Plant hormones and homeoboxes: bridging the gap?

Genome-wide characterization of two homeobox families identifies key genes associated with grain-related traits in wheat

Homeodomain proteins encoded by BEL1- and KNAT1-type genes are ubiquitously distributed across plant species and play important roles in growth and development, whereby a comprehensive investigation of their molecular interactions and potential functions in wheat is of great significance. In this study, we systematically investigated the phylogenetic relationships, gene structures, conserved domains, and cis-acting elements of 34 TaBEL and 34 TaKNAT genes in the wheat genome. Our analysis revealed these genes evolved under different selective pressures and showed variable transcript levels in different wheat tissues. Subcellular localization analysis further indicated the proteins encoded by these genes were either exclusively located in the nucleus or both in the nucleus and the cytoplasm. Additionally, a comprehensive protein-protein interaction network was constructed with representative genes in which each TaBEL or TaKNAT proteins interact with at least two partners. The evaluation of wheat mutants identified key genes, including TaBEL-5B, TaBEL-4A.4, and TaKNAT6, which are involved in grain-related traits. Finally, haplotype analysis suggests TaKNAT-6B is associated with grain-related traits and is preferentially selected among a large set of wheat accessions. Our study provides important information on BEL1- and KNAT1-type gene families in wheat, and lays the foundation for functional research in the future.

Development of SSR Markers Linked to Stress Responsive Genes along Tomato Chromosome 3 (Solanum lycopersicum L.)

This study aimed to develop novel SSR markers in tomato. Several BAC clones along chromosome 3 in tomato were selected based on their content. The criteria was the availability of genes, either directly or indirectly related to stress response (drought, salinity, and heat) in tomato. A total of 20 novel in silico SSR markers were developed and 96 important nearby genes were identified. The identified nearby genes represent different tomato genes involved in plant growth and development and biotic and abiotic stress tolerance. The developed SSR markers were assessed using tomato landraces. A total of 29 determinate and semi-determinate local tomato landraces collected from diverse environments were utilized. A total of 33 alleles with mean of 1.65 alleles per locus were scored, showing 100% polymorphic patterns, with a mean of 0.18 polymorphism information content (PIC) values. The mean of observed and expected heterozygosity were 0.19 and 0.24, respectively. The mean value of the Jaccard similarity index was used for clustering the landraces. The developed microsatellite markers showed potential to assess genetic variability among tomato landraces. The genetic distance information reported in this study can be used by breeders in future genetic improvement of tomato for tolerance against diverse stresses.

microRNAs and Their Roles in Plant Development

Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.

Developmental Analysis of Compound Leaf Development in Arachis hypogaea

Leaves are the primary photosynthetic structures, while photosynthesis is the direct motivation of crop yield formation. As a legume plant, peanut (Arachis hypogaea) is one of the most economically essential crops as well as an important source of edible oil and protein. The leaves of A. hypogaea are in the tetrafoliate form, which is different from the trifoliate leaf pattern of Medicago truncatula, a model legume species. In A. hypogaea, an even-pinnate leaf with a pair of proximal and distal leaflets was developed; however, only a single terminal leaflet and a pair of lateral leaflets were formed in the odd-pinnate leaf in M. truncatula. In this study, the development of compound leaf in A. hypogaea was investigated. Transcriptomic profiles revealed that the common and unique differentially expressed genes were identified in a proximal leaflet and a distal leaflet, which provided a research route to understand the leaf development in A. hypogaea. Then, a naturally occurring mutant line with leaf developmental defects in A. hypogaea was obtained, which displayed a pentafoliate form with an extra terminal leaflet. The characterization of the mutant indicated that cytokinin and class I KNOTTED-LIKE HOMEOBOX were involved in the control of compound leaf pattern in A. hypogaea. These results expand our knowledge and provide insights into the molecular mechanism underlying the formation of different compound leaf patterns among species.

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

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

Over-expression of transcription factor ARK1 gene leads to down-regulation of lignin synthesis related genes in hybrid poplar '717'

Improving wood growth rate and wood quality are worthy goals in forest genetics and breeding research. The ARK1 gene is one member of the ARBORKNOX family in all plants, which play an essential role in the process of plant growth and development, but the mechanism associated with its gene network regulation is poorly investigated. In order to generate over-expression transgenic hybrid poplar, the agrobacterium-mediated transformation was used to obtain transgenic hybrid poplar ‘717’ plants to provide insight into the function of the ARK1 gene in poplar. Moreover, the morphology of transgenic plants was observed, and transcriptome analysis was performed to explore the ARK1 gene function. The results showed that there were significant differences in pitch, stem diameter, petiole length, leaf width, leaf length and seedling height between ARK1 transgenic seedlings and non-transgenic seedlings. The transgenic seedlings usually had multiple branches and slender leaves, with some leaves not being fully developed. The results of transcriptome analysis showed that the differentially expressed genes were involved in the growth of poplars, including proteins, transcription factors and protein kinases. Genes related to the positive regulation in plant hormone signal transduction pathways were up-regulated, and the genes related to lignin synthesis were down-regulated. The RT-qPCR analysis confirmed the expression levels of the genes involved in the plant hormone signal transduction pathways and phenylpropanoid pathway. In conclusion, the ARK1 gene had a positive regulatory effect on plant growth, and the gene’s coding enzymes related to lignin synthesis were down-regulated.

RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines

BACKGROUND

Gibberellins (GAs) and their regulator DELLA are involved in many aspects of plant growth and development and most of our current knowledge in the DELLA-facilitated GA signaling was obtained from the studies of annual species. To understand GA-DELLA signaling in perennial species, we created ten GA-insensitive transgenic grapevines carrying a DELLA mutant allele (Vvgai1) in the background of Vitis vinifera 'Thompson Seedless' and conducted comprehensive analysis of their RNA expression profiles in the shoot, leaf and root tissues.

RESULTS

The transgenic lines showed varying degrees of dwarf stature and other typical DELLA mutant phenotypes tightly correlated with the levels of Vvgai1 expression. A large number of differentially expressed genes (DEGs) were identified in the shoot, leaf and root tissues of the transgenic lines and these DEGs were involved in diverse biological processes; many of the DEGs showed strong tissue specificity and about 30% them carried a DELLA motif. We further discovered unexpected expression patterns of several key flowering induction genes VvCO, VvCOL1 and VvTFL1.

CONCLUSIONS

Our results not only confirmed many previous DELLA study findings in annual species, but also revealed new DELLA targets and responses in grapevine, including the roles of homeodomain transcription factors as potential co-regulators with DELLA in controlling the development of grapevine which uniquely possess both vegetative and reproductive meristems at the same time. The contrasting responses of some key flowering induction pathway genes provides new insights into the divergence of GA-DELLA regulations between annual and perennial species in GA-DELLA signaling.

Genome-wide Identification, Classification, and Expression Pattern of Homeobox Gene Family in Brassica rapa under Various Stresses

Homeobox (HB) genes are crucial for plant growth and development processes. They encode transcription factors and responses to various stresses, as reported by recent emerging evidence. In this study, a total of 113 BraHB genes were identified in Brassica rapa. On the basis of domain organization and phylogenetic analysis, the BraHBs were grouped into nine subclasses, in which homeobox leucine-zipper (HB LZP-III) showed the highest number of genes (28) compared to other subclasses. The BraHBs exhibited similarities in exon-intron organization and motif composition among the members of the same subclasses. The analysis revealed that HB-Knotted was more preferentially retained than any other subclass of BraHB. Furthermore, we evaluated the impact of whole-genome triplication on the evolution of BraHBs. In order to analyze the subgenomes of B. rapa, we identified 39 paralogous pairs for which synonymous substitution values were lower than 1.00 for further purifying selection. Finally, the expression patterns of BraHBs across six tissues expressed dynamic variations combined with their responses against multiple stresses. The current study provides brief information on the homeobox gene family in B. rapa. Our findings can serve as a reference for further functional analysis of BraHBs.

Cytokinin-induced expression of OSH1 in a shoot-regenerating rice callus

The expression of a KNOX class 1 gene OSH1 is induced by cytokinin during regeneration of shoots from callus in Oryza sativa L. (rice). This cytokinin-induced expression was enhanced by overexpression of homologues of cytokinin-signalling phosphorelay genes such as a histidine kinase gene OHK3, a phosphotransmitter gene OHP2 and a response regulator gene ORR1 in cultured cells. Regionally overlapped expression of these genes and OSH1 was observed in shoot apex. These results suggest that these cytokinin-signalling genes are positive regulators of the expression of OSH1, and mediate the OSH expression upon shoot regeneration from callus in rice.

Barley NARROW LEAFED DWARF1 encoding a WUSCHEL-RELATED HOMEOBOX 3 (WOX3) regulates the marginal development of lateral organs

Barley (Hordeum vulgare L.) is the fourth most-produced cereal in the world and is mainly utilized as animal feed and malts. Recently barley attracts considerable attentions as healthy food rich in dietary fiber. However, limited knowledge is available about developmental aspects of barley leaves. In the present study, we investigated barley narrow leafed dwarf1 (nld1) mutants, which exhibit thin leaves accompanied by short stature. Detailed histological analysis revealed that leaf marginal tissues, such as sawtooth hairs and sclerenchymatous cells, were lacked in nld1, suggesting that narrowed leaf of nld1 was attributable to the defective development of the marginal regions in the leaves. The defective marginal developments were also appeared in internodes and glumes in spikelets. Map-based cloning revealed that NLD1 encodes a WUSCHEL-RELATED HOMEOBOX 3 (WOX3), an ortholog of the maize NARROW SHEATH genes. In situ hybridization showed that NLD1 transcripts were localized in the marginal edges of leaf primordia from the initiating stage. From these results, we concluded that NLD1 plays pivotal role in the increase of organ width and in the development of marginal tissues in lateral organs in barley.

Diversity of maize shoot apical meristem architecture and its relationship to plant morphology

The shoot apical meristem contains a pool of undifferentiated stem cells and controls initiation of all aerial plant organs. In maize (Zea mays), leaves are formed throughout vegetative development; on transition to floral development, the shoot meristem forms the tassel. Due to the regulated balance between stem cell maintenance and organogenesis, the structure and morphology of the shoot meristem are constrained during vegetative development. Previous work identified loci controlling meristem architecture in a recombinant inbred line population. The study presented here expanded on this by investigating shoot apical meristem morphology across a diverse set of maize inbred lines. Crosses of these lines to common parents showed varying phenotypic expression in the F1, with some form of heterosis occasionally observed. An investigation of meristematic growth throughout vegetative development in diverse lines linked the timing of reproductive transition to flowering time. Phenotypic correlations of meristem morphology with adult plant traits showed an association between the meristem and flowering time, leaf shape, and yield traits, revealing links between the control and architecture of undifferentiated and differentiated plant organs. Finally, quantitative trait loci mapping was utilized to map the genetic architecture of these meristem traits in two divergent populations. Control of meristem architecture was mainly population-specific, with 15 total unique loci mapped across the two populations with only one locus identified in both populations.

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.

Phenotypic characterization of the CRISPA (ARP gene) mutant of pea (Pisum sativum; Fabaceae): a reevaluation

PREMISE OF THE STUDY

Leaf form and development are controlled genetically. The ARP genes encode MYB transcription factors that interact with Class 1 KNOX genes in a regulatory module that controls meristem-leaf determinations and is highly conserved in plants. ARP loss of function alleles and subsequent KNOX1 overexpression cause many unusual leaf phenotypes including loss or partial loss of the ability to produce a lamina and production of "knots" on leaf blades. CRISPA (CRI) is the ARP gene in pea, and a number of its mutant alleles are known.

METHODS

We made morphological and anatomical evaluations of cri-1 mutant plants while controlling for genetic background and for heteroblastic effects, and we used aldehyde fixation and resin preparations for anatomical analysis. Further, we compared gene expression in WT and cri-1 shoot tips and HOP1/PsKN1 and CRI expression in other leaf mutants.

KEY RESULTS

The cri-1 plants had more extensive abnormalities in the proximal than in the distal regions of the leaf, including ectopic stipules, narrow leaflets, and shortened petioles with excessive adaxial expansion. "Knots" were morphologically and anatomically variable but consisted of vascularized out-pocketing of the adaxial leaflet surface. HOP1/PsKN1 and UNI mRNA levels were higher in cri-1 shoot tips, and some auxin-regulated genes were lower. Low LE expression suggests that the GA level is high in cri-1 shoot tips.

CONCLUSIONS

The CRISPA gene of pea suppresses KNOX1 genes and UNI and functions to (1) maintain proximal-distal regions in their appropriate positions, (2) restrict excessive adaxial cell proliferation, and (3) promote laminar expansion.

Early transcriptional response of soybean contrasting accessions to root dehydration

Drought is a significant constraint to yield increase in soybean. The early perception of water deprivation is critical for recruitment of genes that promote plant tolerance. DeepSuperSAGE libraries, including one control and a bulk of six stress times imposed (from 25 to 150 min of root dehydration) for drought-tolerant and sensitive soybean accessions, allowed to identify new molecular targets for drought tolerance. The survey uncovered 120,770 unique transcripts expressed by the contrasting accessions. Of these, 57,610 aligned with known cDNA sequences, allowing the annotation of 32,373 unitags. A total of 1,127 unitags were up-regulated only in the tolerant accession, whereas 1,557 were up-regulated in both as compared to their controls. An expression profile concerning the most representative Gene Ontology (GO) categories for the tolerant accession revealed the expression "protein binding" as the most represented for "Molecular Function", whereas CDPK and CBL were the most up-regulated protein families in this category. Furthermore, particular genes expressed different isoforms according to the accession, showing the potential to operate in the distinction of physiological behaviors. Besides, heat maps comprising GO categories related to abiotic stress response and the unitags regulation observed in the expression contrasts covering tolerant and sensitive accessions, revealed the unitags potential for plant breeding. Candidate genes related to "hormone response" (LOX, ERF1b, XET), "water response" (PUB, BMY), "salt stress response" (WRKY, MYB) and "oxidative stress response" (PER) figured among the most promising molecular targets. Additionally, nine transcripts (HMGR, XET, WRKY20, RAP2-4, EREBP, NAC3, PER, GPX5 and BMY) validated by RT-qPCR (four different time points) confirmed their differential expression and pointed that already after 25 minutes a transcriptional reorganization started in response to the new condition, with important differences between both accessions.

Modulation of root-skewing responses by KNAT1 in Arabidopsis thaliana

The KNOTTED1 homeobox (KNOX) family transcription factors are essential for stem cell establishment and maintenance and regulate various aspects of development in all green plants. Expression patterns of the KNOX genes in the roots of plants have been reported, but their role in development remains unclear. Here we show how the KNAT1 gene is specifically involved in root skewing in Arabidopsis. The roots of two mutant alleles of KNAT1 (bp-1 and bp-5) exhibited exaggerated skewing to the right of gravity when grown on both vertical and tilted agar medium surfaces. This skewing phenotype was enhanced by treatments with low concentrations of propyzamide, and required auxin transport. The KNAT1 mutation substantially decreased basipetal auxin transport and increased auxin accumulation in the roots. Using a PIN2-GFP reporter and western blot analysis, we found that this alteration in auxin transport was accompanied by a decrease in PIN2 levels in the root tip. Decreased PIN2 expression in the mutant roots was not accompanied by reduced mRNA levels, suggesting that the KNAT1 mutations affected PIN2 expression at the posttranscriptional level. In vivo visualization of intracellular vacuolar targeting indicated that vacuolar degradation of PIN2-GFP was significantly promoted in the root tips of the bp allelic mutants. Together, these results demonstrate that KNAT1 negatively modulates root skewing, possibly by regulating auxin transport.

A role for APETALA1/fruitfull transcription factors in tomato leaf development

Flexible maturation rates underlie part of the diversity of leaf shape, and tomato (Solanum lycopersicum) leaves are compound due to prolonged organogenic activity of the leaf margin. The CINCINNATA-teosinte branched1, cycloidea, PCF (CIN-TCP) transcription factor lanceolate (LA) restricts this organogenic activity and promotes maturation. Here, we show that tomato APETALA1/fruitfull (AP1/FUL) MADS box genes are involved in tomato leaf development and are repressed by LA. AP1/FUL expression is correlated negatively with LA activity and positively with the organogenic activity of the leaf margin. LA binds to the promoters of the AP1/FUL genes MBP20 and TM4. Overexpression of MBP20 suppressed the simple-leaf phenotype resulting from upregulation of LA activity or from downregulation of class I knotted like homeobox (KNOXI) activity. Overexpression of a dominant-negative form of MBP20 led to leaf simplification and partly suppressed the increased leaf complexity of plants with reduced LA activity or increased KNOXI activity. Tomato plants overexpressing miR319, a negative regulator of several CIN-TCP genes including LA, flower with fewer leaves via an SFT-dependent pathway, suggesting that miR319-sensitive CIN-TCPs delay flowering in tomato. These results identify a role for AP1/FUL genes in vegetative development and show that leaf and plant maturation are regulated via partially independent mechanisms.

KNOX1 is expressed and epigenetically regulated during in vitro conditions in Agave spp

BACKGROUND

The micropropagation is a powerful tool to scale up plants of economical and agronomical importance, enhancing crop productivity. However, a small but growing body of evidence suggests that epigenetic mechanisms, such as DNA methylation and histone modifications, can be affected under the in vitro conditions characteristic of micropropagation. Here, we tested whether the adaptation to different in vitro systems (Magenta boxes and Bioreactors) modified epigenetically different clones of Agave fourcroydes and A. angustifolia. Furthermore, we assessed whether these epigenetic changes affect the regulatory expression of KNOTTED1-like HOMEOBOX (KNOX) transcription factors.

RESULTS

To gain a better understanding of epigenetic changes during in vitro and ex vitro conditions in Agave fourcroydes and A. angustifolia, we analyzed global DNA methylation, as well as different histone modification marks, in two different systems: semisolid in Magenta boxes (M) and temporary immersion in modular Bioreactors (B). No significant difference was found in DNA methylation in A. fourcroydes grown in either M or B. However, when A. fourcroydes was compared with A. angustifolia, there was a two-fold difference in DNA methylation between the species, independent of the in vitro system used. Furthermore, we detected an absence or a low amount of the repressive mark H3K9me2 in ex vitro conditions in plants that were cultured earlier either in M or B. Moreover, the expression of AtqKNOX1 and AtqKNOX2, on A. fourcroydes and A. angustifolia clones, is affected during in vitro conditions. Therefore, we used Chromatin ImmunoPrecipitation (ChIP) to know whether these genes were epigenetically regulated. In the case of AtqKNOX1, the H3K4me3 and H3K9me2 were affected during in vitro conditions in comparison with AtqKNOX2.

CONCLUSIONS

Agave clones plants with higher DNA methylation during in vitro conditions were better adapted to ex vitro conditions. In addition, A. fourcroydes and A. angustifolia clones displayed differential expression of the KNOX1 gene during in vitro conditions, which is epigenetically regulated by the H3K4me3 and H3K9me2 marks. The finding of an epigenetic regulation in key developmental genes will make it important in future studies to identify factors that help to find climate-resistant micropropagated plants.

The tomato (Solanum lycopersicum cv. Micro-Tom) natural genetic variation Rg1 and the DELLA mutant procera control the competence necessary to form adventitious roots and shoots

Despite the wide use of plant regeneration for biotechnological purposes, the signals that allow cells to become competent to assume different fates remain largely unknown. Here, it is demonstrated that the Regeneration1 (Rg1) allele, a natural genetic variation from the tomato wild relative Solanum peruvianum, increases the capacity to form both roots and shoots in vitro; and that the gibberellin constitutive mutant procera (pro) presented the opposite phenotype, reducing organogenesis on either root-inducing medium (RIM) or shoot-inducing medium (SIM). Mutants showing alterations in the formation of specific organs in vitro were the auxin low-sensitivity diageotropica (dgt), the lateral suppresser (ls), and the KNOX-overexpressing Mouse ears (Me). dgt failed to form roots on RIM, Me increased shoot formation on SIM, and the high capacity for in vitro shoot formation of ls contrasted with its recalcitrance to form axillary meristems. Interestingly, Rg1 rescued the in vitro organ formation capacity in proRg1 and dgtRg1 double mutants and the ex vitro low lateral shoot formation in pro and ls. Such epistatic interactions were also confirmed in gene expression and histological analyses conducted in the single and double mutants. Although Me phenocopied the high shoot formation of Rg1 on SIM, it failed to increase rooting on RIM and to rescue the non-branching phenotype of ls. Taken together, these results suggest REGENERATION1 and the DELLA mutant PROCERA as controlling a common competence to assume distinct cell fates, rather than the specific induction of adventitious roots or shoots, which is controlled by DIAGEOTROPICA and MOUSE EARS, respectively.

The peach (Prunus persica L. Batsch) genome harbours 10 KNOX genes, which are differentially expressed in stem development, and the class 1 KNOPE1 regulates elongation and lignification during primary growth

The KNOTTED-like (KNOX) genes encode homeodomain transcription factors and regulate several processes of plant organ development. The peach (Prunus persica L. Batsch) genome was found to contain 10 KNOX members (KNOPE genes); six of them were experimentally located on the Prunus reference map and the class 1 KNOPE1 was found to link to a quantitative trait locus (QTL) for the internode length in the peach×Ferganensis population. All the KNOPE genes were differentially transcribed in the internodes of growing shoots; the KNOPE1 mRNA abundance decreased progressively from primary (elongation) to secondary growth (radial expansion). During primary growth, the KNOPE1 mRNA was localized in the cortex and in the procambium/metaphloem zones, whereas it was undetected in incipient phloem and xylem fibres. KNOPE1 overexpression in the Arabidopsis bp4 loss-of-function background (35S:KNOPE1/bp genotype) restored the rachis length, suggesting, together with the QTL association, a role for KNOPE1 in peach shoot elongation. Several lignin biosynthesis genes were up-regulated in the bp4 internodes but repressed in the 35S:KNOPE1/bp lines similarly to the wild type. Moreover, the lignin deposition pattern of the 35S:KNOPE1/bp and the wild-type internodes were the same. The KNOPE1 protein was found to recognize in vitro one of the typical KNOX DNA-binding sites that recurred in peach and Arabidopsis lignin genes. KNOPE1 expression was inversely correlated with that of lignin genes and lignin deposition along the peach shoot stems and was down-regulated in lignifying vascular tissues. These data strongly support that KNOPE1 prevents cell lignification by repressing lignin genes during peach stem primary growth.

Flower-specific KNOX phenotype in the orchid Dactylorhiza fuchsii

The KNOTTED1-like homeobox (KNOX) genes are best known for maintaining a pluripotent stem-cell population in the shoot apical meristem that underlies indeterminate vegetative growth, allowing plants to adapt their development to suit the prevailing environmental conditions. More recently, the function of the KNOX gene family has been expanded to include additional roles in lateral organ development such as complex leaf morphogenesis, which has come to dominate the KNOX literature. Despite several reports implicating KNOX genes in the development of carpels and floral elaborations such as petal spurs, few authors have investigated the role of KNOX genes in flower development. Evidence is presented here of a flower-specific KNOX function in the development of the elaborate flowers of the orchid Dactylorhiza fuchsii, which have a three-lobed labellum petal with a prominent spur. Using degenerate PCR, four Class I KNOX genes (DfKN1-4) have been isolated, one from each of the four major Class I KNOX subclades and by reverse transcription PCR (RT-PCR), it is demonstrated that DfKNOX transcripts are detectable in developing floral organs such as the spur-bearing labellum and inferior ovary. Although constitutive expression of the DfKN2 transcript in tobacco produces a wide range of floral abnormalities, including serrated petal margins, extra petal tissue, and fused organs, none of the vegetative phenotypes typical of constitutive KNOX expression were produced. These data are highly suggestive of a role for KNOX expression in floral development that may be especially important in taxa with elaborate flowers.

Gibberellin partly mediates LANCEOLATE activity in tomato

Elaboration of a compound leaf shape depends on extended morphogenetic activity in developing leaves. In tomato (Solanum lycopersicum), the CIN-TCP transcription factor LANCEOLATE (LA) promotes leaf differentiation. LA is negatively regulated by miR319 during the early stages of leaf development, and decreased sensitivity of LA mRNA to miR319 recognition in the semi-dominant mutant La leads to prematurely increased LA expression, precocious leaf differentiation and a simpler and smaller leaf. Increased levels or responses of the plant hormone gibberellin (GA) in tomato leaves also led to a simplified leaf form. Here, we show that LA activity is mediated in part by GA. Expression of the SlGA20 oxidase1 (SlGA20ox1) gene, which encodes an enzyme in the GA biosynthesis pathway, is increased in gain-of-function La mutants and reduced in plants that over-express miR319. Conversely, the transcript levels of the GA deactivation gene SlGA2 oxidase4 (SlGA2ox4) are increased in plants over-expressing miR319. The miR319 over-expression phenotype is suppressed by exogenous GA application and by a mutation in the PROCERA (PRO) gene, which encodes an inhibitor of the GA response. SlGA2ox4 is expressed in initiating leaflets during early leaf development. Its expression expands as a result of miR319 over-expression, and its over-expression leads to increased leaf complexity. These results suggest that LA activity is partly mediated by positive regulation of the GA response, probably by regulation of GA levels.

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.

Ectopic expression of class 1 KNOX genes induce adventitious shoot regeneration and alter growth and development of tobacco (Nicotiana tabacum L) and European plum (Prunus domestica L)

Transgenic plants of tobacco (Nicotiana tabacum L) and European plum (Prunus domestica L) were produced by transforming with the apple class 1 KNOX genes (MdKN1 and MdKN2) or corn KNOX1 gene. Transgenic tobacco plants were regenerated in vitro from transformed leaf discs cultured in a medium lacking cytokinin. Ectopic expression of KNOX genes retarded shoot growth by suppressing elongation of internodes in transgenic tobacco plants. Expression of each of the three KNOX1 genes induced malformation and extensive lobbing in tobacco leaves. In situ regeneration of adventitious shoots was observed from leaves and roots of transgenic tobacco plants expressing each of the three KNOX genes. In vitro culture of leaf explants and internode sections excised from in vitro grown MdKN1 expressing tobacco shoots regenerated adventitious shoots on MS (Murashige and Skoog 1962) basal medium in the absence of exogenous cytokinin. Transgenic plum plants that expressed the MdKN2 or corn KNOX1 gene grew normally but MdKN1 caused a significant reduction in plant height, leaf shape and size and produced malformed curly leaves. A high frequency of adventitious shoot regeneration (96%) was observed in cultures of leaf explants excised from corn KNOX1-expressing transgenic plum shoots. In contrast to KNOX1-expressing tobacco, leaf and internode explants of corn KNOX1-expressing plum required synthetic cytokinin (thidiazuron) in the culture medium to induce adventitious shoot regeneration. The induction of high-frequency regeneration of adventitious shoots in vitro from leaves and stem internodal sections of plum through the ectopic expression of a KNOX1 gene is the first such report for a woody perennial fruit trees.

Plant hormone interactions: how complex are they?

Models describing plant hormone interactions are often complex and web-like. Here we assess several suggested interactions within one experimental system, elongating pea internodes. Results from this system indicate that at least some suggested interactions between auxin, gibberellins (GAs), brassinosteroids (BRs), abscisic acid (ABA) and ethylene do not occur in this system or occur in the reverse direction to that suggested. Furthermore, some of the interactions are relatively weak and may be of little physiological relevance. This is especially true if plant hormones are assumed to show a log-linear response curve as many empirical results suggest. Although there is strong evidence to support some interactions between hormones (e.g. auxin stimulating ethylene and bioactive GA levels), at least some of the web-like complexities do not appear to be justified or are overstated. Simpler and more targeted models may be developed by dissecting out key interactions with major physiological effects.

MACCHI-BOU 2 is required for early embryo patterning and cotyledon organogenesis in Arabidopsis

The phytohormone auxin is a key regulator of organogenesis in plants and is distributed asymmetrically via polar transport. However, the precise mechanisms underlying auxin-mediated organogenesis remain elusive. Here, we have analyzed the macchi-bou 2 (mab2) mutant identified in a pinoid (pid) enhancer mutant screen. Seedlings homozygous for either mab2 or pid showed only mild phenotypic effects on cotyledon positions and/or numbers. In contrast, mab2 pid double mutant seedlings completely lacked cotyledons, indicating a synergistic interaction. We found that mab2 homozygous embryos had defective patterns of cell division and showed aberrant cotyledon organogenesis. Further analysis revealed that the mab2 mutation affected auxin response but not auxin transport in the embryos, suggesting the involvement of MAB2 in auxin response during embryogenesis. MAB2 encodes an Arabidopsis ortholog of MED13, a putative regulatory module component of the Mediator complex. Mediator is a multicomponent complex that is evolutionarily conserved in eukaryotes and its regulatory module associates with Mediator to control the interaction of Mediator and RNA polymerase II. MAB2 interacts with a regulatory module component in yeast cells. Taken together, our data suggest that MAB2 plays a crucial role in embryo patterning and cotyledon organogenesis, possibly through modulating expression of specific genes such as auxin-responsive genes.

Class I KNOX genes are associated with organogenesis during bulbil formation in Agave tequilana

Bulbil formation in Agave tequilana was analysed with the objective of understanding this phenomenon at the molecular and cellular levels. Bulbils formed 14-45 d after induction and were associated with rearrangements in tissue structure and accelerated cell multiplication. Changes at the cellular level during bulbil development were documented by histological analysis. In addition, several cDNA libraries produced from different stages of bulbil development were generated and partially sequenced. Sequence analysis led to the identification of candidate genes potentially involved in the initiation and development of bulbils in Agave, including two putative class I KNOX genes. Real-time reverse transcription-PCR and in situ hybridization revealed that expression of the putative Agave KNOXI genes occurs at bulbil initiation and specifically in tissue where meristems will develop. Functional analysis of Agave KNOXI genes in Arabidopsis thaliana showed the characteristic lobed phenotype of KNOXI ectopic expression in leaves, although a slightly different phenotype was observed for each of the two Agave genes. An Arabidopsis KNOXI (knat1) mutant line (CS30) was successfully complemented with one of the Agave KNOX genes and partially complemented by the other. Analysis of the expression of the endogenous Arabidopsis genes KNAT1, KNAT6, and AS1 in the transformed lines ectopically expressing or complemented by the Agave KNOX genes again showed different regulatory patterns for each Agave gene. These results show that Agave KNOX genes are functionally similar to class I KNOX genes and suggest that spatial and temporal control of their expression is essential during bulbil formation in A. tequilana.

Co-ordination of developmental processes by small RNAs during leaf development

Leaf development entails the transition from a small group of undifferentiated cells to a structure of defined size and shape, highly organized into different cell types with specialized functions. During this developmental sequence, patterning, growth, and differentiation have to be tightly coordinated by intricate regulatory networks in which small RNAs [microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs)] have emerged during the last years as essential players. In this review, after having given an overview of miRNA and ta-siRNA biogenesis and mode of action, their contribution to the life of a leaf from initiation to senescence is described. MiRNA and ta-siRNA are not merely regulators of gene expression patterns, but, by acting both locally and at the whole organ scale, they have an essential role in the coordination of complex developmental processes and are fully integrated in genetic networks and signalling pathways.

KNOX overexpression in transgenic Kohleria (Gesneriaceae) prolongs the activity of proximal leaf blastozones and drastically alters segment fate

KNOX (knotted1-like homeobox) genes have a widely conserved role in the generation of dissected leaves. Ectopic KNOX activity in leaves in various angiosperm lineages causes leaf form changes that can elucidate how the configuration of leaf development evolved. We present an analysis of leaf morphology and morphogenesis in transgenic Kohleria lines overexpressing a heterologous KNOX gene. Kohleria, like many members of Gesneriaceae, has simple-serrated leaves with pinnate venation. KNOX overexpression causes prolonged segment proliferation in proximal, but not distal, parts of leaf blades. Elaborate dissected segments reiterate the zonation of the whole leaf, with organogenic activity persisting between a distal maturation zone and a proximal intercalary elongation zone. The architecture of vascular bundles is severely altered, with a reduced midvein and a more palmate venation. The initial establishment of organogenically competent primordial margins (marginal blastozones) and the onset of tissue differentiation in early stages of leaf development were similar in wild-type and KNOX overexpressing lines. However, leaves overexpressing KNOX often failed to fully mature, and persistent marginal blastozones were found at the base of blades in mature portions of the shoot. We conclude that KNOX-mediated perpetuation of marginal blastozones in Kohleria is sufficient to induce a set of processes that result in highly dissected leaflets, which are unusual in this plant family. Spatial confinement of blastozones between an early maturing tip and a late elongating petiole zone reflects the presence of distinct maturation processes that limit the ability of the leaf margins to respond to ectopic KNOX gene expression.

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 homologs are linked to the expression of lateral dominance in the acaulescent Streptocarpus rexii (Gesneriaceae)

Acaulescent species of Streptocarpus Lindl. show unusual patterns of growth, characterized by anisocotyly (i.e. the unequal growth of cotyledons after germination) and lack of a conventional embryonic shoot apical meristem (SAM). A SAM-like structure appears during post-embryonic development on the axis of the continuously growing cotyledon. Since we have shown previously that KNOX genes are involved in this unusual morphology of Streptocarpus rexii, here we investigated the expression pattern of WUSCHEL (WUS), which is also required for the indeterminacy of the SAM, but is expressed independently from KNOX in Arabidopsis thaliana. In A. thaliana WUSCHEL is involved in the maintenance of the stem cell fate in the organizing centre. The expression pattern of the WUS ortholog in S. rexii (SrWUS) strongly deviates from that of the model plant, suggesting a fundamentally different spatial and temporal regulation of signalling involved in meristem initiation and maintenance. In S. rexii, exogenous application of growth regulators, i.e. gibberellin (GA(3)), cytokinin (CK) and a gibberellin biosynthesis inhibitor (PAC), prevents anisocotyly and relocates meristematic cells to a position of conventional SAMs; this coincides with a re-localization of the two main pathways controlling meristem formation, the SrWUS and the KNOX pathways. Our results suggest that the establishment of a hormone imbalance in the seedlings is the basis of anisocotyly, causing a lateral dominance of the macrocotyledon over the microcotyledon. The peculiar morphogenetic program in S. rexii is linked to this delicate hormone balance and is the result of crosstalk between endogenous hormones and regulatory genes.

The peach (Prunus persica [L.] Batsch) homeobox gene KNOPE3, which encodes a class 2 knotted-like transcription factor, is regulated during leaf development and triggered by sugars

Class 1 KNOTTED1-like transcription factors (KNOX) are known to regulate plant development, whereas information on class 2 KNOX has been limited. The peach KNOPE3 gene was cloned, belonged to a family of few class 2 members and was located at 66 cM in the Prunus spp. G1 linkage-group. The mRNA localization was diversified in leaf, stem, flower and drupe, but recurred in all organ sieves, suggesting a role in sap nutrient transport. During leaf development, the mRNA earliest localized to primordia sieves and subsequently to mesophyll cells of growing leaves. Consistently, its abundance augmented with leaf expansion. The transcription was monitored in leaves responding to darkening, supply and transport block of sugars. It peaked at 4 h after darkness and dropped under prolonged obscurity, showing a similar kinetic to that of sucrose content variation. Feeding leaflets via the transpiration stream caused KNOPE3 up-regulation at 3 h after fructose, glucose and sucrose absorption and at 12 h after sorbitol. In girdling experiments, leaf KNOPE3 was triggered from 6 h onwards along with sucrose and sorbitol raise. Both the phloem-associated expression and sugar-specific gene modulation suggest that KNOPE3 may play a role in sugar translocation during the development of agro-relevant organs such as drupe.

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.

Small RNA regulation of rice homeobox genes

Recently, we reported the genome-wide identification of 107 homeobox genes in rice and classified them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. Microarray analysis revealed the tissue-specific and overlapping expression profiles of these genes during various stages of floral transition, panicle development and seed set. Several homeobox genes were also found to be differentially expressed under abiotic stress conditions. Based on massively parallel signature sequencing (MPSS) data analysis, we report here that a large number of small RNA signatures are associated with rice homeobox genes, which may be involved in their tissue-specific/developmental regulation and stress responses. The association of a very large number of small RNA signatures suggested an unusually high degree of regulation of homeobox genes by small RNAs during inflorescence development.

Evolution of developmental mechanisms in plants

As our understanding of developmental mechanisms in flowering plant species has become more advanced, an appreciation of the need to understand how distinct plant morphologies are generated has grown. This has led to an awareness of the key morphological differences in distinct land plant groups and to an assessment of the major innovations that occurred during land plant evolution. Recent advances demonstrate how developmental toolkits have been recruited for related purposes in different land plant groups, but the limited number of examples highlights both the infancy of the field and the difficulty of working with non-flowering plants.

Modulation of the hormone setting by Rhodococcus fascians results in ectopic KNOX activation in Arabidopsis

The biotrophic actinomycete Rhodococcus fascians has a profound impact on plant development and a common aspect of the symptomatology is the deformation of infected leaves. In Arabidopsis (Arabidopsis thaliana), the serrated leaf margins formed upon infection resemble the leaf phenotype of transgenic plants with ectopic expression of KNOTTED-like homeobox (KNOX) genes. Through transcript profiling, we demonstrate that class-I KNOX genes are transcribed in symptomatic leaves. Functional analysis revealed that BREVIPEDICELLUS/KNOTTED-LIKE1 and mainly SHOOT MERISTEMLESS were essential for the observed leaf dissection. However, these results also positioned the KNOX genes downstream in the signaling cascade triggered by R. fascians infection. The much faster activation of ARABIDOPSIS RESPONSE REGULATOR5 and the establishment of homeostatic and feedback mechanisms to control cytokinin (CK) levels support the overrepresentation of this hormone in infected plants due to the secretion by the pathogen, thereby placing the CK response high up in the cascade. Hormone measurements show a net decrease of tested CKs, indicating either that secretion by the bacterium and degradation by the plant are in balance, or, as suggested by the strong reaction of 35S:CKX plants, that other CKs are at play. At early time points of the interaction, activation of gibberellin 2-oxidase presumably installs a local hormonal setting favorable for meristematic activity that provokes leaf serrations. The results are discussed in the context of symptom development, evasion of plant defense, and the establishment of a specific niche by R. fascians.

Peach [Prunus persica (L.) Batsch] KNOPE1, a class 1 KNOX orthologue to Arabidopsis BREVIPEDICELLUS/KNAT1, is misexpressed during hyperplasia of leaf curl disease

Class 1 KNOTTED-like (KNOX) transcription factors control cell meristematic identity. An investigation was carried out to determine whether they maintain this function in peach plants and might act in leaf curliness caused by the ascomycete Taphrina deformans. KNOPE1 function was assessed by overexpression in Arabidopsis and by yeast two-hybrid assays with Arabidopsis BELL proteins. Subsequently, KNOPE1 mRNA and zeatin localization was monitored during leaf curl disease. KNOPE1 and Arabidopsis BREVIPEDICELLUS (BP) proteins fell into the same phyletic group and recognized the same BELL factors. 35S:KNOPE1 Arabidopsis lines exhibited altered traits resembling those of BP-overexpressing lines. In peach shoot apical meristem, KNOPE1 was expressed in the peripheral and central zones but not in leaf primordia, identically to the BP expression pattern. These results strongly suggest that KNOPE1 must be down-regulated for leaf initiation and that it can control cell meristem identity equally as well as all class 1 KNOX genes. Leaves attacked by T. deformans share histological alterations with class 1 KNOX-overexpressing leaves, including cell proliferation and loss of cell differentiation. Both KNOPE1 and a cytokinin synthesis ISOPENTENYLTRANSFERASE gene were found to be up-regulated in infected curled leaves. At early disease stages, KNOPE1 was uniquely triggered in the palisade cells interacting with subepidermal mycelium, while zeatin vascular localization was unaltered compared with healthy leaves. Subsequently, when mycelium colonization and asci development occurred, both KNOPE1 and zeatin signals were scattered in sectors of cell disorders. These results suggest that KNOPE1 misexpression and de novo zeatin synthesis of host origin might participate in hyperplasia of leaf curl disease.

Patterning and polarity in seed plant shoots

Leaves and stems are ultimately derived from the shoot apical meristem (SAM); leaves arise from the peripheral zone of the SAM and stem tissue is derived from both the peripheral and central zones of the SAM. Both the peripheral and central regions of the SAM are formed during embryogenesis when the basic body plan of the plant is established. Interplay between points of maximal concentration of auxin and specific patterns of transcription of both auxin-responsive transcription factors and other patterning genes subdivide the embryo along both the apical-basal and central-peripheral axes. Differential gene expression along these axes leads to the differentiation of tissues, lateral organs, meristems, and boundary regions, each with varying responsiveness to auxin. Subsequent shoot growth and development is a reiteration of basic patterning processes established during embryogenesis.

EFFECTOR OF TRANSCRIPTION2 is involved in xylem differentiation and includes a functional DNA single strand cutting domain

EFFECTORS OF TRANSCRIPTION2 (ET) are plant-specific regulatory proteins characterized by the presence of two to five C-terminal DNA- and Zn-binding repeats, and a highly conserved cysteine pattern. We describe the structural characterization of the three member Arabidopsis thaliana ET gene family and reveal some allelic sequence polymorphisms. A mutation analysis showed that AtET2 affects the expression of various KNAT genes involved in the maintenance of the undifferentiated state of cambial meristem cells. It also plays a role in the regulation of GA5 (gibberellin 3-beta-dioxygenase) and the cell-cycle-related GASA4. A correlation was established between AtET2 expression and the cellular differentiation state. AtET-GFP fusion proteins shuttle between the cytoplasm and nucleus, with the AtET2 product prevented from entering the nucleus in non-differentiating cells. Within the nucleus, AtET2 probably acts via a single strand cutting domain. A more general regulatory role for ET factors is proposed, governing cell differentiation in cambial meristems, a crucial process for the development of plant vascular tissues.

ATHB23, an Arabidopsis class I homeodomain-leucine zipper gene, is expressed in the adaxial region of young leaves

Homeobox genes are essential regulators of plant development. ATHB23, a class I homeodomain leucine zipper gene of Arabidopsis, was found to be induced by treatment with the phytohormone gibberellin (GA). In order to clarify its role in development, we performed a histochemical analysis of transgenic plants containing a construct with a GUS::GFP reporter under the control of the 1.5 kb upstream region of ATHB23. The construct was mainly expressed in young leaves and the styles of flowers but not in mature leaves. Microscopic examination of young leaves revealed that it was expressed in the adaxial domain of leaf primordia and the rib meristem. Expression of ATHB23, like that of GA5 encoding GA 20-oxidase, was reduced in mutants related to adaxial-abaxial leaf polarity (phb-1d, se-2, and kan1 kan2). Reduced expression of the GUS::GFP reporter gene was also observed in an se-2 background. These results indicate that ATHB23 is under the control of GA and other activators such as PHB, and is involved in establishing polarity during leaf development.

Differential transcription initiation and alternative RNA splicing of Knox7, a class 2 homeobox gene of maize

Knox7, a class 2 homeobox gene has been characterized in maize. A combination of experimental (3'- and 5'-RACE) and bioinformatics approaches supported the idea that Knox7 would be transcribed into two alternative transcripts by differential initiation of transcription. Sequence differences between alternative transcripts, Knox7L the larger and Knox7S the smaller, were confined to their 5' end regions and exon 1 was only found in Knox7L transcripts. Deduced proteins shared the same homeodomain, while an Ala and Ala/Gly rich domain was found only in KNOX7L protein. We hypothesize that KNOX7L and KNOX7S might regulate (differentially) the expression of the same gene(s) by binding competitively to the same cis-acting element(s). Further expression analysis using RT-PCR to amplify cDNA portions corresponding to ORFs of both Knox7 alternative transcripts showed that seven cDNA clones were probably generated by alternative splicing of Knox7L. Alignment of these sequences showed that they are in frame suggesting the existence of the corresponding proteins. Quantitative RT-PCR experiments indicated that Knox7S and Knox7L were expressed in maize embryos during germination. In the same tissue, expression of Knox7S was stimulated by light and ABA and inhibited by GA, two hormones that control germination process.

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.

The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism

Gibberellin (GA) biosynthesis is regulated by feedback control providing a mechanism for GA homeostasis in plants. However, regulatory elements involved in the feedback control are not known. In this report, we show that a rice (Oryza sativa) YABBY1 (YAB1) gene had a similar expression pattern as key rice GA biosynthetic genes GA3ox2 and GA20ox2. Overexpression of YAB1 in transgenic rice resulted in a semidwarf phenotype that could be fully rescued by applied GA. Quantification of the endogenous GA content revealed increases of GA(20) and decreases of GA(1) levels in the overexpression plants, in which the transcripts of the biosynthetic gene GA3ox2 were decreased. Cosuppression of YAB1 in transgenic plants induced expression of GA3ox2. The repression of GA3ox2 could be obtained upon treatment by dexamethasone of transgenic plants expressing a YAB1-glucocorticoid receptor fusion. Importantly, we show that YAB1 bound to a GA-responsive element within the GA3ox2 promoter. In addition, the expression of YAB1 was deregulated in GA biosynthesis and signaling mutants and could be either transiently induced by GA or repressed by a GA inhibitor. Finally, either overexpression or cosuppression of YAB1 impaired GA-mediated repression of GA3ox2. These data together suggest that YAB1 is involved in the feedback regulation of GA biosynthesis in rice.

A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development

YABBY and WUSCHEL-LIKE HOMEOBOX (WOX) genes have been shown to play important roles in lateral organ formation and meristem function. Here, we report the characterization of functional relationship between rice (Oryza sativa) YAB3 and WOX3 in rice leaf development. Rice YAB3 is closely related to maize (Zea mays) ZmYAB14 and Arabidopsis (Arabidopsis thaliana) FILAMENTOUS FLOWER (FIL), whereas rice WOX3 is highly conserved with maize narrow sheath1 (NS1) and NS2 and Arabidopsis PRESSED FLOWER (PRS). In situ hybridization experiments revealed that the expression of both genes was excluded from the shoot apical meristem, but the transcripts were detected in leaf primordia, young leaves, and reproductive organs without any polar distribution. The function of the two genes was studied by both overexpression and RNA interference (RNAi) in transgenic rice. YAB3 RNAi induced twisted and knotted leaves lacking specialized structures such as ligule and auricles, while no phenotypic change was observed in YAB3 overexpression plants, suggesting that rice YAB3 may be required for leaf cell growth and differentiation. Overexpression of WOX3 repressed YAB3 and showed a YAB3 RNAi phenotype. The expression of class I KNOTTED-LIKE HOMEOBOX (KNOX) genes was ectopically induced in leaves of YAB3 RNAi or WOX3 overexpression plants. Data from inducible WOX3 expression and DNA-protein interaction assays suggested that WOX3 acted as a transcriptional repressor of YAB3. These data reveal a regulatory network involving YAB3, WOX3, and KNOX genes required for rice leaf development.

Anisocotyly and meristem initiation in an unorthodox plant, Streptocarpus rexii (Gesneriaceae)

In common with most Old World Gesneriaceae; Streptocarpus Lindl. shows anisocotylous growth, i.e., the continuous growth of one cotyledon after germination. Linked to this phenomenon is an unorthodox behaviour of the shoot apical meristem (SAM) that determines the growth pattern of acaulescent species (subgenus Streptocarpus). In contrast caulescent species develop a conventional central post-embryonic SAM (mainly subgenus Streptocarpella). We used S. rexii Lindl. as a model to investigate anisocotyly and meristem initiation in Streptocarpus by using histological techniques and analyses of the expression pattern of the meristematic marker SrSTM1 during ontogeny. In contrast to Arabidopsis thaliana (L.) Heynh., S. rexii does not establish a SAM during embryogenesis, and the first evidence of a SAM-like structure occurs during post-embryonic development on the axis (the petiolode) between the two cotyledons. The expression pattern of SrSTM1 suggests a function in maintaining cell division activity in the cotyledons before becoming localized in the basal meristem, initially at the proximal ends of both cotyledons, later at the base of the continuously growing macrocotyledon, and the groove meristem on the petiolode. The latter is equivalent to a displaced SAM seemingly originating de novo under the influence of endogenous factors. Applied cytokinin retains SrSTM1expression in the small cotyledon, thus promoting isocotyly and re-establishment of a central post-embryonic SAM. Hormone-dependent delocalization of the process of meristem development could underlie anisocotyly and the unorthodox SAM formation in Streptocarpus.

The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis

CUP-SHAPED COTYLEDON1 (CUC1), CUC2, and CUC3 define the boundary domain around organs in the Arabidopsis thaliana meristem. CUC1 and CUC2 transcripts are targeted by a microRNA (miRNA), miR164, encoded by MIR164A, B, and C. We show that each MIR164 is transcribed to generate a large population of primary miRNAs of variable size with a locally conserved secondary structure around the pre-miRNA. We identified mutations in the MIR164A gene that deepen serration of the leaf margin. By contrast, leaves of plants overexpressing miR164 have smooth margins. Enhanced leaf serration was observed following the expression of an miR164-resistant CUC2 but not of an miR164-resistant CUC1. Furthermore, CUC2 inactivation abolished serration in mir164a mutants and the wild type, whereas CUC1 inactivation did not. Thus, CUC2 specifically controls leaf margin development. CUC2 and MIR164A are transcribed in overlapping domains at the margins of young leaf primordia, with transcription gradually restricted to the sinus, where the leaf margins become serrated. We suggest that leaf margin development is controlled by a two-step process in Arabidopsis. The pattern of serration is determined first, independently of CUC2 and miR164. The balance between coexpressed CUC2 and MIR164A then determines the extent of serration.

The role of hormones in shoot apical meristem function

Plant organs are produced in meristems in a continuous and predictable but nevertheless flexible manner. Phytohormones and transcription factors cooperate to balance meristem maintenance and organ production. Recent research has provided clues to the mechanisms underlying this cooperation. KNOTTED1-like homeobox (KNOX) and WUSCHEL (WUS) transcription factors facilitate high cytokinin activity in the shoot apical meristem (SAM), whereas high gibberellin and auxin activities promote the initiation of lateral organs at specific sites in the SAM flanks.

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.