SEMAPHORE1 functions during the regulation of ancestrally duplicated knox genes and polar auxin transport in maize

Identification and expression analysis of the KNOX genes during organogenesis and stress responseness in Camellia sinensis (L.) O. Kuntze

Tea plant (Camellia sinensis L.), whose leaves are the major reproductive organs, has been cultivated and consumed widely for its economic and health benefits. The Knotted1-like Homeobox (KNOX) proteins play significant roles in leaf morphology formation and development. However, the functions of KNOX proteins in tea plants are still unknown. Here, 11 CsKNOX genes from the tea plants were cloned and divided into Class I, II, and KNATM clades based on their protein sequences. These 11 CsKNOX genes were mapped on 8 out of 15 tea plant chromosomes, all localized in the nucleus. Specific spatiotemporal expression patterns of CsKNOX genes were found in various tissues and different development periods of buds, flowers, and roots of tea plants. Meanwhile, transcript levels of CsKNOX in tea leaves were strongly correlated with the accumulation of flavan-3-ols and proanthocyanidins. It was found that most of the CsKNOX genes could respond to drought, salt, cold, and exogenous MeJA and GA3 by analysis of transcriptomics data and promoter elements. The protein interaction analysis showed that CsKNOX could cooperate with CsAS1 and other critical functional proteins. In conclusion, this research provided the basic information for the functions of the CsKNOX family during organogenesis and stress response in tea plants, which was necessary for further functional characterization verification.

Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization

In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.

grasviq: an image analysis framework for automatically quantifying vein number and morphology in grass leaves

Beyond facilitating transport and providing mechanical support to the leaf, veins have important roles in the performance and productivity of plants and the ecosystem. In recent decades, computational image analysis has accelerated the extraction and quantification of vein traits, benefiting fields of research from agriculture to climatology. However, most of the existing leaf vein image analysis programs have been developed for the reticulate venation found in dicots. Despite the agroeconomic importance of cereal grass crops, like Oryza sativa (rice) and Zea mays (maize), a dedicated image analysis program for the parallel venation found in monocots has yet to be developed. To address the need for an image-based vein phenotyping tool for model and agronomic grass species, we developed the grass vein image quantification (grasviq) framework. Designed specifically for parallel venation, this framework automatically segments and quantifies vein patterns from images of cleared leaf pieces using classical computer vision techniques. Using image data sets from maize inbred lines and auxin biosynthesis and transport mutants in maize, we demonstrate the utility of grasviq for quantifying important vein traits, including vein density, vein width and interveinal distance. Furthermore, we show that the framework can resolve quantitative differences and identify vein patterning defects, which is advantageous for genetic experiments and mutant screens. We report that grasviq can perform high-throughput vein quantification, with precision on a par with that of manual quantification. Therefore, we envision that grasviq will be adopted for vein phenomics in maize and other grass species.

The retromer protein ZmVPS29 regulates maize kernel morphology likely through an auxin-dependent process(es)

Kernel size and morphology are two important yield-determining traits in maize, but their molecular and genetic mechanisms are poorly characterized. Here, we identified a major QTL, qKM4.08, which explains approximately 24.20% of the kernel morphology variance in a recombinant population derived from two elite maize inbred lines, Huangzaosi (HZS, round kernel) and LV28 (slender kernel). Positional cloning and transgenic analysis revealed that qKM4.08 encodes ZmVPS29, a retromer complex component. Compared with the ZmVPS29 HZS allele, the ZmVPS29 LV28 allele showed higher expression in developing kernels. Overexpression of ZmVPS29 conferred a slender kernel morphology and increased the yield per plant in different maize genetic backgrounds. Sequence analysis revealed that ZmVPS29 has been under purifying selection during maize domestication. Association analyses identified two significant kernel morphology-associated polymorphic sites in the ZmVPS29 promoter region that were significantly enriched in modern maize breeding lines. Further study showed that ZmVPS29 increased auxin accumulation during early kernel development by enhancing auxin biosynthesis and transport and reducing auxin degradation and thereby improved kernel development. Our results suggest that ZmVPS29 regulates kernel morphology, most likely through an auxin-dependent process(es).

Is auxin involved in the induction of genetic instability in barley homeotic double mutants?

The triggers of genetic instability in barley homeotic double mutants are tweaky spike -type mutations associated with an auxin imbalance in separate spike phytomeres. Barley homeotic tweaky spike;Hooded (tw;Hd) double mutants are characterized by an inherited instability of spike and flower development, which is absent in the single parental constituents. The aim of the present study was to show that the trigger of genetic instability in the double mutants is the tw mutations, which are associated with an auxin imbalance in the developing spikes. Their pleiotropic effects on genes related to spike/flower development may cause the genetic instability of double mutants. The study of four double-mutant groups composed of different mutant alleles showed that the instability arose only if the mutant allele tw was a constituent of the double mutants. Application of auxin inhibitors and 2,4-dichlorophenoxyacetic acid (2,4-D) demonstrated the relationship of the instability of the double mutants and the phenotype of the tw mutants to auxin imbalance. 2,4-D induced phenocopies of the tw mutation in wild-type plants and rescued the phenotypes of three allelic tw mutants. The differential display (dd-PCR) method allowed the identification of several putative candidate genes in tw that may be responsible for the initiation of instability in the double mutants by pleiotropic variations of their expression in the tw mutant associated with auxin imbalance in the developing spikes. The results of the present study linked the genetic instability of homeotic double mutants with an auxin imbalance caused by one of the constituents (tw). The genetic instability of the double mutants in relation to auxin imbalance was studied for the first time. A matrocliny on instability expression was also observed.

Water-deficit-induced changes in transcription factor expression in maize seedlings

Plants tolerate water deficits by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. In this study, reverse transcription quantitative PCR (RT-qPCR) was used to examine the abundance of 618 transcripts from 536 TF genes in individual root and shoot tissues of maize seedlings grown in vermiculite under well-watered (water potential of -0.02 MPa) and water-deficit conditions (water potentials of -0.3 and -1.6 MPa). A linear mixed model identified 433 TF transcripts representing 392 genes that differed significantly in abundance in at least one treatment, including TFs that intersect growth and development and environmental stress responses. TFs were extensively differentially regulated across stressed maize seedling tissues. Hierarchical clustering revealed TFs with stress-induced increased abundance in primary root tips that likely regulate root growth responses to water deficits, possibly as part of abscisic acid and/or auxin-dependent signaling pathways. Ten of these TFs were selected for validation in nodal root tips of drought-stressed field-grown plants (late V1 to early V2 stage). Changes in abundance of these TF transcripts under a field drought were similar to those observed in the seedling system.

Signaling in Early Maize Kernel Development

Developing the next plant generation within the seed requires the coordination of complex programs driving pattern formation, growth, and differentiation of the three main seed compartments: the embryo (future plant), the endosperm (storage compartment), representing the two filial tissues, and the surrounding maternal tissues. This review focuses on the signaling pathways and molecular players involved in early maize kernel development. In the 2 weeks following pollination, functional tissues are shaped from single cells, readying the kernel for filling with storage compounds. Although the overall picture of the signaling pathways regulating embryo and endosperm development remains fragmentary, several types of molecular actors, such as hormones, sugars, or peptides, have been shown to be involved in particular aspects of these developmental processes. These molecular actors are likely to be components of signaling pathways that lead to transcriptional programming mediated by transcriptional factors. Through the integrated action of these components, multiple types of information received by cells or tissues lead to the correct differentiation and patterning of kernel compartments. In this review, recent advances regarding the four types of molecular actors (hormones, sugars, peptides/receptors, and transcription factors) involved in early maize development are presented.

N-glycan containing a core α1,3-fucose residue is required for basipetal auxin transport and gravitropic response in rice (Oryza sativa)

In plants, α1,3-fucosyltransferase (FucT) catalyzes the transfer of fucose from GDP-fucose to asparagine-linked GlcNAc of the N-glycan core in the medial Golgi. To explore the physiological significance of this processing, we isolated two Oryza sativa (rice) mutants (fuct-1 and fuct-2) with loss of FucT function. Biochemical analyses of the N-glycan structure confirmed that α1,3-fucose is missing from the N-glycans of allelic fuct-1 and fuct-2. Compared with the wild-type cv Kitaake, fuct-1 displayed a larger tiller angle, shorter internode and panicle lengths, and decreased grain filling as well as an increase in chalky grains with abnormal shape. The mutant allele fuct-2 gave rise to similar developmental abnormalities, although they were milder than those of fuct-1. Restoration of a normal tiller angle in fuct-1 by complementation demonstrated that the phenotype is caused by the loss of FucT function. Both fuct-1 and fuct-2 plants exhibited reduced gravitropic responses. Expression of the genes involved in tiller and leaf angle control was also affected in the mutants. We demonstrate that reduced basipetal auxin transport and low auxin accumulation at the base of the shoot in fuct-1 account for both the reduced gravitropic response and the increased tiller angle.

Genome-wide analysis reveals phytohormone action during cassava storage root initiation

Development of storage roots is a process associated with a phase change from cell division and elongation to radial growth and accumulation of massive amounts of reserve substances such as starch. Knowledge of the regulation of cassava storage root formation has accumulated over time; however, gene regulation during the initiation and early stage of storage root development is still poorly understood. In this study, transcription profiling of fibrous, intermediate and storage roots at eight weeks old were investigated using a 60-mer-oligo microarray. Transcription and gene expression were found to be the key regulating processes during the transition stage from fibrous to intermediate roots, while homeostasis and signal transduction influenced regulation from intermediate roots to storage roots. Clustering analysis of significant genes and transcription factors (TF) indicated that a number of phytohormone-related TF were differentially expressed; therefore, phytohormone-related genes were assembled into a network of correlative nodes. We propose a model showing the relationship between KNOX1 and phytohormones during storage root initiation. Exogeneous treatment of phytohormones N (6) -benzylaminopurine and 1-Naphthaleneacetic acid were used to induce the storage root initiation stage and to investigate expression patterns of the genes involved in storage root initiation. The results support the hypothesis that phytohormones are acting in concert to regulate the onset of cassava storage root development. Moreover, MeAGL20 is a factor that might play an important role at the onset of storage root initiation when the root tip becomes swollen.

Organogenesis in plants: initiation and elaboration of leaves

Plant organs initiate from meristems and grow into diverse forms. After initiation, organs enter a morphological phase where they develop their shape, followed by differentiation into mature tissue. Investigations into these processes have revealed numerous factors necessary for proper development, including transcription factors such as the KNOTTED-LIKE HOMEOBOX (KNOX) genes, the hormone auxin, and miRNAs. Importantly, these factors have been shown to play a role in organogenesis in various diverse model species, revealing both deep conservation of regulatory strategies and evolutionary novelties that led to new plant forms. We review here recent work in understanding the regulation of organogenesis and in particular leaf formation, highlighting how regulatory modules are often redeployed in different organ types and stages of development to achieve diverse forms through the balance of growth and differentiation.

Inherited phenotype instability of inflorescence and floral organ development in homeotic barley double mutants and its specific modification by auxin inhibitors and 2,4-D

BACKGROUND AND AIMS

Barley (Hordeum vulgare) double mutants Hv-Hd/tw2, formed by hybridization, are characterized by inherited phenotypic instability and by several new features, such as bract/leaf-like structures, long naked gaps in the spike, and a wide spectrum of variations in the basic and ectopic flowers, which are absent in single mutants. Several of these features resemble those of mutations in auxin distribution, and thus the aim of this study was to determine whether auxin imbalances are related to phenotypic variations and instability. The effects of auxin inhibitors and 2,4-D (2,4-dichlorophenoxyacetic acid) on variation in basic and ectopic flowers were therefore examined, together with the effects of 2,4-D on spike structure.

METHODS

The character of phenotypic instability and the effects of auxin inhibitors and 2,4-D were compared in callus cultures and intact plants of single homeotic Hv-tw2 and Hv-Hooded/Kap (in the BKn3 gene) mutants and alternative double mutant lines: offspring from individual plants in distal hybrid generations (F9-F10) that all had the same BKn3 allele as determined by DNA sequencing. For intact plants, two auxin inhibitors, 9-hydroxyfluorene-9-carboxylic acid (HFCA) and p-chlorophenoxyisobutyric acid (PCIB), were used.

KEY RESULTS

Callus growth and flower/spike structures of the Hv-tw2 mutant differed in their responses to HFCA and PCIB. An increase in normal basic flowers after exposure to auxin inhibitors and a decrease in their frequencies caused by 2,4-D were observed, and there were also modifications in the spectra of ectopic flowers, especially those with sexual organs, but the effects depended on the genotype. Exposure to 2,4-D decreased the frequency of short gaps and lodicule transformations in Hv-tw2 and of long naked gaps in double mutants.

CONCLUSIONS

The effects of auxin inhibitors and 2,4-D suggest that ectopic auxin maxima or deficiencies arise in various regions of the inflorescence/flower primordia. Based on the phenotypic instability observed, definite trends in the development of ectopic flower structures may be detected, from insignificant outgrowths on awns to flowers with sterile organs. Phenotypically unstable barley double mutants provide a highly promising genetic system for the investigation of gene expression modules and trend orders.

Leaf development and morphogenesis

The development of plant leaves follows a common basic program that is flexible and is adjusted according to species, developmental stage and environmental circumstances. Leaves initiate from the flanks of the shoot apical meristem and develop into flat structures of variable sizes and forms. This process is regulated by plant hormones, transcriptional regulators and mechanical properties of the tissue. Here, we review recent advances in the understanding of how these factors modulate leaf development to yield a substantial diversity of leaf forms. We discuss these issues in the context of leaf initiation, the balance between morphogenesis and differentiation, and patterning of the leaf margin.

Transcriptomic analyses indicate that maize ligule development recapitulates gene expression patterns that occur during lateral organ initiation

Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize (Zea mays) leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialized ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally derived fringe. Recessive liguleless1 mutants lack ligules and auricles and have upright leaves. We used laser microdissection and RNA sequencing to identify genes that are differentially expressed in discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation and compared transcript accumulation in wild-type and liguleless1-R mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these "ligule genes" have also been shown to function during leaf initiation or lateral branching and intersect multiple hormonal signaling pathways. We propose that genetic modules utilized in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia.

Genetic control of maize shoot apical meristem architecture

The shoot apical meristem contains a pool of undifferentiated stem cells and generates all above-ground organs of the plant. During vegetative growth, cells differentiate from the meristem to initiate leaves while the pool of meristematic cells is preserved; this balance is determined in part by genetic regulatory mechanisms. To assess vegetative meristem growth and genetic control in Zea mays, we investigated its morphology at multiple time points and identified three stages of growth. We measured meristem height, width, plastochron internode length, and associated traits from 86 individuals of the intermated B73 × Mo17 recombinant inbred line population. For meristem height-related traits, the parents exhibited markedly different phenotypes, with B73 being very tall, Mo17 short, and the population distributed between. In the outer cell layer, differences appeared to be related to number of cells rather than cell size. In contrast, B73 and Mo17 were similar in meristem width traits and plastochron internode length, with transgressive segregation in the population. Multiple loci (6−9 for each trait) were mapped, indicating meristem architecture is controlled by many regions; none of these coincided with previously described mutants impacting meristem development. Major loci for height and width explaining 16% and 19% of the variation were identified on chromosomes 5 and 8, respectively. Significant loci for related traits frequently coincided, whereas those for unrelated traits did not overlap. With the use of three near-isogenic lines, a locus explaining 16% of the parental variation in meristem height was validated. Published expression data were leveraged to identify candidate genes in significant regions.

Current perspectives on the hormonal control of seed development in Arabidopsis and maize: a focus on auxin

The seed represents the unit of reproduction of flowering plants, capable of developing into another plant, and to ensure the survival of the species under unfavorable environmental conditions. It is composed of three compartments: seed coat, endosperm and embryo. Proper seed development depends on the coordination of the processes that lead to seed compartments differentiation, development and maturation. The coordination of these processes is based on the constant transmission/perception of signals by the three compartments. Phytohormones constitute one of these signals; gradients of hormones are generated in the different seed compartments, and their ratios comprise the signals that induce/inhibit particular processes in seed development. Among the hormones, auxin seems to exert a central role, as it is the only one in maintaining high levels of accumulation from fertilization to seed maturation. The gradient of auxin generated by its PIN carriers affects several processes of seed development, including pattern formation, cell division and expansion. Despite the high degree of conservation in the regulatory mechanisms that lead to seed development within the Spermatophytes, remarkable differences exist during seed maturation between Monocots and Eudicots species. For instance, in Monocots the endosperm persists until maturation, and constitutes an important compartment for nutrients storage, while in Eudicots it is reduced to a single cell layer, as the expanding embryo gradually replaces it during the maturation. This review provides an overview of the current knowledge on hormonal control of seed development, by considering the data available in two model plants: Arabidopsis thaliana, for Eudicots and Zea mays L., for Monocots. We will emphasize the control exerted by auxin on the correct progress of seed development comparing, when possible, the two species.

The role of auxin in shaping shoot architecture

The variety of plant architectures observed in nature is predominantly determined by vegetative and reproductive branching patterns, the positioning of lateral organs, and differential stem elongation. Branches, lateral organs, and stems are the final products of the activity of meristems, groups of stem cells whose function is genetically determined and environmentally influenced. Several decades of studies in different plant species have shed light on the essential role of the hormone auxin in plant growth and development. Auxin influences stem elongation and regulates the formation, activity, and fate of meristems, and has therefore been recognized as a major hormone shaping plant architecture. Increasing our knowledge of the molecular mechanisms that regulate auxin function is necessary to understand how different plant species integrate a genetically determined developmental programme, the establishment of a body plan, with constant inputs from the surrounding environment. This information will allow us to develop the molecular tools needed to modify plant architecture in several crop species and in rapidly changing environments.

Studies on the rice LEAF INCLINATION1 (LC1), an IAA-amido synthetase, reveal the effects of auxin in leaf inclination control

The angle of rice leaf inclination is an important agronomic trait and closely related to the yields and architecture of crops. Although few mutants with altered leaf angles have been reported, the molecular mechanism remains to be elucidated, especially whether hormones are involved in this process. Through genetic screening, a rice gain-of-function mutant leaf inclination1, lc1-D, was identified from the Shanghai T-DNA Insertion Population (SHIP). Phenotypic analysis confirmed the exaggerated leaf angles of lc1-D due to the stimulated cell elongation at the lamina joint. LC1 is transcribed in various tissues and encodes OsGH3-1, an indole-3-acetic acid (IAA) amido synthetase, whose homolog of Arabidopsis functions in maintaining the auxin homeostasis by conjugating excess IAA to various amino acids. Indeed, recombinant LC1 can catalyze the conjugation of IAA to Ala, Asp, and Asn in vitro, which is consistent with the decreased free IAA amount in lc1-D mutant. lc1-D is insensitive to IAA and hypersensitive to exogenous BR, in agreement with the microarray analysis that reveals the altered transcriptions of genes involved in auxin signaling and BR biosynthesis. These results indicate the crucial roles of auxin homeostasis in the leaf inclination control.

The role of PIN auxin efflux carriers in polar auxin transport and accumulation and their effect on shaping maize development

In plants, proper seed development and the continuing post-embryonic organogenesis both require that different cell types are correctly differentiated in response to internal and external stimuli. Among internal stimuli, plant hormones and particularly auxin and its polar transport (PAT) have been shown to regulate a multitude of plant physiological processes during vegetative and reproductive development. Although our current auxin knowledge is almost based on the results from researches on the eudicot Arabidopsis thaliana, during the last few years, many studies tried to transfer this knowledge from model to crop species, maize in particular. Applications of auxin transport inhibitors, mutant characterization, and molecular and cell biology approaches, facilitated by the sequencing of the maize genome, allowed the identification of genes involved in auxin metabolism, signaling, and particularly in polar auxin transport. PIN auxin efflux carriers have been shown to play an essential role in regulating PAT during both seed and post-embryonic development in maize. In this review, we provide a summary of the recent findings on PIN-mediated polar auxin transport during maize development. Similarities and differences between maize and Arabidopsis are analyzed and discussed, also considering that their different plant architecture depends on the differentiation of structures whose development is controlled by auxins.

The physiological mechanism of a drooping leaf2 mutation in rice

Here we characterized a classic rice (Oryza sativa) drooping leaf2 mutant (named dl2). The dl2 allele affects both the midrib development and the total leaf venation pattern. Leaf anatomy results revealed the central vein lacks both clear cells and the adaxial small vascular bundle in dl2 mutant, which seemed to cause the drooping leaf phenotype. The dl2 leaves contain more small veins, and the size of the vascular cylinder in dl2 leaf is also altered. Furthermore, similar anatomy alteration was found in the dl2 roots. A reduction in the number of xylem and phloem poles in the central vascular cylinder in dl2 roots was observed and the diameter of cortical cell is also reduced. In addition, the alterations of the vegetative development such as the longer leaf blade and fewer adventitious and lateral roots were also observed in dl2. The physiological mechanism underlying the morphological and vascular alterations of dl2 was further studied. The result demonstrated that the dl2 vascular patterning distortions are strictly associated with a defective PAT (polar auxin transport) activity and sensitivity to different classes of polar auxin transport inhibitors. Finally, the drooping leaf phenotype of dl2 is coupled to a defective response to auxin.

Distal expression of knotted1 in maize leaves leads to reestablishment of proximal/distal patterning and leaf dissection

Maize (Zea mays) leaves provide a useful system to study how proximal/distal patterning is established because of the distinct tissues found in the distal blade and the proximal sheath. Several mutants disrupt this pattern, including the dominant knotted1-like homeobox (knox) mutants. knox genes encode homeodomain proteins of the TALE superclass of transcription factors. Class I knox genes are expressed in the meristem and down-regulated as leaves initiate. Gain-of-function phenotypes result from misexpression in leaves. We identified a new dominant allele of maize knotted1, Kn1-DL, which contains a transposon insertion in the promoter in addition to a tandem duplication of the kn1 locus. In situ hybridization shows that kn1 is misexpressed in two different parts of the blade that correlate with the different phenotypes observed. When kn1 is misexpressed along the margins, flaps of sheath-like tissue form along the margins. Expression in the distal tip leads to premature termination of the midrib into a knot and leaf bifurcation. The gain-of-function phenotypes suggest that kn1 establishes proximal/distal patterning when expressed in distal locations and lead to the hypothesis that kn1 normally participates in the establishment of proximal/distal polarity in the incipient leaf.

Microdissection of shoot meristem functional domains

The shoot apical meristem (SAM) maintains a pool of indeterminate cells within the SAM proper, while lateral organs are initiated from the SAM periphery. Laser microdissection-microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes that function during leaf development. Nine hundred and sixty-two differentially expressed maize genes were detected; control genes known to be upregulated in the initiating leaf (P0/P1) or in the SAM proper verified the precision of the microdissections. Genes involved in cell division/growth, cell wall biosynthesis, chromatin remodeling, RNA binding, and translation are especially upregulated in initiating leaves, whereas genes functioning during protein fate and DNA repair are more abundant in the SAM proper. In situ hybridization analyses confirmed the expression patterns of six previously uncharacterized maize genes upregulated in the P0/P1. P0/P1-upregulated genes that were also shown to be downregulated in leaf-arrested shoots treated with an auxin transport inhibitor are especially implicated to function during early events in maize leaf initiation. Reverse genetic analyses of asceapen1 (asc1), a maize D4-cyclin gene upregulated in the P0/P1, revealed novel leaf phenotypes, less genetic redundancy, and expanded D4-CYCLIN function during maize shoot development as compared to Arabidopsis. These analyses generated a unique SAM domain-specific database that provides new insight into SAM function and a useful platform for reverse genetic analyses of shoot development in maize.

Hormone mediated regulation of the shoot apical meristem

Recent work on hormone mediated regulation of the SAM is reviewed, emphasizing how combinations of genetic, molecular and modelling approaches have refined models based on classic experimental and physiological work. Special emphasis is given to newly described mechanisms that modulate the responsiveness of specific tissues to hormones and their potential to direct position dependent determination processes.

Developmental disaster1: A novel mutation causing defects during vegetative and inflorescence development in maize (Zea mays, Poaceae)

Axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. To understand how axillary meristems initiate, we have screened for mutants with defects in axillary meristem initiation to uncover the genes controlling this process. These mutants, called the barren class of mutants in maize (Zea mays), have defects in axillary meristem initiation during both vegetative and reproductive development. Here, we identify and characterize a new member of the barren class of mutants named Developmental disaster1 (Dvd1), due to the pleiotropic effects of the mutation. Similar to the barren mutants, Dvd1 mutants have fewer branches, spikelets, florets, and floral organs in the inflorescence due to defects in the initiation of axillary meristems. Furthermore, double mutant analysis with teosinte branched1 shows that dvd1 also functions in axillary meristems during vegetative development. However, unlike the barren mutants, Dvd1 mutants are semidwarf due to the production of shorter internodes, and they produce leaves in the inflorescence due to the outgrowth of bract leaf primordia. The suite of defects seen in Dvd1 mutants, together with the genetic interaction of Dvd1 with barren inflorescence2, suggests that dvd1 is a novel regulator of axillary meristem and internode development.

Expression of class I knotted1-like homeobox genes in the storage roots of sweetpotato (Ipomoea batatas)

As a first step in clarifying the involvement of class I knotted1-like homeobox (KNOXI) genes in the storage root development of sweetpotato (Ipomoea batatas), we isolated three KNOXI genes, named Ibkn1, Ibkn2 and Ibkn3, expressed in the storage roots. Phylogenetic analysis showed that Ibkn1 was homologous to the SHOOT MERISTEMLESS (STM) gene of Arabidopsis, while Ibkn2 and Ibkn3 were homologous to the BREVIPEDICELLUS (BP) gene. Of these, expression of Ibkn1 and Ibkn2 were upregulated in developing and mature storage roots compared with fibrous roots. Ibkn1 and Ibkn2 showed different expression patterns in the storage roots. Ibkn1 was preferentially expressed at the proximal end and around the primary vascular cambium, while Ibkn2 expression was highest in the thickest part and lower in both the proximal and distal ends. In contrast to Ibkn1 and Ibkn2, expression of Ibkn3 in roots was not consistent among sweetpotato cultivars. The distribution of endogenous trans-zeatin riboside (t-ZR) in sweetpotato roots showed a similarity to the expression pattern of KNOXI genes, supporting the idea that KNOXI genes control cytokinin levels in the storage roots. The physiological functions of these KNOXI genes in storage root development are discussed.

Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis

KNOTTED1-like homeobox (KNOX) genes promote stem cell activity and must be repressed to form determinate lateral organs. Stable KNOX gene silencing during organogenesis is known to involve the predicted DNA binding proteins ASYMMETRIC LEAVES1 (AS1) and AS2 as well as the chromatin-remodeling factor HIRA. However, the mechanism of silencing is unknown. Here, we show that AS1 and AS2 form a repressor complex that binds directly to the regulatory motifs CWGTTD and KMKTTGAHW present at two sites in the promoters of the KNOX genes BREVIPEDICELLUS (BP) and KNAT2. The two binding sites act nonredundantly, and interaction between AS1-AS2 complexes at these sites is required to repress BP. Promoter deletion analysis further indicates that enhancer elements required for BP expression in the leaf are located between the AS1-AS2 complex binding sites. We propose that AS1-AS2 complexes interact to create a loop in the KNOX promoter and, likely through recruitment of HIRA, form a repressive chromatin state that blocks enhancer activity during organogenesis. Our model for AS1-AS2-mediated KNOX gene silencing is conceptually similar to the action of an insulator. This regulatory mechanism may be conserved in simple leafed species of monocot and dicot lineages and constitutes a potential key determinant in the evolution of compound leaves.

Arabidopsis JAGGED LATERAL ORGANS is expressed in boundaries and coordinates KNOX and PIN activity

Plant lateral organs are initiated as small protrusions on the flanks of shoot apical meristems. Organ primordia are separated from the remainder of the meristem by distinct cell types that create a morphological boundary. The Arabidopsis thaliana gain-of-function mutant jagged lateral organs-D (jlo-D) develops strongly lobed leaves, indicative of KNOX gene misexpression, and the shoot apical meristem arrests organ initiation prematurely, terminating in a pin-like structure. The JLO gene, a member of the LATERAL ORGAN BOUNDARY DOMAIN gene family, is expressed in boundaries between meristems and organ primordia and during embryogenesis. Inducible JLO misexpression activates expression of the KNOX genes SHOOT MERISTEMLESS and KNAT1 in leaves and downregulates the expression of PIN auxin export facilitators. Consequently, bulk auxin transport through the inflorescence stem is drastically reduced. During embryogenesis, JLO is required for the initiation of cotyledons and development beyond the globular stage. Converting JLO into a transcriptional repressor causes organ fusions, showing that during postembryonic development, JLO function is required to maintain the integrity of boundaries between cell groups with indeterminate or determinate fates.

L1 division and differentiation patterns influence shoot apical meristem maintenance

Plant development requires regulation of both cell division and differentiation. The class 1 KNOTTED1-like homeobox (KNOX) genes such as knotted1 (kn1) in maize (Zea mays) and SHOOTMERISTEMLESS in Arabidopsis (Arabidopsis thaliana) play a role in maintaining shoot apical meristem indeterminacy, and their misexpression is sufficient to induce cell division and meristem formation. KNOX overexpression experiments have shown that these genes interact with the cytokinin, auxin, and gibberellin pathways. The L1 layer has been shown to be necessary for the maintenance of indeterminacy in the underlying meristem layers. This work explores the possibility that the L1 affects meristem function by disrupting hormone transport pathways. The semidominant Extra cell layers1 (Xcl1) mutation in maize leads to the production of multiple epidermal layers by overproduction of a normal gene product. Meristem size is reduced in mutant plants and more cells are incorporated into the incipient leaf primordium. Thus, Xcl1 may provide a link between L1 division patterns, hormonal pathways, and meristem maintenance. We used double mutants between Xcl1 and dominant KNOX mutants and showed that Xcl1 suppresses the Kn1 phenotype but has a synergistic interaction with gnarley1 and rough sheath1, possibly correlated with changes in gibberellin and auxin signaling. In addition, double mutants between Xcl1 and crinkly4 had defects in shoot meristem maintenance. Thus, proper L1 development is essential for meristem function, and XCL1 may act to coordinate hormonal effects with KNOX gene function at the shoot apex.

The auxin-induced K(+) channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development

The transcript level and in turn protein density of the K(+)-uptake channel ZMK1 in maize (Zea mays) coleoptiles is controlled by the phytohormone auxin. ZMK1 is involved in auxin-regulated coleoptile elongation as well as gravi- and phototropism. To provide unequivocal evidence for the role of ZMK1 in these elementary processes we screened for maize plants containing a Mutator-tagged Zmk1 gene. In a site-selected approach, we were able to identify three independent alleles of Mutator-transposon insertions in Zmk1. zmk1-m1::Mu1 plants were characterised by a Mu1 transposon inside intron 1 of ZMK1. When we analysed the Zmk1-transcript abundance in growing coleoptiles of these homozygous mutants, however, we found the K(+)-channel allele overexpressed. In consequence, elevated levels of K(+)-channel transcripts resulted in a growth phenotype as expected from more efficient K(+)-uptake, representing a central factor for turgor formation. Following Zmk1 expression during maize embryogenesis, we found this K(+)-channel gene constitutively expressed throughout embryo development and upregulated in late stages. In line with a vital role in embryogenesis, the mutations of exon 2 and intron 2 of Zmk1-zmk1-m2::Mu8 and zmk1-m3::MuA2-caused a lethal, defective-kernel phenotype. Thus, these results demonstrate the central role of the auxin-regulated K(+)-channel gene Zmk1 in coleoptile growth and embryo development.

Auxin immunolocalization implicates vesicular neurotransmitter-like mode of polar auxin transport in root apices

Immunolocalization of auxin using a new specific antibody revealed, besides the expected diffuse cytoplasmic signal, enrichments of auxin at end-poles (cross-walls), within endosomes and within nuclei of those root apex cells which accumulate abundant F-actin at their end-poles. In Brefeldin A (BFA) treated roots, a strong auxin signal was scored within BFA-induced compartments of cells having abundant actin and auxin at their end-poles, as well as within adjacent endosomes, but not in other root cells. Importantly, several types of polar auxin transport (PAT) inhibitors exert similar inhibitory effects on endocytosis, vesicle recycling, and on the enrichments of F-actin at the end-poles. These findings indicate that auxin is transported across F-actin-enriched end-poles (synapses) via neurotransmitter-like secretion. This new concept finds genetic support from the semaphore1, rum1 and rum1/lrt1 mutants of maize which are impaired in PAT, endocytosis and vesicle recycling, as well as in recruitment of F-actin and auxin to the auxin transporting end-poles. Although PIN1 localizes abundantly to the end-poles, and they also fail to support the formation of in these mutants affected in PAT, auxin and F-actin are depleted from their end-poles which also fail to support formation of the large BFA-induced compartments.

KNOX gene function in plant stem cell niches

Homeobox genes encode transcriptional regulators that control development in multicellular eukaryotes. In plants, post-embryonic shoot growth relies on the activity of indeterminate cell populations termed shoot meristems, within which members of the class-1 KNOX sub-family of homeobox genes are expressed. KNOX genes are differentially required for meristem development and function to inhibit cell expansion and differentiation associated with organogenesis. Mechanisms must therefore be employed to prevent KNOX gene expression in developing lateral organs such as leaves. This review focuses on the expression patterns, meristematic functions and regulation of KNOX genes, and how the activities of these genes are integrated within the framework of pathways that control plant development.

Lateral root initiation or the birth of a new meristem

Root branching happens through the formation of new meristems out of a limited number of pericycle cells inside the parent root. As opposed to shoot branching, the study of lateral root formation has been complicated due to its internal nature, and a lot of questions remain unanswered. However, due to the availability of new molecular tools and more complete genomic data in the model species Arabidopsis, the probability to find new and crucial elements in the lateral root formation pathway has increased. Increasingly more data are supporting the idea that lateral root founder cells become specified in young root parts before differentiation is accomplished. Next, pericycle founder cells undergo anticlinal asymmetric, divisions followed by an organized cell division pattern resulting in the formation of a new organ. The whole process of cell cycle progression and stimulation of the molecular pathway towards lateral root initiation is triggered by the plant hormone auxin. In this review, we aim to give an overview on the developmental events taking place from the very early specification of founder cells in the pericycle until the first anticlinal divisions by combining the knowledge originating from classical physiology studies with new insights from genetic-molecular analyses. Based on the current knowledge derived from recent genetic and developmental studies, we propose here a hypothetical model for LRI.

Stem cell signalling networks in plants

The essential nature of meristematic tissues is addressed with reference to conceptual frameworks that have been developed to explain the behaviour of animal stem cells. Comparisons are made between different types of plant meristems with the objective of highlighting common themes that might illuminate underlying mechanisms. A more in depth comparison of the root and shoot apical meristems is made which suggests a common mechanism for maintaining stem cells. The relevance of organogenesis to stem cell maintenance is discussed, along with the nature of underlying mechanisms which help ensure that stem cell production is balanced with the depletion of cells through differentiation. Mechanisms that integrate stem cell behaviour in the whole plant are considered, with a focus on the roles of auxin and cytokinin. The review concludes with a brief discussion of epigenetic mechanisms that act to stabilise and maintain stem cell populations.

Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1

The monogenic recessive maize (Zea mays) mutant rootless with undetectable meristems 1 (rum1) is deficient in the initiation of the embryonic seminal roots and the postembryonic lateral roots at the primary root. Lateral root initiation at the shoot-borne roots and development of the aerial parts of the mutant rum1 are not affected. The mutant rum1 displays severely reduced auxin transport in the primary root and a delayed gravitropic response. Exogenously applied auxin does not induce lateral roots in the primary root of rum1. Lateral roots are initiated in a specific cell type, the pericycle. Cell-type-specific transcriptome profiling of the primary root pericycle 64 h after germination, thus before lateral root initiation, via a combination of laser capture microdissection and subsequent microarray analyses of 12k maize microarray chips revealed 90 genes preferentially expressed in the wild-type pericycle and 73 genes preferentially expressed in the rum1 pericycle (fold change >2; P-value <0.01; estimated false discovery rate of 13.8%). Among the 51 annotated genes predominately expressed in the wild-type pericycle, 19 genes are involved in signal transduction, transcription, and the cell cycle. This analysis defines an array of genes that is active before lateral root initiation and will contribute to the identification of checkpoints involved in lateral root formation downstream of rum1.

Evolution of leaf developmental mechanisms

Leaves are determinate organs produced by the shoot apical meristem. Land plants demonstrate a large range of variation in leaf form. Here we discuss evolution of leaf form in the context of our current understanding of leaf development, as this has emerged from molecular genetic studies in model organisms. We also discuss specific examples where parallel studies of development in different species have helped understanding how diversification of leaf form may occur in nature.

Genetic analysis as a tool to investigate the molecular mechanisms underlying seed development in maize

BACKGROUND

In angiosperms the seed is the outcome of double fertilization, a process leading to the formation of the embryo and the endosperm. The development of the two seed compartments goes through three main phases: polarization, differentiation of the main tissues and organs and maturation.

SCOPE

This review focuses on the maize kernel as a model system for developmental and genetic studies of seed development in angiosperms. An overview of what is known about the genetic and molecular aspects underlying embryo and endosperm formation and maturation is presented. The role played by embryonic meristems in laying down the plant architecture is discussed. The acquisition of the different endosperm domains are presented together with the use of molecular markers available for the detection of these domains. Finally the role of programmed cell death in embryo and endosperm development is considered.

CONCLUSIONS

The sequence of events occurring in the developing maize seed appears to be strictly regulated. Proper seed development requires the co-ordinated expression of embryo and endosperm genes and relies on the interaction between the two seed components and between the seed and the maternal tissues. Mutant analysis is instrumental in unravelling the genetic control underlying the formation of each compartment as well as the molecular signals interplaying between the two compartments.

CORKSCREW1 defines a novel mechanism of domain specification in the maize shoot

In higher plants, determinate leaf primordia arise in regular patterns on the flanks of the indeterminate shoot apical meristem (SAM). The acquisition of leaf form is then a gradual process, involving the specification and growth of distinct domains within the three leaf axes. The recessive corkscrew1 (cks1) mutation of maize (Zea mays) disrupts both leaf initiation patterns in the SAM and domain specification within the mediolateral and proximodistal leaf axes. Specifically, cks1 mutant leaves exhibit multiple midribs and leaf sheath tissue differentiates in the blade domain. Such perturbations are a common feature of maize mutants that ectopically accumulate KNOTTED1-like homeobox (KNOX) proteins in leaf tissue. Consistent with this observation, at least two knox genes are ectopically expressed in cks1 mutant leaves. However, ectopic KNOX proteins cannot be detected. We therefore propose that CKS1 primarily functions within the SAM to establish boundaries between meristematic and leaf zones. Loss of gene function disrupts boundary formation, impacts phyllotactic patterns, and leads to aspects of indeterminate growth within leaf primordia. Because these perturbations arise independently of ectopic KNOX activity, the cks1 mutation defines a novel component of the developmental machinery that facilitates leaf-versus-shoot development in maize.

The role of knox genes in plant development

knox genes encode homeodomain-containing transcription factors that are required for meristem maintenance and proper patterning of organ initiation. In plants with simple leaves, knox genes are expressed exclusively in the meristem and stem, but in dissected leaves, they are also expressed in leaf primordia, suggesting that they may play a role in the diversity of leaf form. This hypothesis is supported by the intriguing phenotypes found in gain-of-function mutations where knox gene misexpression affects leaf and petal shape. Similar phenotypes are also found in recessive mutations of genes that function to negatively regulate knox genes. KNOX proteins function as heterodimers with other homeodomains in the TALE superclass. The gibberellin and lignin biosynthetic pathways are known to be negatively regulated by KNOX proteins, which results in indeterminate cell fates.

Pattern formation in the vascular system of monocot and dicot plant species

Plant vascular tissues are organised in continuous strands, the longitudinal and radial patterns of which are intimately linked to the signals that direct plant architecture as a whole. Therefore, understanding the mechanisms underlying vascular tissue patterning is expected to shed light on patterning events beyond those that organise the vascular system, and thus represents a central issue in plant developmental biology. A number of recent advances, reviewed here, are leading to a more precise definition of the signals that control the formation of vascular tissues and their integration into a larger organismal context. Contents Summary 209 I. Introduction 209 II. The plant vascular system 210 III. Ontogeny of the vascular tissues 210 IV. Procambium development 210 V. The organisation of the vascular tissues 212 VI. The regulation of longitudinal vascular pattern formation 214 VII. The regulation of radial vascular pattern formation 220 VIII. Genetic screens for vascular development mutants 231 IX. Genes involved in vascular development identified through reverse genetics approaches 235 X. Conclusions and perspectives 235 Note added at the revision stage 236 Acknowledgements 236 References 236.

The extended auricle1 (eta1) gene is essential for the genetic network controlling postinitiation maize leaf development

The maize leaf is composed of distinct regions with clear morphological boundaries. The ligule and auricle mark the boundary between distal blade and proximal sheath and are amenable to genetic study due to the array of mutants that affect their formation without severely affecting viability. Herein, we describe the novel maize gene extended auricle1 (eta1), which is essential for proper formation of the blade/sheath boundary. Homozygous eta1 individuals have a wavy overgrowth of auricle tissue and the blade/sheath boundary is diffuse. Double-mutant combinations of eta1 with genes in the knox and liguleless pathways result in synergistic and, in some cases, dosage-dependent interactions. While the phenotype of eta1 mutant individuals resembles that of dominant knox overexpression phenotypes, eta1 mutant leaves do not ectopically express knox genes. In addition, eta1 interacts synergistically with lg1 and lg2, but does not directly affect the transcription of either gene in leaf primordia. We present evidence based on genetic and molecular analyses that eta1 provides a downstream link between the knox and liguleless pathways.

Plant hormones and homeoboxes: bridging the gap?

Plant hormones are signalling molecules that control growth and development. Growth of the aerial parts of higher plants requires the continuous activity of the shoot apical meristem, a small mound of cells at the apex of a plant. KNOTTED1-like HOMEOBOX (KNOX) genes are involved in regulating meristem activity, however, little is known about how this regulation is mediated. Recent evidence suggests that KNOX transcription factors may control meristem development by regulating the balance of activities of multiple hormones.

Shaping up: the genetic control of leaf shape

Leaf initiation at the shoot apical meristem involves a balance between cell proliferation and commitment to make primordia. Several genes, such as CLAVATA1, CLAVATA3, WUSCHEL, KNOTTED1, and PHANTASTICA, play key roles in these processes. When expressed in the leaf primordium, however, these 'meristem' genes can profoundly affect leaf shape and size, possibly by regulating hormone gradients and transport. The KNOTTED1-like genes are involved in regulating changes in hormonal levels. Recent studies have elaborated on the role that hormones, such as auxin, play in releasing biophysical constraints on leaf initiation and growth. Final leaf form is elaborated by a coordination of these hormonally regulated processes, cell division and cellular differentiation.

Determination of cell fate in apical meristems

Although roots and shoots exhibit profound differences in their pattern of organogenesis, both apices share the capacity for indeterminate growth. Ongoing molecular and genetic analyses have revealed relatively little overlap between the genes that regulate organogenesis in the root and shoot apices. In the shoot, an ensemble of transcription factors lays the foundations for the leaf, in which indeterminacy is exchanged for more limited and polarized growth. Class-I KNOX genes are downregulated in the anlagen of the leaf early in its establishment, but are maintained in other regions of the shoot apex. This persistent expression of KNOX genes may serve to prevent the precocious determination of apical initial derivatives, and thus may allow the production of a large number of pluripotent cells from a relatively small number of stem cells. Greater commonality between roots and shoots is seen in mechanisms that underlie histogenesis and radial-patterning processes. Recent work suggests that undetermined stem cells in both the root and the shoot may be maintained by related mechanisms, which feature regulation of WUSCHEL-like organizer activities by feedback mechanisms that involve receptor-like kinases.

The polar auxin transport inhibitor N-1-naphthylphthalamic acid disrupts leaf initiation, KNOX protein regulation, and formation of leaf margins in maize

Maize (Zea mays) leaves develop basipetally (tip to base); the upper blade emerges from the shoot apical meristem (SAM) before the expansion of the lower sheath. Founder cells, leaf initials located in the periphery of the SAM, are distinguished from the SAM proper by the differential accumulation of KNOX proteins. KNOX proteins accumulate in the SAM, but are excluded from maize leaf primordia and leaf founder cells. As in Arabidopsis and tomato (Lycopersicon esculentum), maize shoots failed to initiate new leaves when cultured in the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). We demonstrate that NPA-induced arrest of leaf initiation in maize is correlated with the failure to down-regulate KNOX accumulation in the SAM. In addition, NPA-cultured shoots formed abnormal tubular leaf bases in which the margins failed to separate in the lower leaf zone. The tubular leaf bases always formed in the fourth leaf from the arrested meristem. Moreover, the unseparated margin domains of these tubular leaf bases accumulated ectopic KNOX protein(s). Transfer of NPA-cultured apices to NPA-free media resulted in the resumption of leaf initiation from the SAM and the restoration of normal patterns of KNOX down-regulation, accordingly. These data suggest that the lower sheath margins emerge from the leaf base late in maize leaf development and that the separation of these leaf margin domains is correlated with auxin transport and down-regulation of KNOX proteins. In addition, these results suggest that the down-regulation of KNOX accumulation in maize apices is not upstream of polar auxin transport, although a more complicated feedback network may exist. A model for L1-derived margin development in maize leaves is presented.