Regulation of SHOOT MERISTEMLESS genes via an upstream-conserved noncoding sequence coordinates leaf development

Application of Developmental Regulators for Enhancing Plant Regeneration and Genetic Transformation

Establishing plant regeneration systems and efficient genetic transformation techniques plays a crucial role in plant functional genomics research and the development of new crop varieties. The inefficient methods of transformation and regeneration of recalcitrant species and the genetic dependence of the transformation process remain major obstacles. With the advancement of plant meristematic tissues and somatic embryogenesis research, several key regulatory genes, collectively known as developmental regulators, have been identified. In the field of plant genetic transformation, the application of developmental regulators has recently garnered significant interest. These regulators play important roles in plant growth and development, and when applied in plant genetic transformation, they can effectively enhance the induction and regeneration capabilities of plant meristematic tissues, thus providing important opportunities for improving genetic transformation efficiency. This review focuses on the introduction of several commonly used developmental regulators. By gaining an in-depth understanding of and applying these developmental regulators, it is possible to further enhance the efficiency and success rate of plant genetic transformation, providing strong support for plant breeding and genetic engineering research.

The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions

Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.

Heritable, multinucleotide deletions in plants using viral delivery of a repair exonuclease and guide RNAs

CRISPR/Cas9-mediated mutagenesis typically results in short insertion/deletion mutations, which are often too small to disrupt the function of cis-acting regulatory elements. Here, we describe a highly efficient in planta gene editing approach called VirTREX2-HLDel that achieves heritable multinucleotide deletions in both protein-coding genes and noncoding DNA regulatory elements. VirTREX2-HLDel uses RNA viruses to deliver both the 3 prime repair exonuclease 2 (TREX2) and single-guide RNAs. Our method enables recovery of multiplexed heritable deletions and increases the heritable gene editing frequency at poorly edited sites. We identified functional conservation and divergence of MICRORNA164 (miR164) in Nicotiana benthamiana and tomato (Solanum lycopersicum) using VirTREX2-HLDel and observed previously uncharacterized phenotypes in plants with large deletions at this locus. Our viral delivery method reduces the need for tissue culture and will accelerate the understanding of protein-coding and regulatory regions in plants.

A Small Compound, HYGIC, Promotes Hypocotyl Growth Through Ectopic Ethylene Response

Plant seedlings adjust the growth of the hypocotyl in response to surrounding environmental changes. Genetic studies have revealed key players and pathways in hypocotyl growth, such as phytohormones and light signaling. However, because of genetic redundancy in the genome, it is expected that not-yet-revealed mechanisms can be elucidated through approaches different from genetic ones. Here, we identified a small compound, HYGIC (HG), that simultaneously induces hypocotyl elongation and thickening, accompanied by increased nuclear size and enlargement of cortex cells. HG-induced hypocotyl growth required the ethylene signaling pathway activated by endogenous ethylene, involving CONSTITUTIVE PHOTOMORPHOGENIC 1, ETHYLENE INSENSITIVE 2 (EIN2) and redundant transcription factors for ethylene responses, ETHYLENE INSENSITIVE 3 (EIN3) and EIN3 LIKE 1. By using EBS:GUS, a transcriptional reporter of ethylene responses based on an EIN3-binding-cis-element, we found that HG treatment ectopically activates ethylene responses at the epidermis and cortex of the hypocotyl. RNA-seq and subsequent gene ontology analysis revealed that a significant number of HG-induced genes are related to responses to hypoxia. Indeed, submergence, a representative environment where the hypoxia response is induced in nature, promoted ethylene-signaling-dependent hypocotyl elongation and thickening accompanied by ethylene responses at the epidermis and cortex, which resembled the HG treatment. Collectively, the identification and analysis of HG revealed that ectopic responsiveness to ethylene promotes hypocotyl growth, and this mechanism is activated under submergence.

Identification of a pluripotency-inducing small compound, PLU, that induces callus formation via Heat Shock Protein 90-mediated activation of auxin signaling

Plants retain the ability to generate a pluripotent tissue called callus by dedifferentiating somatic cells. A pluripotent callus can also be artificially induced by culturing explants with hormone mixtures of auxin and cytokinin, and an entire body can then be regenerated from the callus. Here we identified a pluripotency-inducing small compound, PLU, that induces the formation of callus with tissue regeneration potency without the external application of either auxin or cytokinin. The PLU-induced callus expressed several marker genes related to pluripotency acquisition via lateral root initiation processes. PLU-induced callus formation required activation of the auxin signaling pathway though the amount of active auxin was reduced by PLU treatment. RNA-seq analysis and subsequent experiments revealed that Heat Shock Protein 90 (HSP90) mediates a significant part of the PLU-initiated early events. We also showed that HSP90-dependent induction of TRANSPORT INHIBITOR RESPONSE 1, an auxin receptor gene, is required for the callus formation by PLU. Collectively, this study provides a new tool for manipulating and investigating the induction of plant pluripotency from a different angle from the conventional method with the external application of hormone mixtures.

SHOOT MERISTEMLESS participates in the heterophylly of Hygrophila difformis (Acanthaceae)

In heterophyllous plants, leaf shape shows remarkable plasticity in response to environmental conditions. However, transgenic studies of heterophylly are lacking and the molecular mechanism remains unclear. Here, we cloned the KNOTTED1-LIKE HOMEOBOX family gene SHOOT MERISTEMLESS (STM) from the heterophyllous plant Hygrophila difformis (Acanthaceae). We used molecular, morphogenetic, and biochemical tools to explore its functions in heterophylly. HdSTM was detected in different organs of H. difformis, and its expression changed with environmental conditions. Heterologous, ectopic expression of HdSTM in Arabidopsis (Arabidopsis thaliana) increased leaf complexity and CUP-SHAPED COTYLEDON (CUC) transcript levels. However, overexpression of HdSTM in H. difformis did not induce the drastic leaf change in the terrestrial condition. Overexpression of HdSTM in H. difformis induced quick leaf variations in submergence, while knockdown of HdSTM led to disturbed leaf development and weakened heterophylly in H. difformis. HdCUC3 had the same spatiotemporal expression pattern as HdSTM. Biochemical analysis revealed a physical interaction between HdSTM and HdCUC3. Our results provide genetic evidence that HdSTM is involved in regulating heterophylly in H. difformis.

Overexpression of PdeGATA3 results in a dwarf phenotype in poplar by promoting the expression of PdeSTM and altering the content of gibberellins

In previous studies, GA20 oxidase (GA20ox) has been identified to be an important enzyme in the biosynthesis of GA, and SHOOTMERISTEMLESS (STM) can repress the expression of GA20ox. In this study, the GATA transcription factor PdeGATA3 was identified in the poplar line NL895, and its overexpression (OE) transgenic lines showed a dwarf phenotype. RNA sequencing (RNA-Seq) analysis suggested that OE PdeGATA3 could promote the expression of PdeSTM and repress the expression of PdeGA20ox. Therefore, we hypothesized that PdeGATA3 would directly promote the expression of PdeSTM and that PdeSTM would repress the expression of PdeGA20ox. Four experiments, a dual-luciferase reporter assay, GUS transient coexpression assay, yeast one-hybrid assay and electrophoretic mobility shift assay, were conducted and verified that PdeGATA3 could promote the expression of PdeSTM by binding GATA-Boxes in its promoter. OE PdeSTM in poplar resulted in a dwarf phenotype and repressed the expression of PdeGA20ox. GA measurement of the OE PdeSTM and PdeGATA3 lines showed that GA3 and GA4 contents were significantly lower than those in the wild type (WT). Accordingly, we put forward a regulation model involving plant height regulation by PdeGATA3, PdeSTM and PdeGA20ox.

Molecular mechanisms underlying leaf development, morphological diversification, and beyond

The basic mechanisms of leaf development have been revealed through a combination of genetics and intense analyses in select model species. The genetic basis for diversity in leaf morphology seen in nature is also being unraveled through recent advances in techniques and technologies related to genomics and transcriptomics, which have had a major impact on these comparative studies. However, this has led to the emergence of new unresolved questions about the mechanisms that generate the diversity of leaf form. Here, we provide a review of the current knowledge of the fundamental molecular genetic mechanisms underlying leaf development with an emphasis on natural variation and conserved gene regulatory networks involved in leaf development. Beyond that, we discuss open questions/enigmas in the area of leaf development, how recent technologies can best be deployed to generate a unified understanding of leaf diversity and its evolution, and what untapped fields lie ahead.

The PagKNAT2/6b-PagBOP1/2a Regulatory Module Controls Leaf Morphogenesis in Populus

Leaf morphogenesis requires precise regulation of gene expression to achieve organ separation and flat-leaf form. The poplar KNOTTED-like homeobox gene PagKNAT2/6b could change plant architecture, especially leaf shape, in response to drought stress. However, its regulatory mechanism in leaf development remains unclear. In this work, gene expression analyses of PagKNAT2/6b suggested that PagKNAT2/6b was highly expressed during leaf development. Moreover, the leaf shape changes along the adaxial-abaxial, medial-lateral, and proximal-distal axes caused by the mis-expression of PagKNAT2/6b demonstrated that its overexpression (PagKNAT2/6b OE) and SRDX dominant repression (PagKNAT2/6b SRDX) poplars had an impact on the leaf axial development. The crinkle leaf of PagKNAT2/6b OE was consistent with the differential expression gene PagBOP1/2a (BLADE-ON-PETIOLE), which was the critical gene for regulating leaf development. Further study showed that PagBOP1/2a was directly activated by PagKNAT2/6b through a novel cis-acting element "CTCTT". Together, the PagKNAT2/6b-PagBOP1/2a module regulates poplar leaf morphology by affecting axial development, which provides insights aimed at leaf shape modification for further improving the drought tolerance of woody plants.

Structural and functional analyses of the PPIase domain of Arabidopsis thaliana CYP71 reveal its catalytic activity toward histone H3

Arabidopsis thaliana CYP71 (AtCYP71) is a chromatin-remodeling protein that promotes shoot apical meristem (SAM) differentiation. The N terminus of AtCYP71 contains a noncanonical WD domain, and the C terminus contains an enzymatic peptidyl-prolyl isomerase (PPIase) cyclophilin (CYP) domain. To date, there has been no characterization of CYP71, and its mode of action remains unknown. Here, we report the crystal structure of the CYP domain of AtCYP71 at 1.9 Å resolution. The structure shows key differences when compared to the canonical CYP fold of human CypA. To the best our knowledge, this is the first A. thaliana CYP structure with a conserved active site loop. Using nuclear magnetic resonance spectroscopy, we demonstrate that the CYP domain is active toward histone H3. Our findings suggest that the PPIase activity of the CYP domain is important for the function of AtCYP71 in chromatin remodeling during organogenesis.

PcG Proteins MSI1 and BMI1 Function Upstream of miR156 to Regulate Aerial Tuber Formation in Potato

Polycomb Repressive Complexes (PRC1 and PRC2) regulate developmental transitions in plants. AtBMI1, a PRC1 member, represses micro RNA156 (miR156) to trigger the onset of adult phase in Arabidopsis (Arabidopsis thaliana). miR156 overexpression (OE) reduces below-ground tuber yield, but stimulates aerial tubers in potato (Solanum tuberosum ssp andigena) under short-day (SD) photoperiodic conditions. Whether PRC members could govern tuber development through photoperiod-mediated regulation of miR156 is unknown. Here, we investigated the role of two PRC proteins, StMSI1 (PRC2 member) and StBMI1-1, in potato development. In wild-type andigena plants, StMSI1 and miR156 levels increased in stolon, whereas StBMI1-1 decreased under SD conditions. StMSI1-OE and StBMI1-1-antisense (AS) lines produced pleiotropic effects, including altered leaf architecture/compounding and reduced below-ground tuber yield. Notably, these lines showed enhanced miR156 accumulation accompanied by aerial stolons and tubers from axillary nodes, similar to miR156-OE lines. Further, grafting of StMSI1-OE or StBMI1-1-AS on wild-type stock resulted in reduced root biomass and showed increased accumulation of miR156a/b and -c precursors in the roots of wild-type stocks. RNA-sequencing of axillary nodes from StMSI1-OE and StBMI1-1-AS lines revealed downregulation of auxin and brassinosteroid genes, and upregulation of cytokinin transport/signaling genes, from 1,023 differentially expressed genes shared between the two lines. Moreover, we observed downregulation of genes encoding H2A-ubiquitin ligase and StBMI1-1/3, and upregulation of Trithorax group H3K4-methyl-transferases in StMSI1-OE Chromatin immunoprecipitation-quantitative PCR confirmed H3K27me3-mediated suppression of StBMI1-1/3, and H3K4me3-mediated activation of miR156 in StMSI1-OE plants. In summary, we show that cross talk between histone modifiers regulates miR156 and alters hormonal response during aerial tuber formation in potato under SD conditions.

Spatiotemporal control of axillary meristem formation by interacting transcriptional regulators

Branching is a common feature of plant development. In seed plants, axillary meristems (AMs) initiate in leaf axils to enable lateral shoot branching. AM initiation requires a high level of expression of the meristem marker SHOOT MERISTEMLESS (STM) in the leaf axil. Here, we show that modules of interacting transcriptional regulators control STM expression and AM initiation. Two redundant AP2-type transcription factors, DORNRÖSCHEN (DRN) and DORNRÖSCHEN-LIKE (DRNL), control AM initiation by regulating STM expression. DRN and DRNL directly upregulate STM expression in leaf axil meristematic cells, as does another transcription factor, REVOLUTA (REV). The activation of STM expression by DRN/DRNL depends on REV, and vice versa. DRN/DRNL and REV have overlapping expression patterns and protein interactions in the leaf axil, which are required for the upregulation of STM expression. Furthermore, LITTLE ZIPPER3, another REV-interacting protein, is expressed in the leaf axil and interferes with the DRN/DRNL-REV interaction to negatively modulate STM expression. Our results support a model in which interacting transcriptional regulators fine-tune the expression of STM to precisely regulate AM initiation. Thus, shoot branching recruits the same conserved protein complexes used in embryogenesis and leaf polarity patterning.

Summary: Shoot branching uses interacting transcriptional regulators to fine-tune the spatiotemporal expression of STM and, thus, to precisely regulate axillary meristem initiation.

Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics

Many plant species exhibit different leaf morphologies within a single plant, or heterophylly. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, at different stages of development, were sequenced using high-throughput sequencing (RNA-Seq), in order to aid gene discovery and functional studies of genes involved in heterophylly. A total of 81,103 unigenes were identified in submerged and floating leaves and 6,822 differentially expressed genes (DEGs) were identified by comparing samples at differing time points of development. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways. A total of 24,025 differentially expressed genes were involved in carbon metabolic pathways, biosynthesis of amino acids, ribosomal processes, and plant-pathogen interactions. In particular, KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. The high-throughput transcriptomic results presented here highlight the potential for understanding the molecular mechanisms underlying heterophylly, which is still poorly understood. Further, these data provide a framework to better understand heterophyllous leaf development in P. octandrus via targeted studies utilizing gene cloning and functional analyses.

Regulation, overexpression, and target gene identification of Potato Homeobox 15 (POTH15) - a class-I KNOX gene in potato

Potato Homeobox 15 (POTH15) is a KNOX-I (Knotted1-like homeobox) family gene in potato that is orthologous to Shoot Meristemless (STM) in Arabidopsis. Despite numerous reports on KNOX genes from different species, studies in potato are limited. Here, we describe photoperiodic regulation of POTH15, its overexpression phenotype, and identification of its potential targets in potato (Solanum tuberosum ssp. andigena). qRT-PCR analysis showed a higher abundance of POTH15 mRNA in shoot tips and stolons under tuber-inducing short-day conditions. POTH15 promoter activity was detected in apical and axillary meristems, stolon tips, tuber eyes, and meristems of tuber sprouts, indicating its role in meristem maintenance and leaf development. POTH15 overexpression altered multiple morphological traits including leaf and stem development, leaflet number, and number of nodes and branches. In particular, the rachis of the leaf was completely reduced and leaves appeared as a bouquet of leaflets. Comparative transcriptomic analysis of 35S::GUS and two POTH15 overexpression lines identified more than 6000 differentially expressed genes, including 2014 common genes between the two overexpression lines. Functional analysis of these genes revealed their involvement in responses to hormones, biotic/abiotic stresses, transcription regulation, and signal transduction. qRT-PCR of selected candidate target genes validated their differential expression in both overexpression lines. Out of 200 randomly chosen POTH15 targets, 173 were found to have at least one tandem TGAC core motif, characteristic of KNOX interaction, within 3.0kb in the upstream sequence of the transcription start site. Overall, this study provides insights to the role of POTH15 in controlling diverse developmental processes in potato.

Transcriptional, posttranscriptional, and posttranslational regulation of SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function in the shoot apex

The activity of SHOOT MERISTEMLESS (STM) is required for the functioning of the shoot apical meristem (SAM). STM is expressed in the SAM but is down-regulated at the site of leaf initiation. STM is also required for the formation of compound leaves. However, how the activity of STM is regulated at the transcriptional, posttranscriptional, and posttranslational levels is poorly understood. We previously found two conserved noncoding sequences in the promoters of STM-like genes across angiosperms, the K-box and the RB-box. Here, we characterize the function of the RB-box in Arabidopsis (Arabidopsis thaliana). The RB-box, along with the K-box, regulates the expression of STM in leaf sinuses, which are areas on the leaf blade with meristematic potential. The RB-box also contributes to restrict STM expression to the SAM. We identified FAR1-RELATED SEQUENCES-RELATED FACTOR1 (FRF1) as a binding factor to the RB-box region. FRF1 is an uncharacterized member of a subfamily of four truncated proteins related to the FAR1-RELATED SEQUENCES factors. Internal deletion analysis of the STM promoter identified a region required to repress the expression of STM in hypocotyls. Expression of STM in leaf primordia under the control of the JAGGED promoter produced plants with partially undifferentiated leaves. We further found that the ELK domain has a role in the posttranslational regulation of STM by affecting the nuclear localization of STM.

The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis

The histone modification H3K27me3 is involved in repression of transcription and plays a crucial role in developmental transitions in both animals and plants. It is deposited by PRC2 (Polycomb repressive complex 2), a conserved protein complex. In Arabidopsis thaliana, H3K27me3 is found at 15% of all genes. These tend to encode transcription factors and other regulators important for development. However, it is not known how PRC2 is recruited to target loci nor how this set of target genes arose during Arabidopsis evolution. To resolve the latter, we integrated A. thaliana gene families with five independent genome-wide H3K27me3 data sets. Gene families were either significantly enriched or depleted of H3K27me3, showing a strong impact of shared ancestry to H3K27me3 distribution. To quantify this, we performed ancestral state reconstruction of H3K27me3 on phylogenetic trees of gene families. The set of H3K27me3-marked genes changed less than expected by chance, suggesting that H3K27me3 was retained after gene duplication. This retention suggests that the PRC2-recruiting signal could be encoded in the DNA and also conserved among certain duplicated genes. Indeed, H3K27me3-marked genes were overrepresented among paralogs sharing conserved noncoding sequences (CNSs) that are enriched with transcription factor binding sites. The association of upstream CNSs with H3K27me3-marked genes represents the first genome-wide connection between H3K27me3 and potential regulatory elements in plants. Thus, we propose that CNSs likely function as part of the PRC2 recruitment in plants.

Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection

BACKGROUND

Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem development are known to regulate also fruit morphology. To decipher the genetic variation underlying tomato fruit morphology, we assessed the nucleotide diversity and selection footprints of candidate genes involved in flower and fruit development and performed genome-wide association studies.

RESULTS

Thirty candidate genes were selected according to their similarity with genes involved in meristem development or their known causal function in Arabidopsis thaliana. In tomato, these genes and flanking regions were sequenced in a core collection of 96 accessions (including cultivated, cherry-type and wild relative accessions) maximizing the molecular diversity, using the Roche 454 technology. A total amount of 17 Mb was sequenced allowing the discovery of 6,106 single nucleotide polymorphisms (SNPs). The annotation of the 30 gene regions identified 231 exons carrying 517 SNPs. Subsequently, the nucleotide diversity (π) and the neutral evolution of each region were compared against genome-wide values within the collection, using a SNP array carrying 7,667 SNPs mainly distributed in coding sequences.About half of the genes revealed footprints of selection and polymorphisms putatively involved in fruit size variation by showing negative Tajima's D and nucleotide diversity reduction in cultivated tomato compared to its wild relative. Among the candidates, FW2.2 and BAM1 sequences revealed selection footprints within their promoter regions suggesting their potential involvement in their regulation. Two associations co-localized with previously identified loci: LC (locule number) and Ovate (fruit shape).

CONCLUSION

Compared to whole genome genotypic data, a drastic reduction of nucleotide diversity was shown for several candidate genes. Strong selection patterns were identified in 15 candidates highlighting the critical role of meristem maintenance genes as well as the impact of domestication on candidates. The study highlighted a set of polymorphisms putatively important in the evolution of these genes.

Class I BASIC PENTACYSTEINE factors regulate HOMEOBOX genes involved in meristem size maintenance

The BASIC PENTACYSTEINE (BCP) family is a poorly characterized plant transcription factor family of GAGA BINDING PROTEINS. In Arabidopsis, there are seven members (BPC1-7) that are broadly expressed, and they can potentially bind more than 3000 Arabidopsis GAGA-repeat-containing genes. To date, BPCs are known to be direct regulators of the INNER NO OUTER (INO), SEEDSTICK (STK), and LEAFY COTYLEDON 2 (LEC2) genes. Because of the high functional redundancy, neither single knockout nor double bpc mutant combinations cause aberrant phenotypes. The bpc1-2 bpc2 bpc3 triple mutant shows several pleiotropic developmental defects, including enlargement of the inflorescence meristem and flowers with supernumerary floral organs. Here, we demonstrated through expression analysis and chromatin immunoprecipitation assays that this phenotype is probably due to deregulation of the expression of the SHOOTMERISTEMLESS (STM) and BREVIPEDICELLUS/KNAT1 (BP) genes, which are both direct targets of BPCs. Moreover, we assigned a role to BPCs in the fine regulation of the cytokinin content in the meristem, as both ISOPENTENYLTRANSFERASE 7 (IPT7) and ARABIDOPSIS RESPONSE REGULATOR 7 (ARR7) genes were shown to be overexpressed in the bpc1-2 bpc2 bpc3 triple mutant.

Acquisition and diversification of tendrilled leaves in Bignonieae (Bignoniaceae) involved changes in expression patterns of SHOOTMERISTEMLESS (STM), LEAFY/FLORICAULA (LFY/FLO), and PHANTASTICA (PHAN)

Leaves have undergone structural modifications over evolutionary time, and presently exist in many forms. For instance, in Fabaceae and Bignoniaceae, leaf parts can be modified into tendrils. Currently, no data are available on genic control of tendrilled leaf development outside Fabaceae. Here, we conducted a detailed study of three representatives of Bignonieae: Amphilophium buccinatorium, Dolichandra unguis-cati, and Bignonia callistegioides, bearing multifid, trifid, and simple-tendrilled leaves, respectively. We investigated the structure of their petioles, petiolules, leaflets, and tendrils through histological analyses. Additionally, the expression of SHOOTMERISTEMLESS (STM), PHANTASTICA (PHAN), and LEAFY/FLORICAULA (LFY/FLO) during leaf development was analyzed by in situ hybridizations. Tendrils share some anatomical similarities with leaflets, but not with other leaf parts. Transcripts of both STM and LFY/FLO were detected in leaf primordia, associated with regions from which leaflets and tendril branches originate. PHAN expression was found to be polarized in branched tendrils, but not in simple tendrils. In Bignonieae, tendrils are modified leaflets that, as a result of premature completion of development, become bladeless organs. Bignonieae leaves develop differently from those of peas, as both LFY/FLO and STM are expressed in developing leaves of Bignonieae. Moreover, PHAN is probably involved in tendril diversification in Bignonieae, as it has distinct expression patterns in different leaf types.

Regulation of plant vascular stem cells by endodermis-derived EPFL-family peptide hormones and phloem-expressed ERECTA-family receptor kinases

Plant vasculatures are complex tissues consisting of (pro)cambium, phloem, and xylem. The (pro)cambium serves as vascular stem cells that produce all vascular cells. The Arabidopsis ERECTA (ER) receptor kinase is known to regulate the architecture of inflorescence stems. It was recently reported that the er mutation enhances a vascular phenotype induced by a mutation of TDR/PXY, which plays a significant role in procambial proliferation, suggesting that ER participates in vascular development. However, detailed molecular mechanisms of the ER-dependent vascular regulation are largely unknown. Here, this work found that ER and its paralogue, ER-LIKE1, were redundantly involved in procambial development of inflorescence stems. Interestingly, their activity in the phloem was sufficient for vascular regulation. Furthermore, two endodermis-derived peptide hormones, EPFL4 and EPFL6, were redundantly involved in such regulation. It has been previously reported that EPFL4 and EPFL6 act as ligands of phloem-expressed ER for stem elongation. Therefore, these findings indicate that cell-cell communication between the endodermis and the phloem plays an important role in procambial development as well as stem elongation. Interestingly, similar EPFL-ER modules control two distinct developmental events by slightly changing their components: the EPFL4/6-ER module for stem elongation and the EPFL4/6-ER/ERL1 module for vascular development.

Dynamic evolution of rht-1 homologous regions in grass genomes

Hexaploid bread wheat contains A, B, and D three subgenomes with its well-characterized ancestral genomes existed at diploid and tetraploid levels, making the wheat act as a good model species for studying evolutionary genomic dynamics. Here, we performed intra- and inter-species comparative analyses of wheat and related grass genomes to examine the dynamics of homologous regions surrounding Rht-1, a well-known "green revolution" gene. Our results showed that the divergence of the two A genomes in the Rht-1 region from the diploid and tetraploid species is greater than that from the tetraploid and hexaploid wheat. The divergence of D genome between diploid and hexaploid is lower than those of A genome, suggesting that D genome diverged latter than others. The divergence among the A, B and D subgenomes was larger than that among different ploidy levels for each subgenome which mainly resulted from genomic structural variation of insertions and, perhaps deletions, of the repetitive sequences. Meanwhile, the repetitive sequences caused genome expansion further after the divergence of the three subgenomes. However, several conserved non-coding sequences were identified to be shared among the three subgenomes of wheat, suggesting that they may have played an important role to maintain the homolog of three subgenomes. This is a pilot study on evolutionary dynamics across the wheat ploids, subgenomes and differently related grasses. Our results gained new insights into evolutionary dynamics of Rht-1 region at sequence level as well as the evolution of wheat during the plolyploidization process.

Haplotype dictionary for the Rht-1 loci in wheat

The introduction of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties was a key component of the 'green revolution' and today these alleles are the primary sources of semi-dwarfism in wheat. The Rht-1 loci encode DELLA proteins, which are transcription factors that affect plant growth and stress tolerance. In bread wheat, Rht-D1b and Rht-B1b influence resistance to the disease Fusarium Head Blight. To identify Rht-1 variants, locus specific primers were developed and used to sequence the entire open reading frame (ORF) and 1.7 kb of the 5' and 0.5 kb of the 3' flanking regions of Rht-A1 (Rht-A1+f), Rht-B1 (Rht-B1+f), and Rht-D1 (Rht-D1+f) in bread wheat (36 sequences from each genome) and tetraploid and diploid wheat (TDW) (one to three sequences from each genome). Among the bread wheat accessions, the Rht-A1+f and Rht-D1+f sequences contained relatively low genetic diversity and few haplotypes relative to the Rht-B1+f sequences. The TDW accessions were relatively rich in genetic diversity and contained the majority of the polymorphic sites. Novel polymorphisms, relative to 'Chinese Spring', discovered among the accessions include 160 and 197 bp insertions 5' of Rht-B1 and a frameshift in the Rht-B1 ORF. Quantitative real-time PCR using shoot and leaf tissue from 5-day-old seedlings of genotypes lacking or containing the 5' insertions revealed no major effect on Rht-B1 transcript accumulation. This research provides insights into the genetic diversity present at the Rht-1 loci in modern bread wheat and in relation to ancestral wheat accessions.

Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat

The introgression of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties beginning in the 1960s led to improved lodging resistance and yield, providing a major contribution to the 'green revolution'. Although wheat Rht-1 and surrounding sequence is available, the genetic composition of this region has not been examined in a homoeologous series. To determine this, three Rht-1-containing bacterial artificial chromosome (BAC) sequences derived from the A, B, and D genomes of the bread wheat variety Chinese Spring (CS) were fully assembled and analyzed. This revealed that Rht-1 and two upstream genes were highly conserved among the homoeologs. In contrast, transposable elements (TEs) were not conserved among homoeologs with the exception of intronic miniature inverted-repeat TEs (MITEs). In relation to the Triticum urartu ancestral line, CS-A genic sequences were highly conserved and several colinear TEs were present. Comparative analysis of the CS wheat BAC sequences with assembled Poaceae genomes showed gene synteny and amino acid sequences were well preserved. Further 5' and 3' of the wheat BAC sequences, a high degree of gene colinearity is present among the assembled Poaceae genomes. In the 20 kb of sequence flanking Rht-1, five conserved non-coding sequences (CNSs) were present among the CS wheat homoeologs and among all the Poaceae members examined. Rht-A1 was mapped to the long arm of chromosome 4 and three closely flanking genetic markers were identified. The tools developed herein will enable detailed studies of Rht-1 and linked genes that affect abiotic and biotic stress response in wheat.

ERECTA-family receptor kinases regulate stem cell homeostasis via buffering its cytokinin responsiveness in the shoot apical meristem

Shoot apical meristems (SAMs), which are maintained at the tips of stems, are indeterminate structures and sources of stem cells from which all aerial organs are ultimately derived. Although mechanisms that regulate the homeostasis of the stem cells have been extensively investigated, identification of further unknown regulators should provide better understanding of the regulation. Here, we report that members of the Arabidopsis ERECTA (ER) receptor kinase family redundantly play a significant role in the regulation of stem cell homeostasis. In wild-type seedlings, the expression of WUSCHEL (WUS), a central regulator of the stem cell population, is stimulated by cytokinin. Interestingly, however, the SAM morphology and the expression of CLAVATA3 (CLV3), which is expressed in stem cells and therefore serves as a stem cell marker, are relatively stable against cytokinin treatment regardless of increased WUS expression. These findings indicate the presence of a mechanism to buffer stem cell homeostasis against an increase in cytokinin. Mutant seedlings lacking all ER-family members, which are expressed in the SAM, show an increase in the stem cell population and also the up-regulation of a cytokinin-responsive gene in the SAM. In this mutant, WUS expression is stimulated by cytokinin treatment as efficiently as in wild-type plants. However, in contrast to wild-type plants, SAM morphology and CLV3 expression respond drastically to cytokinin treatment, suggesting that the buffering mechanism to maintain stem cell homeostasis against an increase in cytokinin is severely impaired in this mutant. We suggest that the ER family regulates stem cell homeostasis via buffering its cytokinin responsiveness in the SAM.

Analysis of the role of Arabidopsis class I TCP genes AtTCP7, AtTCP8, AtTCP22, and AtTCP23 in leaf development

TCP family of plant-specific transcription factors regulates plant form through control of cell proliferation and differentiation. This gene family is comprised of two groups, class I and class II. While the role of class II TCP genes in plant development is well known, data about the function of some class I TCP genes is lacking. We studied a group of phylogenetically related class I TCP genes: AtTCP7, AtTCP8, AtTCP22, and AtTCP23. The similar expression pattern in young growing leaves found for this group suggests similarity in gene function. Gene redundancy is characteristic in this group, as also seen in the class II TCP genes. We generated a pentuple mutant tcp8 tcp15 tcp21 tcp22 tcp23 and show that loss of function of these genes results in changes in leaf developmental traits. We also determined that these factors are able to mutually interact in a yeast two-hybrid assay and regulate the expression of KNOX1 genes. To circumvent the issue of genetic redundancy, dominant negative forms with SRDX repressor domain were used. Analysis of transgenic plants expressing AtTCP7-SRDX and AtTCP23-SRDX indicate a role of these factors in the control of cell proliferation.

Leaf development

Leaves are the most important organs for plants. Without leaves, plants cannot capture light energy or synthesize organic compounds via photosynthesis. Without leaves, plants would be unable perceive diverse environmental conditions, particularly those relating to light quality/quantity. Without leaves, plants would not be able to flower because all floral organs are modified leaves. Arabidopsis thaliana is a good model system for analyzing mechanisms of eudicotyledonous, simple-leaf development. The first section of this review provides a brief history of studies on development in Arabidopsis leaves. This history largely coincides with a general history of advancement in understanding of the genetic mechanisms operating during simple-leaf development in angiosperms. In the second section, I outline events in Arabidopsis leaf development, with emphasis on genetic controls. Current knowledge of six important components in these developmental events is summarized in detail, followed by concluding remarks and perspectives.

Plant 'evo-devo' goes genomic: from candidate genes to regulatory networks

Plant development gives rise to a staggering complexity of morphological structures with different shapes, colors, and functions. Understanding the evolution of control mechanisms that underlie developmental processes provides insights into causes of morphological diversity and, therefore, is of great interest to biologists. New genomic resources and techniques enable biologists to assess for the first time the evolution of developmental regulatory networks at a global scale. Here, we address the question of how comparative regulatory genomics can be used to reveal the evolutionary dynamics of control networks linked to morphological evolution in plants.

Ectopic expression of Kxhkn5 in the viviparous species Kalanchoe × Houghtonii induces a novel pattern of epiphyll development

KxhKN5 (class 1 KNOX gene) was cloned from Kalanchoe × houghtonii with strong tendency to form epiphylls on leaves. KxhKN5 appear to be homologue of BP of A. thaliana on the basis of phylogeny, expression and phenotype analysis. Beside the modification of several plant and leaf traits, the appearance of epiphylls was drastically reduced by both the silencing and the over-expression of KxhKN5 in most of the generated clones. In silenced clones, epiphyll production followed the morphogenetic pathway of the WT plants: somatic embryos outbreak in the centre of each leaf-pedestal, grown in the notch between leaf indentations and were supported by a suspensor. The connection between the epiphyll and the mother plant did not include any vasculature and as a result, the epiphylls dropped easily from the mother plant. The most represented category of over expressor clones, disclosed a novel pattern of epiphyll development: the leaf-pedestals were absent and single bud outbreaks in each leaf notch. Buds developed into shoots which remained attached to the maternal plant by a strong vascular connection. The leaves supporting shoots, produced a thickened midrib and veins, and their lamina ceased expanding. Finally, the leaf/shoot structure resembles a lateral branch. The ectopic expression of KxhKN5 in K. × houghtonii induces a process comparable to the alternation of leaf and shoot formation in other species and support the idea, that it is the variation in shared molecular and developmental processes which produces the growth of specific structures.

Altered seed oil and glucosinolate levels in transgenic plants overexpressing the Brassica napus SHOOTMERISTEMLESS gene

SHOOTMERISTEMLESS (STM) is a homeobox gene conserved among plant species which is required for the formation and maintenance of the shoot meristem by suppressing differentiation and maintaining an undetermined cell fate within the apical pole. To assess further the role of this gene during seed storage accumulation, transgenic Brassica napus (Bn) plants overexpressing or down-regulating BnSTM under the control of the 35S promoter were generated. Overexpression of BnSTM increased seed oil content without affecting the protein and sucrose level. These changes were accompanied by the induction of genes encoding several transcription factors promoting fatty acid (FA) synthesis: LEAFY COTYLEDON1 (BnLEC1), BnLEC2, and WRINKLE1 (BnWRI1). In addition, expression of key representative enzymes involved in sucrose metabolism, glycolysis, and FA biosynthesis was up-regulated in developing seeds ectopically expressing BnSTM. These distinctive expression patterns support the view of an increased carbon flux to the FA biosynthetic pathway in developing transformed seeds. The overexpression of BnSTM also resulted in a desirable reduction of seed glucosinolate (GLS) levels ascribed to a transcriptional repression of key enzymes participating in the GLS biosynthetic pathway, and possibly to the differential utilization of common precursors for GLS and indole-3-acetic acid synthesis. No changes in oil and GLS levels were observed in lines down-regulating BnSTM. Taken together, these findings provide evidence for a novel function for BnSTM in promoting desirable changes in seed oil and GLS levels when overexpressed in B. napus plants, and demonstrate that this gene can be used as a target for genetic improvement of oilseed species.

LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration

The remarkable regeneration capability of plant tissues or organs under culture conditions has underlain an extensive practice for decades. The initial step in plant in vitro regeneration often involves the induction of a pluripotent cell mass termed callus, which is driven by the phytohormone auxin and occurs via a root development pathway. However, the key molecules governing callus formation remain unknown. Here we demonstrate that Arabidopsis LATERAL ORGAN BOUNDARIES DOMAIN (LBD)/ASYMMETRIC LEAVES2-LIKE (ASL) transcription factors are involved in the control of callus formation program. The four LBD genes downstream of AUXIN RESPONSE FACTORs (ARFs), LBD16, LBD17, LBD18 and LBD29, are rapidly and dramatically induced by callus-inducing medium (CIM) in multiple organs. Ectopic expression of each of the four LBD genes in Arabidopsis is sufficient to trigger spontaneous callus formation without exogenous phytohormones, whereas suppression of LBD function inhibits the callus formation induced by CIM. Moreover, the callus triggered by LBD resembles that induced by CIM by characteristics of ectopically activated root meristem genes and efficient regeneration capacity. These findings define LBD transcription factors as key regulators in the callus induction process, thereby establishing a molecular link between auxin signaling and the plant regeneration program.

Characterization of Linaria KNOX genes suggests a role in petal-spur development

Spurs are tubular outgrowths of perianth organs that have evolved iteratively among angiosperms. They typically contain nectar and often strongly influence pollinator specificity, potentially mediating reproductive isolation. The identification of Antirrhinum majus mutants with ectopic petal spurs suggested that petal-spur development is dependent on the expression of KNOTTED 1-like homeobox (KNOX) genes, which are better known for their role in maintaining the shoot apical meristem. Here, we tested the role of KNOX genes in petal-spur development by isolating orthologs of the A. majus KNOX genes Hirzina (AmHirz) and Invaginata (AmIna) from Linaria vulgaris, a related species that differs from A. majus in possessing long, narrow petal spurs. We name these genes LvHirz and LvIna, respectively. Using quantitative reverse-transcription PCR, we show that LvHirz is expressed at high levels in the developing petals and demonstrate that the expression of petal-associated KNOX genes is sufficient to induce sac-like outgrowths on petals in a heterologous host. We propose a model in which KNOX gene expression during early petal-spur development promotes and maintains further morphogenetic potential of the petal, as previously described for KNOX gene function in compound leaf development. These data indicate that petal spurs could have evolved by changes in regulatory gene expression that cause rapid and potentially saltational phenotypic modifications. Given the morphological similarity of spur ontogeny in distantly related taxa, changes in KNOX gene expression patterns could be a shared feature of spur development in angiosperms.

Developmental analysis of a Medicago truncatula smooth leaf margin1 mutant reveals context-dependent effects on compound leaf development

Compound leaf development requires highly regulated cell proliferation, differentiation, and expansion patterns. We identified loss-of-function alleles at the SMOOTH LEAF MARGIN1 (SLM1) locus in Medicago truncatula, a model legume species with trifoliate adult leaves. SLM1 encodes an auxin efflux carrier protein and is the ortholog of Arabidopsis thaliana PIN-FORMED1 (PIN1). Auxin distribution is impaired in the slm1 mutant, resulting in pleiotropic phenotypes in different organs. The most striking change in slm1 is the increase in the number of terminal leaflets and a simultaneous reduction in the number of lateral leaflets, accompanied by reduced expression of SINGLE LEAFLET1 (SGL1), an ortholog of LEAFY. Characterization of the mutant indicates that distinct developmental domains exist in the formation of terminal and lateral leaflets. In contrast with the pinnate compound leaves in the wild type, the slm1 sgl1 double mutant shows nonpeltately palmate leaves, suggesting that the terminal leaflet primordium in M. truncatula has a unique developmental mechanism. Further investigations on the development of leaf serrations reveal different ontogenies between distal serration and marginal serration formation as well as between serration and leaflet formation. These data suggest that regulation of the elaboration of compound leaves and serrations is context dependent and tightly correlated with the auxin/SLM1 module in M. truncatula.

STENOFOLIA regulates blade outgrowth and leaf vascular patterning in Medicago truncatula and Nicotiana sylvestris

Dicot leaf primordia initiate at the flanks of the shoot apical meristem and extend laterally by cell division and cell expansion to form the flat lamina, but the molecular mechanism of lamina outgrowth remains unclear. Here, we report the identification of STENOFOLIA (STF), a WUSCHEL-like homeobox transcriptional regulator, in Medicago truncatula, which is required for blade outgrowth and leaf vascular patterning. STF belongs to the MAEWEST clade and its inactivation by the transposable element of Nicotiana tabacum cell type1 (Tnt1) retrotransposon insertion leads to abortion of blade expansion in the mediolateral axis and disruption of vein patterning. We also show that the classical lam1 mutant of Nicotiana sylvestris, which is blocked in lamina formation and stem elongation, is caused by deletion of the STF ortholog. STF is expressed at the adaxial-abaxial boundary layer of leaf primordia and governs organization and outgrowth of lamina, conferring morphogenetic competence. STF does not affect formation of lateral leaflets but is critical to their ability to generate a leaf blade. Our data suggest that STF functions by modulating phytohormone homeostasis and crosstalk directly linked to sugar metabolism, highlighting the importance of coordinating metabolic and developmental signals for leaf elaboration.

Arabidopsis ERECTA-family receptor kinases mediate morphological alterations stimulated by activation of NB-LRR-type UNI proteins

Shoot apical meristems (SAMs), which maintain stem cells at the tips of stems, and axillary meristems (AMs), which arise at leaf axils for branch formation, play significant roles in the establishment of plant architecture. Previously, we showed that, in Arabidopsis thaliana, activation of NB-LRR (nucleotide-binding site-leucine-rich repeat)-type UNI proteins affects plant morphology through modulation of the regulation of meristems. However, information about genes involved in the processes was still lacking. Here, we report that ERECTA (ER) receptor kinase family members cooperatively mediate the morphological alterations that are stimulated by activation of UNI proteins. uni-1D is a gain-of-function mutation in the UNI gene and uni-1D mutants exhibit early termination of inflorescence stem growth and also formation of extra AMs at leaf axils. The former defect involves modulation of the SAM activity and is suppressed by er mutation. Though the AM phenotype is not affected by a single er mutation, it is suppressed by simultaneous mutations of ER-family members. It was previously shown that trans-zeatin (tZ)-type cytokinins were involved in the morphological phenotypes of uni-1D mutants and that expression of CYP735A2, which is essential for biosynthesis of tZ-type cytokinins, was modulated in uni-1D mutants. We show that this modulation of CYP735A2 expression requires activities of ER-family members. Moreover, the ER activity in UNI-expressing cells contributes to all morphological phenotypes of uni-1D mutants, suggesting that a cross-talk between ER-family-dependent and UNI-triggered signaling pathways plays a significant role in the morphological alterations observed in uni-1D mutants.

Divergent expression patterns of miR164 and CUP-SHAPED COTYLEDON genes in palms and other monocots: implication for the evolution of meristem function in angiosperms

In order to understand how the morphology of plant species has diversified over time, it is necessary to decipher how the underlying developmental programs have evolved. The regulatory network controlling shoot meristem activity is likely to have played an important role in morphological diversification and useful insights can be gained by comparing monocots and eudicots. These two distinct monophyletic groups of angiosperms diverged 130 Ma and are characterized by important differences in their morphology. Several studies of eudicot species have revealed a conserved role for NAM and CUC3 genes in meristem functioning and pattern formation through the definition of morphogenetic boundaries during development. In this study, we show that NAM- and CUC3-related genes are conserved in palms and grasses, their diversification having predated the radiation of monocots and eudicots. Moreover, the NAM-miR164 posttranscriptional regulatory module is also conserved in palm species. However, in contrast to the CUC3-related genes, which share a similar expression pattern between the two angiosperm groups, the expression domain of the NAM-miR164 module differs between monocot and eudicot species. In our studies of spatial expression patterns, we compared existing eudicot data with novel results from our work using two palm species (date palm and oil palm) and two members of the Poaceae (rice and millet). In addition to contrasting results obtained at the gene expression level, major differences were also observed between eudicot and monocot NAM-related genes in the occurrence of putative cis-regulatory elements in their promoter sequences. Overall, our results suggest that although NAM- and CUC3-related proteins are functionally equivalent between monocots and eudicots, evolutionary radiation has resulted in heterotopy through alterations in the expression domain of the NAM-miR164 regulatory module.

Members of the LATERAL ORGAN BOUNDARIES DOMAIN transcription factor family are involved in the regulation of secondary growth in Populus

Regulation of secondary (woody) growth is of substantial economic and environmental interest but is poorly understood. We identified and subsequently characterized an activation-tagged poplar (Populus tremula × Populus alba) mutant with enhanced woody growth and changes in bark texture caused primarily by increased secondary phloem production. Molecular characterization of the mutation through positioning of the tag and retransformation experiments shows that the phenotype is conditioned by activation of an uncharacterized gene that encodes a novel member of the LATERAL ORGAN BOUNDARIES DOMAIN (LBD) family of transcription factors. Homology analysis showed highest similarity to an uncharacterized LBD1 gene from Arabidopsis thaliana, and we consequently named it Populus tremula × Populus alba (Pta) LBD1. Dominant-negative suppression of Pta LBD1 via translational fusion with the repressor SRDX domain caused decreased diameter growth and suppressed and highly irregular phloem development. In wild-type plants, LBD1 was most highly expressed in the phloem and cambial zone. Two key Class I KNOTTED1-like homeobox genes that promote meristem identity in the cambium were downregulated, while an Altered Phloem Development gene that is known to promote phloem differentiation was upregulated in the mutant. A set of four LBD genes, including the LBD1 gene, was predominantly expressed in wood-forming tissues, suggesting a broader regulatory role of these transcription factors during secondary woody growth in poplar.

KNOX genes: versatile regulators of plant development and diversity

Knotted1-like homeobox (KNOX) proteins are homeodomain transcription factors that maintain an important pluripotent cell population called the shoot apical meristem, which generates the entire above-ground body of vascular plants. KNOX proteins regulate target genes that control hormone homeostasis in the meristem and interact with another subclass of homeodomain proteins called the BELL family. Studies in novel genetic systems, both at the base of the land plant phylogeny and in flowering plants, have uncovered novel roles for KNOX proteins in sculpting plant form and its diversity. Here, we discuss how KNOX proteins influence plant growth and development in a versatile context-dependent manner.

Plant development: a TALE story

Plant development depends on the activity of a group of dividing cells called the meristem. Extensive genetic analyses have identified the major regulators of the shoot apical meristem (SAM), which control the development of all aerial organs. Among them, the three-amino-acid-loop-extension (TALE) class of homeoproteins has been shown to control meristem formation and/or maintenance, organ morphogenesis, organ position, and several aspects of the reproductive phase. This family contains the KNOTTED-like homeodomain (KNOX) and BEL1-like Homeodomain (BELL) members, which function as heterodimers. In this review, we have reported the functions of the TALE members throughout the Arabidopsis life cycle. Genetic analyses revealed a complex network, as TALE members exhibit both overlapping and antagonistic activities. The characterization of a new KNOX member (KNATM), which lacks a homeodomain and interacts with other members to modulate their activities, adds another layer of complexity to this network. While the mode of action of these transcription factors is still largely unknown, they have been implicated in the regulation of several hormonal pathways, providing a link between gene regulatory networks and signaling in the SAM.

Embryogenesis - the humble beginnings of plant life

Each plant starts life from the zygote formed by the fusion of an egg and a sperm cell. The zygote gives rise to a multicellular embryo that displays a basic plant body organization and is surrounded by nutritive endosperm and maternal tissue. How the body organization is generated had already been studied before the genome sequence of Arabidopsis thaliana was completed 10 years ago, but several regulatory mechanisms of embryo development have since been discovered or analysed in more detail. Although this progress did not strictly depend on the availability of the genome sequence itself, several advances were considerably facilitated. In this review, we mainly address early embryo development, highlighting general mechanisms and crucial regulators, including phytohormones, that are involved in patterning the embryo and were mainly analysed in the post-genome decade. We also highlight some unsolved problems, provide a brief outlook on the future of Arabidopsis embryo research, and discuss how the knowledge gained from Arabidopsis could be translated to crop species.

Weeds of change: Cardamine hirsuta as a new model system for studying dissected leaf development

Cardamine hirsuta, a small crucifer closely related to the model organism Arabidopsis thaliana, offers high genetic tractability and has emerged as a powerful system for studying the genetic basis for diversification of plant form. Contrary to A. thaliana, which has simple leaves, C. hirsuta produces dissected leaves divided into individual units called leaflets. Leaflet formation requires activity of Class I KNOTTED1-like homeodomain (KNOX) proteins, which also promote function of the shoot apical meristem (SAM). In C. hirsuta, KNOX genes are expressed in the leaves whereas in A. thaliana their expression is confined to the SAM, and differences in expression arise through cis-regulatory divergence of KNOX regulation. KNOX activity in C. hirsuta leaves delays the transition from proliferative growth to differentiation thus facilitating the generation of lateral growth axes that give rise to leaflets. These axes reflect the sequential generation of cell division foci across the leaf proximodistal axis in response to auxin activity maxima, which are generated by the PINFORMED1 (PIN1) auxin efflux carriers in a process that resembles organogenesis at the SAM. Delimitation of C. hirsuta leaflets also requires the activity of CUP SHAPED COTYLEDON (CUC) genes, which direct formation of organ boundaries at the SAM. These observations show how species-specific deployment of fundamental shoot development networks may have sculpted simple versus dissected leaf forms. These studies also illustrate how extending developmental genetic studies to morphologically divergent relatives of model organisms can greatly help elucidate the mechanisms underlying the evolution of form.

Coordination of leaf development via regulation of KNOX1 genes

Class I KNOTTED1-LIKE HOMEOBOX (KNOX1) genes are expressed in the shoot apical meristem (SAM) to effect its formation and maintenance. KNOX1 genes are also involved in leaf shape control throughout angiosperm evolution. Leaves can be classified as either simple or compound, and KNOX1 expression patterns in leaf primordia are highly correlated with leaf shape; in most simple-leafed species, KNOX1 genes are expressed only in the SAM but not in leaf primordia, while in compound-leafed species they are expressed both in the SAM and leaf primordia. How can KNOX1 expression be maintained to a high degree in the SAM, but simultaneously be so variable in leaves? This dichotomy suggests that the processes of leaf and SAM development have been compartmentalized during evolution. Here, we introduce our findings regarding the regulation of expression of SHOOT MERISTEMLESS, a KNOX1 gene, together with a brief review of KNOX1 genes from an evolutionary viewpoint. We also present our findings regarding another aspect of KNOX1 regulation via a protein-protein interaction network involved in the natural variation in leaf shape. Both aspects of KNOX1 regulation could be utilized for fine-tuning leaf morphology during evolution without affecting the essential function of KNOX genes in the shoot.

Multicellular genesis of leaf primordium was demonstrated via chimaeric transgenic plant of maize (Zea mays L.) regenerated from Type II calli

Type-II embryonic calli were induced from immature embryos of maize (Zea mays L.) genotype YD and bombarded with beta-glucuronidase gene. Bombarded calli were proliferated on normal N6 medium for 2 weeks at 26°C in the dark and selected on N6 medium containing 1 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D) and 5 mg/l phosphinothricin (PPT) but without casamino acids and proline under the same conditions for 14 days. Regeneration was carried out on hormone-free MS medium containing 5 mg/l phosphinothricin at 26°C under 3000 lux illumination. Plants over 8 cm were transplanted into soil and sprayed with 250 mg/l phosphinothricin when two new leaves appeared. Except normal transgenic plants, chimaeric transgenics also were regenerated in the present work. The expression pattern of beta-glucuronidase gene in leaves of chimaeric transgenic plant revealed that more than one cell formed leaf primordium at the initial stage, and filial cells stemed from each cell in leaf primordium arranged in a row longitudinally from leaf base to leaf apex. There was a clear boundary as a straight line between the area formed by transformed cells and the area formed by normal cells. A hypothesis was put forward that the primitive cells in leaf primordium divided in a longitudinal style, resulted in leaf elongation, then the filial cells divided transversally and synchronously toward the outside to broaden the leaf.

Identification and expression of cytokinin signaling and meristem identity genes in sulfur deficient grapevine (Vitis vinifera L.)

In plants, cytokinin (CK) perception and signaling pathway is composed by a histidine kinase receptor (HK) and a response regulator (RR), the signal being mediated by a histidine phosphotransfer (HPt), as described in Arabidopsis, maize and rice. From database searches we identified in grapevine three HKs, three HPs, four A-type RRs and six B-type RRs, suggesting a common mechanism for grapevine. The phylogenetic analysis of these Vitis genes showed a variable but high degree of homology with Arabidopsis sequences. When sulfate was withdrawn from the culture medium (-S) of in vitro Vitis shoots, we assessed a significant reduction in shoot branching. To ascertain the crosstalk of S status with CK signaling in grapevine, control and -S grown shoots and control, -S and -CK cell suspensions were used as experimental systems. Real-time PCR was elected to quantify the expression of key genes. The expression of CK receptor genes was downregulated in -S cells while not affected in -CK cells. In differentiated shoots no response to -S was observed on those genes. A-type VvRRa4 was downregulated in -S or -CK cells while Vitis B-type RRs did not respond either to CK or S starvation. The results suggest that Vitis CK signaling pathway is affected by -S, although differently according to the model system. Transcription of Vitis apical meristem-identity genes VvWUS, VvCLV and VvSTM and axillary meristem genes VvBRC1, VvBRC2, VvLAS, VvRAX and VvREV was estimated and VvSTM and VvLAS showed to be downregulated in -S. Then, the expression levels of VvSTM and VvLAS make them strong candidates to be associated with the branching pattern of Vitis shoots in -S.

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.

A KNOX family TALE

Knotted1 defined the first homeobox gene family to be isolated in plants and was identified from dominant maize mutants that produced 'knots' of mis-specified tissue on the leaf. The Knotted1-like homeobox (KNOX) gene family expanded last year to include members lacking the defining homeobox with exciting implications for KNOX gene regulation and function. Recent evidence for direct KNOX regulation by myb-related ARP proteins and epigenetic silencing by polycomb repressive complexes have also shed light on the mechanisms defining KNOX gene expression.

WUS and STM-based reporter genes for studying meristem development in poplar

We describe the development of a reporter system for monitoring meristem initiation in poplar using promoters of poplar homologs to the meristem-active regulatory genes WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM). When ~3 kb of the 5' flanking regions of close homologs were used to drive expression of the GUSPlus gene, 50-60% of the transgenic events showed expression in apical and axillary meristems. However, expression was also common in other organs, including in leaf veins (40 and 46% of WUS and STM transgenic events, respectively) and hydathodes (56% of WUS transgenic events). Histochemical GUS staining of explants during callogenesis and shoot regeneration using in vitro stems as explants showed that expression was detectable prior to visible shoot development, starting 3-15 days after explants were placed onto callus inducing medium. A minority of WUS and STM events also showed expression in the cambium, phloem, or xylem of regenerated, greenhouse grown plants undergoing secondary growth. Based on microarray gene expression data, a paralog of poplar WUS was detectably up-regulated during shoot initiation, but the other paralog was not. Both paralogs of poplar STM were down-regulated threefold to sixfold during early callus initiation. We identified 15-35 copies of cytokinin response regulator binding motifs (ARR1AT) and one copy of the auxin response element (AuxRE) in both promoters. Several of the events recovered may be useful for studying the process of primary and secondary meristem development, including treatments intended to stimulate meristem development to promote clonal propagation and genetic transformation.