Genetic control of branching in Arabidopsis and tomato

Spatio-temporal analysis of strawberry architecture: insights into the control of branching and inflorescence complexity

Plant architecture plays a major role in flowering and therefore in crop yield. Attempts to visualize and analyse strawberry plant architecture have been few to date. Here, we developed open-source software combining two- and three-dimensional representations of plant development over time along with statistical methods to explore the variability in spatio-temporal development of plant architecture in cultivated strawberry. We applied this software to six seasonal strawberry varieties whose plants were exhaustively described monthly at the node scale. Results showed that the architectural pattern of the strawberry plant is characterized by a decrease of the module complexity between the zeroth-order module (primary crown) and higher-order modules (lateral branch crowns and extension crowns). Furthermore, for each variety, we could identify traits with a central role in determining yield, such as date of appearance and number of branches. By modeling the spatial organization of axillary meristem fate on the zeroth-order module using a hidden hybrid Markov/semi-Markov mathematical model, we further identified three zones with different probabilities of production of branch crowns, dormant buds, or stolons. This open-source software will be of value to the scientific community and breeders in studying the influence of environmental and genetic cues on strawberry architecture and yield.

Plasticity of bud outgrowth varies at cauline and rosette nodes in Arabidopsis thaliana

Shoot branching is a complex mechanism in which secondary shoots grow from buds that are initiated from meristems established in leaf axils. The model plant Arabidopsis (Arabidopsis thaliana) has a rosette leaf growth pattern in the vegetative stage. After flowering initiation, the main stem elongates with the top leaf primordia developing into cauline leaves. Meristems in Arabidopsis initiate in the axils of rosette or cauline leaves, giving rise to rosette or cauline buds, respectively. Plasticity in the process of shoot branching is regulated by resource and nutrient availability as well as by plant hormones. However, few studies have attempted to test whether cauline and rosette branching are subject to the same plasticity. Here, we addressed this question by phenotyping cauline and rosette branching in three Arabidopsis ecotypes and several Arabidopsis mutants with varied shoot architectures. Our results showed no negative correlation between cauline and rosette branch numbers in Arabidopsis, demonstrating that there is no tradeoff between cauline and rosette bud outgrowth. Through investigation of the altered branching pattern of flowering pathway mutants and Arabidopsis ecotypes grown in various photoperiods and light regimes, we further elucidated that the number of cauline branches is closely related to flowering time. The number of rosette branches has an enormous plasticity compared with cauline branches and is influenced by genetic background, flowering time, light intensity, and temperature. Our data reveal different levels of plasticity in the regulation of branching at rosette and cauline nodes, and promote a framework for future branching analyses.

Histone Acetyltransferase SlGCN5 Regulates Shoot Meristem and Flower Development in Solanum lycopersicum

The histone acetyltransferase (HAT) general control non-repressed protein 5 (GCN5) plays important roles in plant development via epigenetic regulation of its target genes. However, the role of GCN5 in tomato, especially in the regulation of tomato shoot meristem and flower development, has not been well-understood. In this study, we found that silencing of Solanum lycopersicum GCN5 (SlGCN5, Solyc10g045400.1.1) by virus-induced gene silencing (VIGS) and RNA interference (RNAi) resulted in the loss of shoot apical dominance, reduced shoot apical meristem (SAM) size, and dwarf and bushy plant phenotype. Besides, we occasionally observed extra carpelloid stamens and carpels fused with stamens at the late stages of flower development. Through gene expression analysis, we noticed that SlGCN5 could enhance SlWUS transcript levels in both SAM and floral meristem (FM). Similar to the known function of GCN5 in Arabidopsis, we demonstrated that SIGCN5 may form a HAT unit with S. lycopersicum alteration/deficiency in activation 2a (SlADA2a) and SlADA2b proteins in tomato. Therefore, our results provide insights in the SlGCN5-mediated regulation of SAM maintenance and floral development in tomato.

How Strigolactone Shapes Shoot Architecture

Despite its central role in the control of plant architecture, strigolactone has been recognized as a phytohormone only 15 years ago. Together with auxin, it regulates shoot branching in response to genetically encoded programs, as well as environmental cues. A central determinant of shoot architecture is apical dominance, i.e., the tendency of the main shoot apex to inhibit the outgrowth of axillary buds. Hence, the execution of apical dominance requires long-distance communication between the shoot apex and all axillary meristems. While the role of strigolactone and auxin in apical dominance appears to be conserved among flowering plants, the mechanisms involved in bud activation may be more divergent, and include not only hormonal pathways but also sugar signaling. Here, we discuss how spatial aspects of SL biosynthesis, transport, and sensing may relate to apical dominance, and we consider the mechanisms acting locally in axillary buds during dormancy and bud activation.

Regulation of Early Plant Development by Red and Blue Light: A Comparative Analysis Between Arabidopsis thaliana and Solanum lycopersicum

In vertical farming, plants are grown in multi-layered growth chambers supplied with energy-efficient LEDs that produce less heat and can thus be placed in close proximity to the plants. The spectral quality control allowed by LED lighting potentially enables steering plant development toward desired phenotypes. However, this requires detailed knowledge on how light quality affects different developmental processes per plant species or even cultivar, and how well information from model plants translates to horticultural crops. Here we have grown the model dicot Arabidopsis thaliana (Arabidopsis) and the crop plant Solanum lycopersicum (tomato) under white or monochromatic red or blue LED conditions. In addition, seedlings were grown in vitro in either light-grown roots (LGR) or dark-grown roots (DGR) LED conditions. Our results present an overview of phenotypic traits that are sensitive to red or blue light, which may be used as a basis for application by tomato nurseries. Our comparative analysis showed that young tomato plants were remarkably indifferent to the LED conditions, with red and blue light effects on primary growth, but not on organ formation or flowering. In contrast, Arabidopsis appeared to be highly sensitive to light quality, as dramatic differences in shoot and root elongation, organ formation, and developmental phase transitions were observed between red, blue, and white LED conditions. Our results highlight once more that growth responses to environmental conditions can differ significantly between model and crop species. Understanding the molecular basis for this difference will be important for designing lighting systems tailored for specific crops.

The Roles of Plant Hormones and Their Interactions with Regulatory Genes in Determining Meristem Activity

Plants, unlike animals, have developed a unique system in which they continue to form organs throughout their entire life cycle, even after embryonic development. This is possible because plants possess a small group of pluripotent stem cells in their meristems. The shoot apical meristem (SAM) plays a key role in forming all of the aerial structures of plants, including floral meristems (FMs). The FMs subsequently give rise to the floral organs containing reproductive structures. Studies in the past few decades have revealed the importance of transcription factors and secreted peptides in meristem activity using the model plant Arabidopsis thaliana. Recent advances in genomic, transcriptomic, imaging, and modeling technologies have allowed us to explore the interplay between transcription factors, secreted peptides, and plant hormones. Two different classes of plant hormones, cytokinins and auxins, and their interaction are particularly important for controlling SAM and FM development. This review focuses on the current issues surrounding the crosstalk between the hormonal and genetic regulatory network during meristem self-renewal and organogenesis.

Deregulation of MADS-box transcription factor genes in a mutant defective in the WUSCHEL-LIKE HOMEOBOX gene EVERGREEN of Petunia hybrida

Angiosperm inflorescences develop in two fundamentally different ways. In monopodial plants, for example in Arabidopsis thaliana, the flowers are initiated as lateral appendages of a central indeterminate inflorescence meristem. In sympodial plants, flowers arise by terminal differentiation of the inflorescence meristem, while further inflorescence development proceeds from new sympodial meristems that are generated at the flank of the terminal flower. We have used the sympodial model species Petunia hybrida to investigate inflorescence development. Here, we describe a mutant, bonsai (bns), which is defective in flower formation, inflorescence branching, and control of meristem size. Detailed microscopic analysis revealed that bns meristems retain vegetative charateristics including spiral phyllotaxis. Consistent with a block in flower formation, bns mutants exhibit a deregulated expression of various MADS-box genes. Molecular analysis revealed that the bns mutant carries a transposon insertion in the previously described EVERGREEN (EVG) gene, which belongs to the WUSCHEL-LIKE HOMEOBOX (WOX) transcription factor gene family. EVG falls in the WOX9 subfamily, which has diverse developmental functions in angiosperms. The comparison of WOX9 orthologues in five model species for flowering shows that these genes play functionally divergent roles in monopodial and sympodial plants, indicating that the WOX9 regulatory node may have played an important role in the evolution of shoot architecture.

BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene

A mutant line, bifurcate flower truss (bif), was recovered from a tomato genetics programme. Plants from the control line produced a mean of 0.16 branches per truss, whereas the value for bif plants was 4.1. This increase in branching was accompanied by a 3.3-fold increase in flower number and showed a significant interaction with exposure to low temperature during truss development. The control line and bif genomes were resequenced and the bif gene was mapped to a 2.01 Mbp interval on chromosome 12; all coding region polymorphisms in the interval were surveyed, and five candidate genes displaying altered protein sequences were detected. One of these genes, SlMAPK1, encoding a mitogen-activated protein (MAP) kinase, contained a leucine to stop codon mutation predicted to disrupt kinase function. SlMAPK1 is an excellent candidate for bif because knock-out mutations of an Arabidopsis orthologue MPK6 were reported to have increased flower number. An introgression browser was used to demonstrate that the origin of the bif genomic DNA at the BIF locus was Solanum galapagense and that the SlMAPK1 null mutant is a naturally occurring allele widespread only on the Galápagos Islands. This work strongly implicates SlMAPK1 as part of the network of genes controlling inflorescence branching in tomato.

Axillary meristem initiation-a way to branch out

Plants differ from most animals in their retained ability to initiate new cycles of growth and development, which relies on the establishment and activity of branch meristems. In seed plants, branching is achieved by axillary meristems, which are established in the axil of each leaf base and develop into lateral branches. Research into axillary meristem initiation has identified transcription factors and phytohormones as key regulators. Based on these findings, a mechanistic framework for understanding axillary meristem initiation has emerged. Taking recent research into account, we discuss mechanisms underlying stem cell fate regulation that enable axillary meristem formation.

Genome-Wide Association Study Identifying Candidate Genes Influencing Important Agronomic Traits of Flax (Linum usitatissimum L.) Using SLAF-seq

Flax (Linum usitatissimum L.) is an important cash crop, and its agronomic traits directly affect yield and quality. Molecular studies on flax remain inadequate because relatively few flax genes have been associated with agronomic traits or have been identified as having potential applications. To identify markers and candidate genes that can potentially be used for genetic improvement of crucial agronomic traits, we examined 224 specimens of core flax germplasm; specifically, phenotypic data for key traits, including plant height, technical length, number of branches, number of fruits, and 1000-grain weight were investigated under three environmental conditions before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome-wide association study (GWAS) for these five agronomic traits. Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the important agronomic traits. Our analyses identified a total of 42 SNP loci that showed significant correlations with the five important agronomic flax traits. Next, candidate genes were screened in the 10 kb zone of each of the 42 SNP loci. These SNP loci were then analyzed by a more stringent screening via co-identification using both a general linear model (GLM) and a mixed linear model (MLM) as well as co-occurrences in at least two of the three environments, whereby 15 final candidate genes were obtained. Based on these results, we determined that UGT and PL are candidate genes for plant height, GRAS and XTH are candidate genes for the number of branches, Contig1437 and LU0019C12 are candidate genes for the number of fruits, and PHO1 is a candidate gene for the 1000-seed weight. We propose that the identified SNP loci and corresponding candidate genes might serve as a biological basis for improving crucial agronomic flax traits.

Genome-Wide Identification and Analysis of the MYB Transcription Factor Superfamily in Solanum lycopersicum

MYB proteins constitute one of the largest transcription factor families in the plant kingdom, members of which perform a variety of functions in plant biological processes. However, there are only very limited reports on the characterization of MYB transcription factors in tomato (Solanum lycopersicum). In our study, a total of 127 MYB genes have been identified in the tomato genome. A complete overview of these MYB genes is presented, including the phylogeny, gene structures, protein motifs, chromosome locations and expression patterns. The 127 SlMYB proteins could be classified into 18 subgroups based on domain similarity and phylogenetic topology. Phylogenetic analysis of SlMYBs along with MYBs from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) indicated 14 subfamilies. Conserved motifs outside the MYB domain may reflect their functional conservation. The identified tomato MYB genes were distributed on 12 chromosomes at various densities but mainly in chromosomes 6 and 10 (12.6% and 11.8%, respectively). Genome-wide segmental and tandem duplications were also found, which may contribute to the expansion of SlMYB genes. RNA-sequencing and microarray data revealed tissue-specific and stress-responsive expression patterns of SlMYB genes. The expression profiles of SlMYB genes in response to salicylic acid (SA) and jasmonic acid methyl ester (MeJA) were also investigated by real-time PCR. Moreover, ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motifs were found in 24 SlMYB proteins. Collectively, our comprehensive analysis of SlMYB genes will facilitate future functional studies of the tomato MYB gene family and probably other Solanaceae plants.

Physiological controls of chrysanthemum DgD27 gene expression in regulation of shoot branching

DgD27 was cloned from D. grandiflorum for the first time and played an important role in shoot branching of chrysanthemum. Shoot branching plays an important role in determining plant architecture. D27 was previously proven to be involved in the strigolactone biosynthetic pathway in rice, Arabidopsis, and Medicago. To investigate the role of D27 in shoot branching of chrysanthemum, we isolated the D27 homolog DgD27. Functional analysis showed that DgD27 was a plastid-localized protein that restored the phenotype of Arabidopsis d27-1. Gene expression analysis revealed that DgD27 was expressed at the highest levels in stem, and was up-regulated by exogenous auxin. Decapitation could down-regulate DgD27 expression, but this effect could be restored by exogenous auxin. DgD27 expression was significantly down-regulated by dark treatment in axillary buds. In addition, DgD27 transcripts produced rapid responses in shoots and roots under conditions of phosphate absence, but only mild variation in responses in buds, stems, and roots with low nitrogen treatment. DgBRC1 transcripts also showed the same response in buds under low nitrogen conditions. Under phosphate deficiency, indole-3-acetic acid (IAA) levels increased, zeatin riboside levels decreased, and abscisic acid (ABA) levels increased in the shoot, while both IAA and ABA levels increased in the shoot under low nitrogen treatments. Gibberellin acid levels were unaffected by phosphate deficiency and low nitrogen treatments. Taken together, these results demonstrated the diverse roles of DgD27 in response to physiological controls in chrysanthemum shoot branching.

Major Contribution of Flowering Time and Vegetative Growth to Plant Production in Common Bean As Deduced from a Comparative Genetic Mapping

Determinacy growth habit and accelerated flowering traits were selected during or after domestication in common bean. Both processes affect several presumed adaptive traits such as the rate of plant production. There is a close association between flowering initiation and vegetative growth; however, interactions among these two crucial developmental processes and their genetic bases remain unexplored. In this study, with the aim to establish the genetic relationships between these complex processes, a multi-environment quantitative trait locus (QTL) mapping approach was performed in two recombinant inbred line populations derived from inter-gene pool crosses between determinate and indeterminate genotypes. Additive and epistatic QTLs were found to regulate flowering time, vegetative growth, and rate of plant production. Moreover, the pleiotropic patterns of the identified QTLs evidenced that regions controlling time to flowering traits, directly or indirectly, are also involved in the regulation of plant production traits. Further QTL analysis highlighted one QTL, on the lower arm of the linkage group Pv01, harboring the Phvul.001G189200 gene, homologous to the Arabidopsis thaliana TERMINAL FLOWER1 (TFL1) gene, which explained up to 32% of phenotypic variation for time to flowering, 66% for vegetative growth, and 19% for rate of plant production. This finding was consistent with previous results, which have also suggested Phvul.001G189200 (PvTFL1y) as a candidate gene for determinacy locus. The information here reported can also be applied in breeding programs seeking to optimize key agronomic traits, such as time to flowering, plant height and an improved reproductive biomass, pods, and seed size, as well as yield.

Roles of DgD14 in regulation of shoot branching in chrysanthemum (Dendranthema grandiflorum 'Jinba')

Shoot branching plays an important role in determining plant architecture. Strigolactones (SLs) negatively regulate shoot branching, and can respond to conditions of low or absent phosphate or nitrogen. The D14 gene is a probable candidate as an SL receptor in rice, petunia, and Arabidopsis. To investigate the roles of D14 in shoot branching of chrysanthemum, we isolated the D14 homolog DgD14. Functional analysis showed that DgD14 was a nuclear-localized protein, and restored the phenotype of Arabidopsis d14-1. Exogenous SL (GR24) could down-regulate DgD14 expression, but this effect could be overridden by apical auxin application. Decapitation could down-regulate DgD14 expression, but this effect could be restored by exogenous auxin. In addition, DgD14 transcripts produced rapid responses in shoot and root under conditions of phosphate absence, but only a mild variation in bud and stem with low nitrogen treatment. Indistinct reductions of P levels in shoot were observed in plants grown under low nitrogen conditions. The absence of phosphate and low levels of nitrogen negatively affected plant growth. These results demonstrate that P levels in shoot had a close relationship with phosphate, whereas nitrogen did not directly regulate DgD14 expression in shoot. Taken together, these results demonstrated that DgD14 was the functional strigolactone signaling component in chrysanthemum.

Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp.)

Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154) derived from a cross between BA3 (C. annuum) and YNXML (C. frutescens). Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147) in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

Capsicum annuum S (CaS) promotes reproductive transition and is required for flower formation in pepper (Capsicum annuum)

The genetic control of the transition to flowering has mainly been studied in model species, while few data are available in crop species such as pepper (Capsicum spp.). To elucidate the genetic control of the transition to flowering in pepper, mutants that lack flowers were isolated and characterized. Genetic mapping and sequencing allowed the identification of the gene disrupted in the mutants. Double mutants and expression analyses were used to characterize the relationships between the mutated gene and other genes controlling the transition to flowering and flower differentiation. The mutants were characterized by a delay in the initiation of sympodial growth, a delay in the termination of sympodial meristems and complete inhibition of flower formation. Capsicum annuum S (CaS), the pepper (Capsicum annuum) ortholog of tomato (Solanum lycopersicum) COMPOUND INFLORESCENCE and petunia (Petunia hybrida) EVERGREEN, was found to govern the mutant phenotype. CaS is required for the activity of the flower meristem identity gene Ca-ANANTHA and does not affect the expression of CaLEAFY. CaS is epistatic over other genes controlling the transition to flowering with respect to flower formation. Comparative homologous mutants in the Solanaceae indicate that CaS has uniquely evolved to have a critical role in flower formation, while its role in meristem maturation is conserved in pepper, tomato and petunia.

What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape

Domestication of fruit and vegetables resulted in a huge diversity of shapes and sizes of the produce. Selections that took place over thousands of years of alleles that increased fruit weight and altered shape for specific culinary uses provide a wealth of resources to study the molecular bases of this diversity. Tomato (Solanum lycopersicum) evolved from a wild ancestor (S. pimpinellifolium) bearing small and round edible fruit. Molecular genetic studies led to the identification of two genes selected for fruit weight: FW2.2 encoding a member of the Cell Number Regulator family; and FW3.2 encoding a P450 enzyme and the ortholog of KLUH. Four genes were identified that were selected for fruit shape: SUN encoding a member of the IQD family of calmodulin-binding proteins leading to fruit elongation; OVATE encoding a member of the OVATE family proteins involved in transcriptional repression leading to fruit elongation; LC encoding most likely the ortholog of WUSCHEL controlling meristem size and locule number; FAS encoding a member in the YABBY family controlling locule number leading to flat or oxheart shape. For this article, we will provide an overview of the putative function of the known genes, when during floral and fruit development they are hypothesized to act and their potential importance in regulating morphological diversity in other fruit and vegetable crops.

Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS

Human immunodeficiency virus intra-host recombination has never been studied in vivo both during early infection and throughout disease progression. The CD8-depleted rhesus macaque model of neuroAIDS was used to investigate the impact of recombination from early infection up to the onset of neuropathology in animals inoculated with a simian immunodeficiency virus (SIV) swarm. Several lymphoid and non-lymphoid tissues were collected longitudinally at 21 days post-infection (p.i.), 61 days p.i. and necropsy (75-118 days p.i.) from four macaques that developed SIV-encephalitis or meningitis, as well as from two animals euthanized at 21 days p.i. The number of recombinant sequences and breakpoints in different tissues and over time from each primate were compared. Breakpoint locations were mapped onto predicted RNA and protein secondary structures. Recombinants were found at each time point and in each primate as early as 21 days p.i. No association was found between recombination rates and specific tissue of origin. Several identical breakpoints were identified in sequences derived from different tissues in the same primate and among different primates. Breakpoints predominantly mapped to unpaired nucleotides or pseudoknots in RNA secondary structures, and proximal to glycosylation sites and cysteine residues in protein sequences, suggesting selective advantage in the emergence of specific recombinant sequences. Results indicate that recombinant sequences can become fixed very early after infection with a heterogeneous viral swarm. Features of RNA and protein secondary structure appear to play a role in driving the production of recombinants and their selection in the rapid disease model of neuroAIDS.

Identification and functional analysis of three MAX2 orthologs in chrysanthemum

MORE AXILLARY BRANCHING 2 (MAX2), initially identified in Arabidopsis thaliana, is a key regulatory gene in strigolactone signal transduction. Three orthologs of MAX2 were cloned from Dendranthema grandiflorum (DgMAX2a, b, and c). Each of the genes has an open reading frame of 2,049 bp and encodes 682 amino acid proteins. The predicted amino acid sequences of the three DgMAX2s are most closely related to the MAX2 orthologs identified in petunia (PhMAX2A and PhMAX2B), and display the highest amino acid sequence similarity with PhMAX2A compared to other MAX2s. Expression analysis revealed that DgMAX2s are predominantly expressed in the stem and axillary buds. On a cellular level, we localized the DgMAX2a::GFP fusion protein to the nucleus in onion epidermal cells, which is consistent with the nuclear localization of MAX2 in Arabidopsis. The chrysanthemum DgMAX2a is able to restore the max2-1 mutant branching to wild-type (WT) Arabidopsis, suggesting that it is a functional MAX2 ortholog. These results suggest that DgMAX2s may be candidate genes for reducing the shoot branching of chrysanthemum.

The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis

Plant-specific DOF (DNA-binding with one finger)-type transcription factors regulate various biological processes. In the present study we characterized a silique-abundant gene AtDOF (Arabidopsis thaliana DOF) 4.2 for its functions in Arabidopsis. AtDOF4.2 is localized in the nuclear region and has transcriptional activation activity in both yeast and plant protoplast assays. The T-M-D motif in AtDOF4.2 is essential for its activation. AtDOF4.2-overexpressing plants exhibit an increased branching phenotype and mutation of the T-M-D motif in AtDOF4.2 significantly reduces branching in transgenic plants. AtDOF4.2 may achieve this function through the up-regulation of three branching-related genes, AtSTM (A. thaliana SHOOT MERISTEMLESS), AtTFL1 (A. thaliana TERMINAL FLOWER1) and AtCYP83B1 (A. thaliana CYTOCHROME P450 83B1). The seeds of an AtDOF4.2-overexpressing plant show a collapse-like morphology in the epidermal cells of the seed coat. The mucilage contents and the concentration and composition of mucilage monosaccharides are significantly changed in the seed coat of transgenic plants. AtDOF4.2 may exert its effects on the seed epidermis through the direct binding and activation of the cell wall loosening-related gene AtEXPA9 (A. thaliana EXPANSIN-A9). The dof4.2 mutant did not exhibit changes in branching or its seed coat; however, the silique length and seed yield were increased. AtDOF4.4, which is a close homologue of AtDOF4.2, also promotes shoot branching and affects silique size and seed yield. Manipulation of these genes should have a practical use in the improvement of agronomic traits in important crops.

The tomato genome: implications for plant breeding, genomics and evolution

The genome sequence of tomato (Solanum lycopersicum), one of the most important vegetable crops, has recently been decoded. We address implications of the tomato genome for plant breeding, genomics and evolutionary studies, and its potential to fuel future crop biology research.

CaBLIND regulates axillary meristem initiation and transition to flowering in pepper

Plant architecture is a major motif in plant diversity. The shape of the plant is regulated by genes that have been found to have similar or related functions in different species. However, changes in gene regulation or their recruitment to additional developmental pathways contribute to the wide range of plant patterns. Our aim was to unravel the genetic mechanisms governing the unique architecture of pepper (Capsicum annuum) and to determine whether these genetic factors have conserved functions in other plant species. We describe the pepper CaBLIND (CaBL) gene that is orthologous to the tomato (Solanum lycopersicum) BLIND (BL) and to the Arabidopsis thaliana REGULATOR OF AXILLARY MERISTEMS (RAX). We identified two allelic Cabl mutants that show dramatic reduction in axillary meristem initiation. In addition, Cabl exhibits late flowering and ectopic vegetative growth during the reproductive phase. Double-mutant and expression analyses suggest that CaBL functions independently of FASCICULATE, the pepper ortholog of SELF PRUNING in regulating sympodial growth, but is epistatic to FASCICULATE in controlling axillary meristem formation. Furthermore, CaBL operates independently of CaREVOLUTA and CaLATERAL SUPPRESSOR in regulating axillary branching. Our results provide evidence of CaBL's conserved function with BL and RAX genes in regulating axillary meristem initiation early in development. In addition, similar to BL but opposite to RAX, CaBL acts to promote the transition from vegetative to reproductive phase. However, in contrast to BL and RAX, CaBL is co-opted to play a role in suppressing vegetative growth during the reproductive phase in pepper.

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.

Mint essential oil can induce or inhibit potato sprouting by differential alteration of apical meristem

Sprouting of potatoes during storage, due to tuber dormancy release, is associated with weight loss and softening. Sprout-preventing chemicals, such as chlorpropham (CIPC), can negatively impact the environment and human health. Monthly thermal fogging with mint (Mentha spicata L.) essential oil (MEO) inhibited sprouting in eight potato cultivars during large-volume 6-month storage: the tubers remained firm with 38% lower weight loss after 140 days of storage. The sprout-inhibitory action may be nullified: treated tubers washed with water resumed sprouting within days, with reduced apical dominance. MEO application caused local necrosis of the bud meristem, and a few weeks later, axillary bud (AX) growth was induced in the same sprouting eye. MEO components analysis showed that 73% of its content is the monoterpene R-carvone. Tubers treated with synthetic R-carvone in equivalent dose, 4.5 microl l(-1), showed an inhibitory effect similar to that of MEO. Surprisingly, 0.5 microl l(-1) of MEO or synthetic R-carvone catalyzed AX sprouting in the tuber. To the best of our knowledge, this is the first report of an essential oil vapor inducing early sprouting of potato tubers. R-carvone caused visible damage to the meristem membrane at sprout-inhibiting, but not sprout-inducing doses, suggesting different underlying mechanisms. After 5 days' exposure to R-carvone, its derivatives transcarveol and neo-dihydrocarveol were found in buds of tubers treated with the inhibitory dose, suggesting biodegradation. These experiments demonstrate the potential of MEO vapor as an environmentally friendly alternative to CIPC in stored potatoes and as a research tool for the control of sprouting in plants.

The making of a compound inflorescence in tomato and related nightshades

Variation in the branching of plant inflorescences determines flower number and, consequently, reproductive success and crop yield. Nightshade (Solanaceae) species are models for a widespread, yet poorly understood, program of eudicot growth, where short side branches are initiated upon floral termination. This “sympodial” program produces the few-flowered tomato inflorescence, but the classical mutants compound inflorescence (s) and anantha (an) are highly branched, and s bears hundreds of flowers. Here we show that S and AN, which encode a homeobox transcription factor and an F-box protein, respectively, control inflorescence architecture by promoting successive stages in the progression of an inflorescence meristem to floral specification. S and AN are sequentially expressed during this gradual phase transition, and the loss of either gene delays flower formation, resulting in additional branching. Independently arisen alleles of s account for inflorescence variation among domesticated tomatoes, and an stimulates branching in pepper plants that normally have solitary flowers. Our results suggest that variation of Solanaceae inflorescences is modulated through temporal changes in the acquisition of floral fate, providing a flexible evolutionary mechanism to elaborate sympodial inflorescence shoots.

Among the most distinguishing features of plants are the flower-bearing shoots, called inflorescences. Despite a solid understanding of flower development, the molecular mechanisms that control inflorescence architecture remain obscure. We have explored this question in tomato, where mutations in two genes, ANANTHA (AN) and COMPOUND INFLORESCENCE (S), transform the well-known tomato “vine” into a highly branched structure with hundreds of flowers. We find that AN encodes an F-box protein ortholog of a gene called UNUSUAL FLORAL ORGANS that controls the identity of floral organs (petals, sepals, and so on), whereas S encodes a transcription factor related to a gene called WUSCHEL HOMEOBOX 9 that is involved in patterning the embryo within the plant seed. (F-box proteins are known for marking other proteins for degradation, but they can also function in hormone regulation and transcriptional activation) Interestingly, these genes have little or no effect on branching in inflorescences that grow continuously (so-called “indeterminate” shoots), as in Arabidopsis. However, we find that transient sequential expression of S followed by AN promotes branch termination and flower formation in plants where meristem growth ends with inflorescence and flower production (“determinate” shoots). We show that mutant alleles of s dramatically increase branch and flower number and have probably been selected for by breeders during modern cultivation. Moreover, the single-flower inflorescence of pepper (a species related to tomato, within the same Solanaceae family) can be converted to a compound inflorescence upon mutating its AN ortholog. Our results suggest a new developmental mechanism whereby inflorescence elaboration can be controlled through temporal regulation of floral fate.

Plant flower production is largely determined by the number of inflorescences, the branches produced on flower stems. Two genes identified in tomato reveal a new phase transition that may explain the mechanism of evolution of compound inflorescences in the Solanaceae family.

Tomato (Solanum lycopersicum): A Model Fruit-Bearing Crop

INTRODUCTIONTomato (Solanum lycopersicum) is one of the most important vegetable plants in the world. It originated in western South America, and domestication is thought to have occurred in Central America. Because of its importance as food, tomato has been bred to improve productivity, fruit quality, and resistance to biotic and abiotic stresses. Tomato has been widely used not only as food, but also as research material. The tomato plant has many interesting features such as fleshy fruit, a sympodial shoot, and compound leaves, which other model plants (e.g., rice and Arabidopsis) do not have. Most of these traits are agronomically important and cannot be studied using other model plant systems. There are 13 recognized wild tomato species that display a great variety of phenotypes and can be crossed with the cultivated tomato. These wild tomatoes are important for breeding, as sources of desirable traits, and for evolutionary studies. Current progress on the tomato genome sequencing project has generated useful information to help in the study of tomato. In addition, the tomato belongs to the extremely large family Solanaceae and is closely related to many commercially important plants such as potato, eggplant, peppers, tobacco, and petunias. Knowledge obtained from studies conducted on tomato can be easily applied to these plants, which makes tomato important research material. Because of these facts, tomato serves as a model organism for the family Solanaceae and, specifically, for fleshy-fruited plants.

Apple shoot architecture: evidence for strong variability of bud size and composition and hydraulics within a branching zone

* In the apple tree (Malus domestica), shoot architecture - the distribution of lateral bud types and growth along the parent shoot - has been extensively investigated. The distal zone of a shoot is characterized by a high proportion of vegetative or floral axillary branches mixed with latent buds and aborted laterals. The hypothesis tested here was that bud development was related to hydraulic conductance of the sap pathway to the bud, independently of an acrotonic (proximal vs distal) effect. * The distal zone of 1-yr-old shoots was studied on five cultivars for bud size and composition (number of appendages) and hydraulic conductance before bud burst. * Bud size, composition and hydraulic conductance were highly variable for all cultivars. A positive correlation was demonstrated between both the number of cataphylls and green-leaf primordia, and hydraulic conductance. Cultivar and bud size affected the intercept of these relationships more than the slope, suggesting similar scaling between these variables, but different hydraulic efficiencies. A great proportion of small buds were also characterized by null values of hydraulic conductance. * This study suggests that hydraulically mediated competition exists between adjacent buds within the same branching zone, prefiguring the variability of lateral types in the following growing season. It is hypothesized that this developmental patterning is driven by hydraulic characteristics of the whole metamer, including the subtending leaf, during bud development.

The origin, initiation and development of axillary shoot meristems in Lotus japonicus

BACKGROUND AND AIMS

Lotus japonicus 'Gifu' develops multiple axillary shoots in the cotyledonary node region throughout the growth of the plant. The origin, initiation and development of these axillary meristems were investigated.

METHODS

Morphological, histological and mRNA in situ analyses were done to characterize the ontogeny of cotyledonary axillary shoot meristems in Lotus. Morphological characterization of a putative Lotus shoot branching mutant (super-accessory branches) sac, is presented.

KEY RESULTS

By using expression of an L. japonicus STM-like gene as a marker for meristematic tissues, it was demonstrated that groups of cells maintained in the meristematic state at the cotyledonary axil region coincide with the sites where additional axillary meristems (accessory meristems) form. A Lotus shoot branching mutant, sac, is a putative Lotus branching mutant characterized by increased proliferation of accessory shoots in all leaf axils including the cotyledons.

CONCLUSION

In Lotus, axillary shoot meristems continually develop at the cotyledonary node region throughout the growth of the plant. These cotyledonary primary and accessory axillaries arise from the position of a meristematic zone of tissue at the cotyledonary node axil region.

Something on the side: axillary meristems and plant development

Axillary meristems allow the production of secondary growth axes in the shoot systems of plants. As such they make a large contribution to the plastic developmental potential of plants, allowing them to alter their architecture to suit the prevailing environment conditions. This review focuses on the formation and activity of axillary meristems, across several model species. Current topics and problems in the field are discussed.

JOINTLESS suppresses sympodial identity in inflorescence meristems of tomato

Unlike monopodial plants, in which flowering terminates growth of a shoot, plants exhibiting sympodial shoot architecture maintain the potential for indeterminate growth even after converting to floral development. This vegetative indeterminacy is conferred by a special type of axillary meristem, the sympodial meristem, which exhibits precocious but determinate growth. The reiterative formation of sympodial meristems as the plant grows results in a shoot composed of a series of modules, each consisting of a limited number of vegetative nodes and terminated by a flower or inflorescence. To determine how sympodial meristems differ from other shoot meristems, we examined interactions between mutations that affect various shoot meristem types in tomato (Lycopersicon esculentum Mill.). Analysis of double mutant combinations of jointless, lateral suppressor, self-pruning, blind, and anantha showed that sympodial meristems share regulatory features with inflorescence meristems. Genetic studies on the jointless mutation implicated this gene in suppressing sympodial meristem fate in the inflorescence. As this mutation has a second phenotype, the elimination of the pedicel abscission zone, we examined the expression pattern of JOINTLESS to test whether pedicel development is involved in directing shoot architecture. We found that this MADS box gene is expressed in a variety of shoot meristems, including inflorescence, floral, sympodial, and axillary meristems, as well as in early staged floral organs, in sporogenous tissues of anthers, and in ovules. Lack of expression in developing pedicels indicates abscission zone development does not rely on JOINTLESS transcription in the differentiating cells. We conclude that the primary role of JOINTLESS is to suppress sympodial meristem identity in inflorescence meristems.

Shoot and inflorescence branching

A major aspect of postembryonic plant development is the formation of secondary axes of growth: vegetative branches, inflorescence branches, or flowers. The first step in side-shoot development is the establishment of lateral meristems in the axils of leaves. GRAS-, MYB-, and bHLH-type transcription factors act as key regulators of early steps in this process. The REVOLUTA subfamily of HD-ZIP transcription factors controls the organization of lateral meristems. Whereas the development of lateral meristems into lateral buds is only poorly understood, recent studies have provided new insights into the regulation of lateral bud outgrowth. The MORE AXILLARY GROWTH (MAX) genes of Arabidopsis and the RAMOSUS (RMS) genes of pea are involved in the production, perception, and transduction of a signal that inhibits lateral bud outgrowth. Synthesis of this not-yet-identified hormone is positively regulated by the main shoot tip through auxin signalling.

Manipulation of the blue light photoreceptor cryptochrome 2 in tomato affects vegetative development, flowering time, and fruit antioxidant content

Cryptochromes are blue light photoreceptors found in plants, bacteria, and animals. In Arabidopsis, cryptochrome 2 (cry2) is involved primarily in the control of flowering time and in photomorphogenesis under low-fluence light. No data on the function of cry2 are available in plants, apart from Arabidopsis (Arabidopsis thaliana). Expression of the tomato (Solanum lycopersicum) CRY2 gene was altered through a combination of transgenic overexpression and virus-induced gene silencing. Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light), but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits. The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes. CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches. Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants, whereas in wild-type plants it causes a minor internode elongation.

Suppression of tiller bud activity in tillering dwarf mutants of rice

In this study, we analyzed five tillering dwarf mutants that exhibit reduction of plant stature and an increase in tiller numbers. We show that, in the mutants, axillary meristems are normally established but the suppression of tiller bud activity is weakened. The phenotypes of tillering dwarf mutants suggest that they play roles in the control of tiller bud dormancy to suppress bud activity. However, tillering dwarf mutants show the dependence of both node position and planting density on their growth, which implies that the functions of tillering dwarf genes are independent of the developmental and environmental control of bud activity. Map-based cloning of the D3 gene revealed that it encodes an F-box leucine-trich repeat (LRR) protein orthologous to Arabidopsis MAX2/ORE9. This indicates the conservation of mechanisms controlling axillary bud activity between monocots and eudicots. We suggest that tillering dwarf mutants are suitable for the study of bud activity control in rice and believe that future molecular and genetic studies using them may enable significant progress in understanding the control of tillering and shoot branching.

Shoot branching

All plant shoots can be described as a series of developmental modules termed phytomers, which are produced from shoot apical meristems. A phytomer generally consists of a leaf, a stem segment, and a secondary shoot meristem. The fate and activity adopted by these secondary, axillary shoot meristems is the major source of evolutionary and environmental diversity in shoot system architecture. Axillary meristem fate and activity are regulated by the interplay of genetic programs with the environment. Recent results show that these inputs are channeled through interacting hormonal and transcription factor regulatory networks. Comparison of the factors involved in regulating the function of diverse axillary meristem types both within and between species is gradually revealing a pattern in which a common basic program has been modified to produce a range of axillary meristem types.

Shoot branching

The mature form of a plant shoot system is an expression of several genetically controlled traits, many of which are also environmentally regulated. A major component of this architectural variation is the degree of shoot branching. Recent results indicate conserved mechanisms for shoot branch development across the monocots and eudicots. The existence of a novel long-range branch-inhibiting signal has been inferred from studies of branching mutants in pea and Arabidopsis.

Meristem fate and bulbil formation in Titanotrichum (Gesneriaceae)

Titanotrichum oldhamii (a monotypic genus from Taiwan, Okinawa, and adjacent regions of China) has inflorescences bearing either showy yellow flowers or asexual bulbils. Asexual reproduction by bulbils is important in natural populations, and bulbil production increases in August and September at the end of the flowering season (which runs from June to the end of September). The bulbils are small (∼1-2.5 mm long) and numerous. They consist of a small portion of stem (bract-stem) topped by opposite storage bracts that enclose a minute apical meristem. A secondary root develops from the side of the bract-stem. The floral meristem of T. oldhamii has three possible fates: (1) bulbil formation, (2) flower formation, or (3) bracteose proliferation. Bracteose proliferation rarely occurs and appears to be a developmental transition between the bulbiliferous and racemose inflorescence forms. It is strongly reminiscent of the floricaula and squamosa mutants of Antirrhinum. In the bulbiliferous form a single floral primordium, which would normally produce one flower, gives rise to ∼50-70 bulbils by repeated subdivision of the meristem. This form of bulbil production appears to be unique to Titanotrichum. Occasionally a floral meristem divides, but the subdivision forms multiflowered units of up to four flowers rather than bulbils, suggesting that meristem fate is reversible up to the first or second meristem subdivision. In Titanotrichum, therefore, primordium fate is apparently not determined at inception but becomes irreversibly determined shortly after the appearance of developmental characteristics of the floral or bulbil pathway.

Regulation of shoot branching by auxin

The idea that apically derived auxin inhibits shoot branching by inhibiting the activity of axillary buds was first proposed 70 years ago, but it soon became clear that its mechanism of action was complex and indirect. Recent advances in the study of axillary bud development and of auxin signal transduction are allowing a better understanding of the role of auxin in controlling shoot branching. These studies have identified a new role for auxin early in bud development as well as some of the second messengers involved in mediating the branch-inhibiting effects of auxin.

Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation

In seed plants, shoot branching is initiated by the formation of new meristems in the axils of leaves, which subsequently develop into new axes of growth. This study describes the genetic control of axillary meristem formation by the LATERAL SUPPRESSOR (LAS) gene in Arabidopsis thaliana. las mutants show a novel phenotype that is characterized by the inability to form lateral shoots during vegetative development. The analysis shows that axillary meristem formation is differently regulated during different phases of development. During reproductive development, axillary meristems initiate in close proximity to the shoot apical meristem and do not require LAS function. In contrast, during the vegetative phase, axillary meristems initiate at a distance to the SAM and require LAS function. This control mechanism is conserved between the distantly related species tomato and Arabidopsis. Monitoring the patterns of LAS and SHOOT MERISTEMLESS transcript accumulation allowed us to identify early steps in the development of leaf axil identity, which seem to be a prerequisite for axillary meristem initiation. Other regulators of shoot branching, like REVOLUTA and AUXIN RESISTANT 1, act downstream of LAS. The results are discussed in the context of the "detached meristem" and the "de novo formation" concepts of axillary meristem formation.

Suppression of a vegetative MADS box gene of potato activates axillary meristem development

Potato MADS box 1 (POTM1) is a member of the SQUAMOSA-like family of plant MADS box genes isolated from an early stage tuber cDNA library. The RNA of POTM1 is most abundant in vegetative meristems of potato (Solanum tuberosum), accumulating specifically in the tunica and corpus layers of the meristem, the procambium, the lamina of new leaves, and newly formed axillary meristems. Transgenic lines with reduced levels of POTM1 mRNA exhibited decreased apical dominance accompanied by a compact growth habit and a reduction in leaf size. Suppression lines produced truncated shoot clusters from stem buds and, in a model system, exhibited enhanced axillary bud growth instead of producing a tuber. This enhanced axillary bud growth was not the result of increased axillary bud formation. Tuber yields were reduced and rooting of cuttings was strongly inhibited in POTM1 suppression lines. Both starch accumulation and the activation of cell division occurred in specific regions of the vegetative meristems of the POTM1 transgenic lines. Cytokinin levels in axillary buds of a transgenic suppression line increased 2- to 3-fold. These results imply that POTM1 mediates the control of axillary bud development by regulating cell growth in vegetative meristems.

Down-regulation of TM29, a tomato SEPALLATA homolog, causes parthenocarpic fruit development and floral reversion

We have characterized the tomato (Lycopersicon esculentum Mill.) MADS box gene TM29 that shared a high amino acid sequence homology to the Arabidopsis SEP1, 2, and 3 (SEPALLATA1, 2, and 3) genes. TM29 showed similar expression profiles to SEP1, with accumulation of mRNA in the primordia of all four whorls of floral organs. In addition, TM29 mRNA was detected in inflorescence and vegetative meristems. To understand TM29 function, we produced transgenic tomato plants in which TM29 expression was down-regulated by either cosuppression or antisense techniques. These transgenic plants produced aberrant flowers with morphogenetic alterations in the organs of the inner three whorls. Petals and stamens were green rather than yellow, suggesting a partial conversion to a sepalloid identity. Stamens and ovaries were infertile, with the later developing into parthenocarpic fruit. Ectopic shoots with partially developed leaves and secondary flowers emerged from the fruit. These shoots resembled the primary transgenic flowers and continued to produce parthenocarpic fruit and additional ectopic shoots. Based on the temporal and spatial expression pattern and transgenic phenotypes, we propose that TM29 functions in floral organ development, fruit development, and maintenance of floral meristem identity in tomato.

Plant architecture

Plant architecture is species specific, indicating that it is under strict genetic control. Although it is also influenced by environmental conditions such as light, temperature, humidity and nutrient status, here we wish to focus only on the endogenous regulatory principles that control plant architecture. We summarise recent progress in the understanding of the basic patterning mechanisms involved in the regulation of leaf arrangement, the genetic regulation of meristem determinacy, i.e. the decision to stop or continue growth, and the control of branching during vegetative and generative development. Finally, we discuss the basis of leaf architecture and the role of cell division and cell growth in morphogenesis.

Quantitative trait loci for inflorescence development in Arabidopsis thaliana

Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler x Col and Cvi x Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi x Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.

The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems

The multitude of forms observed in flowering plants is largely because of their ability to establish new axes of growth during postembryonic development. This process is initiated by the formation of secondary meristems that develop into vegetative or reproductive branches. In the blind and torosa mutants of tomato, initiation of lateral meristems is blocked during shoot and inflorescence development, leading to a strong reduction in the number of lateral axes. In this study, it is shown that blind and torosa are allelic. The Blind gene has been isolated by positional cloning, and it was found that the mutant phenotype is caused by a loss of function of an R2R3 class Myb gene. RNA interference-induced blind phenocopies confirmed the identity of the isolated gene. Double mutant analysis shows that Blind acts in a novel pathway different from the one to which the previously identified Lateral suppressor gene belongs. The findings reported add a new class of transcription factors to the group of genes controlling lateral meristem initiation and reveal a previously uncharacterized function of R2R3 Myb genes.

Control of axillary bud initiation and shoot architecture in Arabidopsis through the SUPERSHOOT gene

The aerial architecture of flowering plants is determined to a large extent by shoot growth and shoot branching arising from the initiation and growth of axillary meristems. We have identified an Arabidopsis mutant, supershoot (sps), which is characterized by a massive overproliferation of shoots, such that a single plant can generate 500 or more inflorescences. Analysis of the mutant plants shows that the primary defect is because of an increase in the number of meristems formed in leaf axils, together with release of bud arrest, resulting in reiterative branch formation from rosette and cauline leaves. The SPS gene is shown here to encode a cytochrome P450, and together with a 3- to 9-fold increase in levels of Z-type cytokinins in sps mutant plants, indicate a role for SPS in modulating hormone levels. The expression pattern of SPS, with strong expression at the leaf axils, correlates well with the phenotypic defects. Our results indicate that control of shoot branching in Arabidopsis may be accomplished in part by suppression of axillary meristem initiation and growth through the localized attenuation of cytokinin levels at sites of bud initiation.

The evolution of plant architecture

The vascular plants have evolved from a simple body plan that has diversified into the vast array of architectures seen in plants today. Much architectural diversity results from the varied growth patterns of apical and axillary meristems. Current research is showing that meristem growth patterns are regulated genetically and hormonally, and the genes that control these processes are being identified and characterized.

Polymerous Leaf Whorls in Vascular Plants: Developmental Morphology and Fuzziness of Organ Identities

In vascular plants there are at least eight ways to develop polymerous whorls, i.e., whorls with four or more leaves. Six ways are presented and compared with literature to estimate organ identity (morphological significance) of the leaflike whorl members. New shoots (also seedlings) may start with dimerous or trimerous whorls. Then leaf number per whorl rises as follows: (1) Many taxa add more leaves per whorl continuously with increasing size of the apical meristem (e.g., Equisetum, Hippuris). (2) Taxa provided with interpetiolar stipules replace their stipules by leaves (e.g., Galium and allies). (3) Taxa with the capacity to form compound leaves shift basal leaflets around the whole node (e.g., Limnophila, probably also Ceratophyllum). Various whorled plants start shoot development with leaf inception along a helix, which is continued into the whorled region. Then polymerous whorls develop as follows: (4) Acacia longipedunculata forms helically arranged fascicles instead of single leaves before the production of complete whorls. (5) Acacia baueri and Acacia verticillata add supernumerary leaves between a first series of helically arranged leaves. (6) Hydrothrix produces an annular bulge around the node of each first-formed leaf. All additional leaves of a whorl arise on this annular bulge. Leaf identity of whorl members cannot be defined unequivocally in whorls with asynchronous (i.e., nonsimultaneous) development, dorsoventral distribution of lateral buds, and/or fewer vascular traces than leaves per node. It is heuristically stimulating to accept structural categories (e.g., shoot, leaf, leaflet, stipule) as fuzzy concepts, as developmental pathways that may overlap to some degree, leading to developmental mosaics (intermediates). For example, the whorled leaves of Utricularia purpurea resemble whole shoots, corroborating Arber's partial-shoot theory.