRC2-mediated H3K27 tri-methylation on OsCKX4 to regulate lateral branching

Lateral branches such as shoot and panicle are determining factors and target traits for rice (Oryza sativa L.) yield improvement. Cytokinin promotes rice lateral branching; however, the mechanism underlying the fine-tuning of cytokinin homeostasis in rice branching remains largely unknown. Here, we report the map-based cloning of RICE LATERAL BRANCH (RLB) encoding a nuclear-localized, KNOX-type homeobox protein from a rice cytokinin-deficient mutant showing more tillers, sparser panicles, defected floret morphology as well as attenuated shoot regeneration from callus. RLB directly binds to the promoter and represses the transcription of OsCKX4, a cytokinin oxidase gene with high abundance in panicle branch meristem. OsCKX4 over-expression lines phenocopied rlb, which showed upregulated OsCKX4 levels. Meanwhile, RLB physically binds to Polycomb repressive complex 2 (PRC2) components OsEMF2b and co-localized with H3K27me3, a suppressing histone modification mediated by PRC2, in the OsCKX4 promoter. We proposed that RLB recruits PRC2 to the OsCKX4 promoter to epigenetically repress its transcription, which suppresses the catabolism of cytokinin, thereby promoting rice lateral branching. Moreover, antisense inhibition of OsCKX4 under the LOG promoter successfully increased panicle size and spikelet number per plant without affecting other major agronomic traits. This study provides insight into cytokinin homeostasis, lateral branching in plants, and also promising target genes for rice genetic improvement.

LF1 regulates the lateral organs polarity development in rice

The patterning of adaxial-abaxial tissues plays a vital role in the morphology of lateral organs, which is maintained by antagonism between the genes that specify adaxial and abaxial tissue identity. The homeo-domain leucine zipper class III (HD-ZIP III) family genes regulate adaxial identity; however, little information is known about the physical interactions or transcriptionally regulated downstream genes of HD-ZIP III. In this study, we identified a dominant rice mutant, lateral floret 1 (lf1), which has defects in lateral organ polarity. LF1 encodes the HD-ZIP III transcription factor, which expressed in the adaxial area of lateral organs. LF1 can activate directly the expression of LITTLE ZIPPER family gene OsZPR4 and HD-ZIP II family gene OsHOX1, and OsZPR4 and OsHOX1 respectively interact with LF1 to form a heterodimer to repress the transcriptional activity of LF1. LF1 influences indole-3-acetic acid (IAA) content by directly regulating the expression of OsYUCCA6. Therefore, LF1 forms negative feedback loops between OsZPR4 and OsHOX1 to affect IAA content, leading to the regulation of lateral organs polarity development. These results reveal the cross-talk among HD-ZIP III, LITTLE ZIPPER, and HD-ZIP II proteins and provide new insights into the molecular mechanisms underlying the polarity development of lateral organs.

BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon

BACKGROUND

The vascular system of plants consists of two main tissue types, xylem and phloem. These tissues are organized into vascular bundles that are arranged into a complex network running through the plant that is essential for the viability of land plants. Despite their obvious importance, the genes involved in the organization of vascular tissues remain poorly understood in grasses.

RESULTS

We studied in detail the vascular network in stems from the model grass Brachypodium distachyon (Brachypodium) and identified a large set of genes differentially expressed in vascular bundles versus parenchyma tissues. To decipher the underlying molecular mechanisms of vascularization in grasses, we conducted a forward genetic screen for abnormal vasculature. We identified a mutation that severely affected the organization of vascular tissues. This mutant displayed defects in anastomosis of the vascular network and uncommon amphivasal vascular bundles. The causal mutation is a premature stop codon in ERECTA, a LRR receptor-like serine/threonine-protein kinase. Mutations in this gene are pleiotropic indicating that it serves multiple roles during plant development. This mutant also displayed changes in cell wall composition, gene expression and hormone homeostasis.

CONCLUSION

In summary, ERECTA has a pleiotropic role in Brachypodium. We propose a major role of ERECTA in vasculature anastomosis and vascular tissue organization in Brachypodium.

Transcriptome Analysis Revealed GhWOX4 Intercedes Myriad Regulatory Pathways to Modulate Drought Tolerance and Vascular Growth in Cotton

Cotton is a paramount cash crop around the globe. Among all abiotic stresses, drought is a leading cause of cotton growth and yield loss. However, the molecular link between drought stress and vascular growth and development is relatively uncharted. Here, we validated a crucial role of GhWOX4, a transcription factor, modulating drought stress with that of vasculature growth in cotton. Knock-down of GhWOX4 decreased the stem width and severely compromised vascular growth and drought tolerance. Conversely, ectopic expression of GhWOX4 in Arabidopsis enhanced the tolerance to drought stress. Comparative RNAseq analysis revealed auxin responsive protein (AUX/IAA), abscisic acid (ABA), and ethylene were significantly induced. Additionally, MYC-bHLH, WRKY, MYB, homeodomain, and heat-shock transcription factors (HSF) were differentially expressed in control plants as compared to GhWOX4-silenced plants. The promotor zone of GhWOX4 was found congested with plant growth, light, and stress response related cis-elements. differentially expressed genes (DEGs) related to stress, water deprivation, and desiccation response were repressed in drought treated GhWOX4-virus-induced gene silencing (VIGS) plants as compared to control. Gene ontology (GO) functions related to cell proliferation, light response, fluid transport, and flavonoid biosynthesis were over-induced in TRV: 156-0 h/TRV: 156-1 h (control) in comparison to TRV: VIGS-0 h/TRV: VIGS-1 h (GhWOX4-silenced) plants. This study improves our context for elucidating the pivotal role of GhWOX4 transcription factors (TF), which mediates drought tolerance, plays a decisive role in plant growth and development, and is likely involved in different regulatory pathways in cotton.

Transcription of the WUSCHEL-RELATED HOMEOBOX 4 gene in Arabidopsis thaliana

Phylogenetic shadowing and chromatin accessibility data suggested that essential regulatory elements are absent in the 2.9 kb immediate upstream region of the published WOX4_pro::YFP cambium marker. Inclusion of an additional 6.3 kb of upstream promoter sequence and confocal imaging with different fluorophores in transgenic Arabidopsis lines revealed a much wider cell-type-specific expression pattern in parenchymous cells of the aerial plant body. The previously demonstrated activity of the WOX4_pro::YFP marker in the cambium of vascular strands in the young Arabidopsis inflorescence stem depicts only sectors of a circular subcortical layer of parenchymous AtWOX4-positive cells. Transcription starts in subepidermal cells within the inflorescence apex in a phyllotactic pattern and extends into successively branching lateral organs, which are connected via small tube-like domains of AtWOX4-expressing cells with the circular subcortical parenchymal layer that extends basipetally down the stem. AtWOX4 expression is most dynamic in leaves, where promoter activity is observed transiently at the adaxial side of the lamina and remains detectable later in the palisade parenchyma, although at a weaker level than in the vasculature. In the root the extended AtWOX4 promoter is active through the proximal root meristem, i.e. in the quiescent centre (QC) and its surrounding initials, a pattern that is broader than transcription of its stem cell promoting relative AtWOX5 in the QC. Outside the proximal meristem AtWOX4 transcription is observed in upper cell layers of the columella root cap beneath or above within the stele in proto- and metaxylem cells, in a ribbon-type pattern which divides the central cylinder in two equal halves. This xylem-specific expression it the root stele relates to established AtWOX4 activity in xylem parenchyma specificity within vascular bundles of the stem.

CURLED LATER1 encoding the largest subunit of the Elongator complex has a unique role in leaf development and meristem function in rice

The Elongator complex, which is conserved in eukaryotes, has multiple roles in diverse organisms. In Arabidopsis thaliana, Elongator is shown to be involved in development, hormone action and environmental responses. However, except for Arabidopsis, our knowledge of its function is poor in plants. In this study, we initially carried out a genetic analysis to characterize a rice mutant with narrow and curled leaves, termed curled later1 (cur1). The cur1 mutant displayed a heteroblastic change, whereby the mutant leaf phenotype appeared specifically at a later adult phase of vegetative development. The shoot apical meristem (SAM) was small and the leaf initiation rate was low, suggesting that the activity of the SAM seemed to be partially reduced in cur1. We then revealed that CUR1 encodes a yeast ELP1-like protein, the largest subunit of Elongator. Furthermore, disruption of OsELP3 encoding the catalytic subunit of Elongator resulted in phenotypes similar to those of cur1, including the timing of the appearance of mutant phenotypes. Thus, Elongator activity seems to be specifically required for leaf development at the late vegetative phase. Transcriptome analysis showed that genes involved in protein quality control were highly upregulated in the cur1 shoot apex at the later vegetative phase, suggesting the restoration of impaired proteins probably produced by partial defects in translational control due to the loss of function of Elongator. The differences in the mutant phenotype and gene expression profile between CUR1 and its Arabidopsis ortholog suggest that Elongator has evolved to play a unique role in rice development.

Orange Leafhopper Cicadulina bipunctata Feeding Induces Gall Formation Nitrogen Dependently and Regulates Gibberellin Signaling

Orange leafhopper Cicadulina bipunctata feeding induces wallaby ear symptoms, namely growth suppression and gall formation characterized by severe swelling of leaf veins, on various Poaceae, thereby leading to low crop yields. Here, we investigated the development of wallaby ear symptoms on rice seedlings due to C. bipunctata feeding. After confirming that C. bipunctata feeding induces growth suppression and gall formation on rice seedlings, we further demonstrated that gall formation score decreased with decreasing levels of nitrogen in the medium and that C. bipunctata feeding induces the expression levels of nitrogen transporter genes. These gene expression changes may participate in the nutrient accumulation observed in galled tissues and in gall formation. In addition, these expression changes should induce growth promotion but the inhibition of gibberellin signaling by C. bipunctata feeding might be the reason why growth is suppressed. Treatment with plant growth regulators did not affect gall formation, suggesting the existence of a complex gall formation mechanism by C. bipunctata feeding.

Receptor-like kinase OsCR4 controls leaf morphogenesis and embryogenesis by fixing the distribution of auxin in rice

Cell differentiation is a key event in organ development; it involves auxin gradient formation, cell signaling, and transcriptional regulation. Yet, how these processes are orchestrated during leaf morphogenesis is poorly understood. Here, we demonstrate an essential role for the receptor-like kinase OsCR4 in leaf development. oscr4 loss-of-function mutants displayed short shoots and roots, with tiny, crinkly, or even dead leaves. The delayed outgrowth of the first three leaves and seminal root in oscr4 was due to defects in plumule and radicle formation during embryogenesis. The deformed epidermal, mesophyll, and vascular tissues observed in oscr4 leaves arose at the postembryo stage; the corresponding expression pattern of proOsCR4:GUS in embryos and young leaves suggests that OsCR4 functions in these tissues. Signals from the auxin reporter DR5rev:VENUS were found to be altered in oscr4 embryos and disorganized in oscr4 leaves, in which indole-3-acetic acid accumulation was further revealed by immunofluorescence. OsWOX3A, which is auxin responsive and related to leaf development, was activated extensively and ectopically in oscr4 leaves, partially accounting for the observed lack of cell differentiation. Our data suggest that OsCR4 plays a fundamental role in leaf morphogenesis and embryogenesis by fixing the distribution of auxin.

The WUSCHEL-related homeobox transcription factor OsWOX4 controls the primary root elongation by activating OsAUX1 in rice

Primary root is the basic component of root system and plays a key role in early seedling growth and survival in rice. However, the molecular mechanism of primary root elongation still needs to be well understood. Here, we showed that OsWOX4, a WUSCHEL-related homeobox (WOX) transcription factor, was involved in the primary root elongation in rice. Silencing of OsWOX4 by RNA interference (RNAi) greatly increased the primary root length, whereas its overexpression reduced primary root elongation significantly. Moreover, the size of meristem zone and epidermal cell length of mature zone in RNAi root tips were drastically enhanced, while they were reduced markedly in overexpression lines, in comparison with that of wild type. Further analysis showed that the accumulation of free IAA was slightly increased in RNAi roots, but drastically reduced in plants overexpressing OsWOX4. The expression of genes responsible for auxin biosynthesis and transport was also changed in OsWOX4 transgenic lines. Transient transcriptional activation and electrophoretic mobility shift assays showed that OsWOX4 directly regulated the transcription of OsAUX1 through binding to its promoter region. Collectively, our results indicated that OsWOX4 played a crucial role in the primary root elongation by regulating auxin transport, suggesting its importance in rice root system architecture.

WUSCHEL: a master regulator in plant growth signaling

This review summarizes recent knowledge on functions of WUS and WUS-related homeobox (WOX) transcription factors in diverse signaling pathways governing shoot meristem biology and several other aspects of plant dynamics. Transcription factors (TFs) are master regulators involved in controlling different cellular and biological functions as well as diverse signaling pathways in plant growth and development. WUSCHEL (WUS) is a homeodomain transcription factor necessary for the maintenance of the stem cell niche in the shoot apical meristem, the differentiation of lateral primordia, plant cell totipotency and other diverse cellular processes. Recent research about WUS has uncovered several unique features including the complex signaling pathways that further improve the understanding of vital network for meristem biology and crop productivity. In addition, several reports bridge the gap between WUS expression and plant signaling pathway by identifying different WUS and WUS-related homeobox (WOX) genes during the formation of shoot (apical and axillary) meristems, vegetative-to-embryo transition, genetic transformation, and other aspects of plant growth and development. In this respect, the WOX family of TFs comprises multiple members involved in diverse signaling pathways, but how these pathways are regulated remains to be elucidated. Here, we review the current status and recent discoveries on the functions of WUS and newly identified WOX family members in the regulatory network of various aspects of plant dynamics.

A cytokinin-activation enzyme-like gene improves grain yield under various field conditions in rice

CRISPR-edited variants at the 3'-end of OsLOGL5's coding sequence (CDS), significantly increased rice grain yield under well-watered, drought, normal nitrogen, and low nitrogen field conditions at multiple geographical locations. Cytokinins impact numerous aspects of plant growth and development. This study reports that constitutive ectopic overexpression of a rice cytokinin-activation enzyme-like gene, OsLOGL5, significantly reduced primary root growth, tiller number, and yield. Conversely, mutations at the 3'-end of OsLOGL5 CDS resulted in normal rice plant morphology but with increased grain yield under well-watered, drought, normal nitrogen, and low nitrogen field conditions at multiple geographical locations. Six gene edited variants (Edit A to F) were created and tested in the field. Edit-B and Edit-F plants increased, but Edit-D and Edit-E plants decreased, the panicle number per plant. All OsLOGL5-edited plants significantly increased seed setting rate, total grain numbers, full-filled grain numbers per panicle, and thousand seed weight under drought conditions, suggesting that OsLOGL5 is likely involved in the regulation of both seed development and grain filling processes. Our results indicate that the C-terminal end of OsLOGL5 protein plays an important role in regulating rice yield improvement under different abiotic stress conditions, and OsLOGL5 is important for rice yield enhancement and stability.

Characterization of a Novel Rice Dynamic Narrow-Rolled Leaf Mutant with Deficiencies in Aromatic Amino Acids

The leaf blade is the main photosynthetic organ and its morphology is related to light energy capture and conversion efficiency. We isolated a novel rice Dynamic Narrow-Rolled Leaf 1 (dnrl1) mutant showing reduced width of leaf blades, rolled leaves and lower chlorophyll content. The narrow-rolled leaf phenotype resulted from the reduced number of small longitudinal veins per leaf, smaller size and irregular arrangement of bulliform cells compared with the wild-type. DNRL1 was mapped to chromosome 7 and encoded a putative 3-deoxy-7-phosphoheptulonate synthase (DAHPS) which catalyzes the conversion of phosphoenolpyruvate and D-erythrose 4-phosphate to DAHP and phosphate. Sequence analysis revealed that a single base substitution (T–A) was detected in dnrl1, leading to a single amino acid change (L376H) in the coding protein. The mutation led to a lower expression level of DNRL1 as well as the lower activity of DAHPS in the mutant compared with the wild type. Genetic complementation and over-expression of DNRL1 could rescue the narrow-rolled phenotype. DNRL1 was constitutively expressed in all tested organs and exhibited different expression patterns from other narrow-rolled leaf genes. DNRL1-GFP located to chloroplasts. The lower level of chlorophyll in dnrl1 was associated with the downregulation of the genes responsible for chlorophyll biosynthesis and photosynthesis. Furthermore, dnrl1 showed significantly reduced levels of aromatic amino acids including Trp, Phe and Tyr. We conclude that OsDAHPS, encoded by DNRL1, plays a critical role in leaf morphogenesis by mediating the biosynthesis of amino acids in rice.

A fern WUSCHEL-RELATED HOMEOBOX gene functions in both gametophyte and sporophyte generations

BACKGROUND

Post-embryonic growth of land plants originates from meristems. Genetic networks in meristems maintain the stem cells and direct acquisition of cell fates. WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors involved in meristem networks have only been functionally characterized in two evolutionarily distant taxa, mosses and seed plants. This report characterizes a WOX gene in a fern, which is located phylogenetically between the two taxa.

RESULTS

CrWOXB transcripts were detected in proliferating tissues, including gametophyte and sporophyte meristems of Ceratopteris richardii. In addition, CrWOXB is expressed in archegonia but not the antheridia of gametophytes. Suppression of CrWOXB expression in wild-type RN3 plants by RNAi produced abnormal morphologies of gametophytes and sporophytes. The gametophytes of RNAi lines produced fewer cells, and fewer female gametes compared to wild-type. In the sporophyte generation, RNAi lines produced fewer leaves, pinnae, roots and lateral roots compared to wild-type sporophytes.

CONCLUSIONS

Our results suggest that CrWOXB functions to promote cell divisions and organ development in the gametophyte and sporophyte generations, respectively. CrWOXB is the first intermediate-clade WOX gene shown to function in both generations in land plants.

Diverse function of plant peptide hormones in local signaling and development

Peptide hormones have emerged as an important class of signaling molecules that mediate developmental signals between plant cells. Membrane-bound receptors bind specific extracellular peptide ligands to mediate communication between cells. In this review, we summarize novel peptide hormones identified in recent studies with an emphasis on their molecular structures. By focusing on the CLE family peptides, we will describe the details of their physiological roles in various plant species, which include Arabidopsis, crop species, and bryophyte models.

HEADLESS Regulates Auxin Response and Compound Leaf Morphogenesis in Medicago truncatula

WUSCHEL (WUS) is thought to be required for the establishment of the shoot stem cell niche in Arabidopsis thaliana. HEADLESS (HDL), a gene that encodes a WUS-related homeobox family transcription factor, is thought to be the Medicago truncatula ortholog of the WUS gene. HDL plays conserved roles in shoot apical meristem (SAM) and axillary meristem (AM) maintenance. HDL is also involved in compound leaf morphogenesis in M. truncatula; however, its regulatory mechanism has not yet been explored. Here, the significance of HDL in leaf development was investigated. Unlike WUS in A. thaliana, HDL was transcribed not only in the SAM and AM but also in the leaf. Both the patterning of the compound leaves and the shape of the leaf margin in hdl mutant were abnormal. The transcriptional profile of the gene SLM1, which encodes an auxin efflux carrier, was impaired and the plants' auxin response was compromised. Further investigations revealed that HDL positively regulated auxin response likely through the recruitment of MtTPL/MtTPRs into the HDL repressor complex. Its participation in auxin-dependent compound leaf morphogenesis is of interest in the context of the functional conservation and neo-functionalization of the products of WUS orthologs.

Comprehensive analysis of WOX genes uncovers that WOX13 is involved in phytohormone-mediated fiber development in cotton

BACKGROUND

The WOX (WUSCHEL-RELATED HOMEOBOX) gene family encodes a class of transcription factors that are unique to green plants, where they are involved in regulating the development of plant tissues and organs by determining cell fate. Although the importance of the WOX gene is well known, there are few studies describing their functions in cotton.

RESULTS

In this study, 32 WOX genes were found in Gossypium hirsutum. Phylogenetic analysis showed that WOX proteins of cotton can be divided into three clades: the ancient, intermediate, and WUS clades. The number of WOX proteins in the WUS clade was greater than the sum of the proteins in the other two clades. Our analysis revealed that 20 GhWOX genes are distributed on 16 cotton chromosomes and that duplication events are likely to have contributed to the expansion of the GhWOX family. All GhWOX genes have introns, and each GhWOX protein contains multiple motifs. RNA-seq data and real-time PCR showed that GhWOX13 gene subfamily is specifically expressed at a high level in cotton fibers. We also identified putative GA, NAA, and BR response elements in the promoter regions of the GhWOX13 genes and GhWOX13 transcripts were significantly induced by GA, NAA, and BR.

CONCLUSIONS

Our data provides a useful resource for future studies on the functional roles of cotton WOX genes and shows that the GhWOX13 genes may influence cotton fiber development. Our results also provide an approach for identifying and characterizing WOX protein genes in other species.

Transcriptional Corepressor ASP1 and CLV-Like Signaling Regulate Meristem Maintenance in Rice

Stem cell homeostasis is maintained by the WUSCHEL-CLAVATA (WUS-CLV) negative feedback loop in Arabidopsis (Arabidopsis thaliana). In rice (Oryza sativa), FLORAL ORGAN NUMBER2 (FON2) functions in the negative regulation of stem cell proliferation, similar to Arabidopsis CLV3 In this study, through genetic enhancer analysis, we found that loss of function of ABERRANT SPIKELET AND PANICLE1 (ASP1), encoding an Arabidopsis TOPLESS (TPL)-like transcriptional corepressor, enhances the fon2 flower phenotype, which displayed an increase in floral organ number. In the fon2 asp1 double mutant, the inflorescence was severely affected, resulting in bifurcation of the main axis (rachis), a phenotype that has not previously been reported. The stem cells showed marked overproliferation in fon2 asp1, resulting in extreme enlargement and splitting of the inflorescence meristem. These results suggest that ASP1 and FON2 synergistically regulate stem cell maintenance in rice. Unexpectedly, genetic analysis indicated that TILLERS ABSENT1, the rice ortholog of WUS, is not involved in promoting stem cell proliferation in this meristem. Transcriptome analysis suggested that ASP1 and FON signaling negatively regulate a set of genes with similar functions, and they act on these genes in concert. Taken together, our results suggest that TPL-like corepressor activity plays a crucial role in meristem maintenance, and that stem cell proliferation is properly maintained via the cooperation of ASP1 and FON2.