Epistatic repression of PHANTASTICA and class 1 KNOTTED genes is uncoupled in tomato

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

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

DEFECTIVE EMBRYO AND MERISTEMS1 (DEM1) Is Essential for Cell Proliferation and Cell Differentiation in Tomato

Most flowering plant species contain at least two copies of the DEFECTIVE EMBRYO AND MERISTEMS (DEM) gene with the encoded DEM proteins lacking homology to proteins of known biochemical function. In tomato (Sl; Solanum lycopersicum), stable mutations in the SlDEM1 locus result in shoot and root meristem defects with the dem1 mutant failing to progress past the cotyledon stage of seedling development. Generation of a Somatic Mutagenesis of DEM1 (SMD) transformant line in tomato allowed for the characterization of SlDEM1 gene function past the seedling stage of vegetative development with SMD plants displaying a range of leaf development abnormalities. Further, the sectored or stable in planta expression of specific regions of the SlDEM1 coding sequence also resulted in the generation of tomato transformants that displayed a range of vegetative development defects, which when considered together with the dem1 mutant seedling and SMD transformant line phenotypic data, allowed for the assignment of SlDEM1 gene function to early embryo development, adaxial epidermis cell development, lateral leaf blade expansion, and mesophyll cell proliferation and differentiation.

Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium

Morphogenesis and differentiation are important stages in organ development and shape determination. However, how they are balanced and tuned during development is not fully understood. In the compound leaved tomato, an extended morphogenesis phase allows for the initiation of leaflets, resulting in the compound form. Maintaining a prolonged morphogenetic phase in early stages of compound-leaf development in tomato is dependent on delayed activity of several factors that promote differentiation, including the CIN-TCP transcription factor (TF) LA, the MYB TF CLAU and the plant hormone Gibberellin (GA), as well as on the morphogenesis-promoting activity of the plant hormone cytokinin (CK). Here, we investigated the genetic regulation of the morphogenesis-differentiation balance by studying the relationship between LA, CLAU, TKN2, CK and GA. Our genetic and molecular examination suggest that LA is expressed earlier and more broadly than CLAU and determines the developmental context of CLAU activity. Genetic interaction analysis indicates that LA and CLAU likely promote differentiation in parallel genetic pathways. These pathways converge downstream on tuning the balance between CK and GA. Comprehensive transcriptomic analyses support the genetic data and provide insights into the broader molecular basis of differentiation and morphogenesis processes in plants.

Morphogenesis and differentiation are crucial steps in the formation and shaping of organs in both plants and animals. A wide array of transcription factors and hormones were shown to act together to support morphogenesis or promote differentiation. However, a comprehensive molecular and genetic understating of how morphogenesis and differentiation are coordinated during development is still missing. We addressed these questions in the context of the development of the tomato compound leaf, for which many regulators have been described. Investigating the coordination among these different actors, we show that several discrete genetic pathways promote differentiation. Downstream of these separate pathways, two important plant hormones, cytokinin and gibberellin, act antagonistically to tweak the morphogenesis-differentiation balance.

The rin, nor and Cnr spontaneous mutations inhibit tomato fruit ripening in additive and epistatic manners

Tomato fruit ripening is regulated by transcription factors (TFs), their downstream effector genes, and the ethylene biosynthesis and signalling pathway. Spontaneous non-ripening mutants ripening inhibitor (rin), non-ripening (nor) and Colorless non-ripening (Cnr) correspond with mutations in or near the TF-encoding genes MADS-RIN, NAC-NOR and SPL-CNR, respectively. Here, we produced heterozygous single and double mutants of rin, nor and Cnr and evaluated their functions and genetic interactions in the same genetic background. We showed how these mutations interact at the level of phenotype, individual effector gene expression, and sensory and quality aspects, in a dose-dependent manner. Rin and nor have broadly similar quantitative effects on all aspects, demonstrating their additivity in fruit ripening regulation. We also found that the Cnr allele is epistatic to rin and nor and that its pleiotropic effects on fruit size and volatile production, in contrast to the well-known dominant effect on ripening, are incompletely dominant, or recessive.

On the mechanisms of development in monocot and eudicot leaves

Contents Summary 706 I. Introduction 707 II. Leaf zones in monocot and eudicot leaves 707 III. Monocot and eudicot leaf initiation: differences in degree and timing, but not kind 710 IV. Reticulate and parallel venation: extending the model? 711 V. Flat laminar growth: patterning and coordination of adaxial-abaxial and mediolateral axes 713 VI. Stipules and ligules: ontogeny of primordial elaborations 715 VII. Leaf architecture 716 VIII. Stomatal development: shared and diverged mechanisms for making epidermal pores 717 IX. Conclusion 719 Acknowledgements 720 References 720 SUMMARY: Comparisons of concepts in monocot and eudicot leaf development are presented, with attention to the morphologies and mechanisms separating these angiosperm lineages. Monocot and eudicot leaves are distinguished by the differential elaborations of upper and lower leaf zones, the formation of sheathing/nonsheathing leaf bases and vasculature patterning. We propose that monocot and eudicot leaves undergo expansion of mediolateral domains at different times in ontogeny, directly impacting features such as venation and leaf bases. Furthermore, lineage-specific mechanisms in compound leaf development are discussed. Although models for the homologies of enigmatic tissues, such as ligules and stipules, are proposed, tests of these hypotheses are rare. Likewise, comparisons of stomatal development are limited to Arabidopsis and a few grasses. Future studies may investigate correlations in the ontogenies of parallel venation and linear stomatal files in monocots, and the reticulate patterning of veins and dispersed stoma in eudicots. Although many fundamental mechanisms of leaf development are shared in eudicots and monocots, variations in the timing, degree and duration of these ontogenetic events may contribute to key differences in morphology. We anticipate that the incorporation of an ever-expanding number of sequenced genomes will enrich our understanding of the developmental mechanisms generating eudicot and monocot leaves.

Silencing SlMED18, tomato Mediator subunit 18 gene, restricts internode elongation and leaf expansion

Mediator complex, a conserved multi-protein, is necessary for controlling RNA polymerase II (Pol II) transcription in eukaryotes. Given little is known about them in tomato, a tomato Mediator subunit 18 gene was isolated and named SlMED18. To further explore the function of SlMED18, the transgenic tomato plants targeting SlMED18 by RNAi-mediated gene silencing were generated. The SlMED18-RNAi lines exhibited multiple developmental defects, including smaller size and slower growth rate of plant and significantly smaller compound leaves. The contents of endogenous bioactive GA3 in SlMED18 silenced lines were slightly less than that in wild type. Furthermore, qRT-PCR analysis indicated that expression of gibberellins biosynthesis genes such as SlGACPS and SlGA20x2, auxin transport genes (PIN1, PIN4, LAX1 and LAX2) and several key regulators, KNOX1, KNOX2, PHAN and LANCEOLATE(LA), which involved in the leaf morphogenesis were significantly down-regulated in SlMED18-RNAi lines. These results illustrated that SlMED18 plays an essential role in regulating plant internode elongation and leaf expansion in tomato plants and it acts as a key positive regulator of gibberellins biosynthesis and signal transduction as well as auxin proper transport signalling. These findings are the basis for understanding the function of the individual Mediator subunits in tomato.

Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program?

Root-knot nematodes (RKNs; Meloidogyne spp.) induce feeding cells (giant cells; GCs) inside a pseudo-organ (gall) from still unknown root cells. Understanding GCs ontogeny is essential to the basic knowledge of RKN-plant interaction and to discover novel and effective control strategies. Hence, we report for the first time in a model plant, Arabidopsis, molecular, and cellular features concerning ectopic de novo organogenesis of RKNs GCs in leaves. RKNs induce GCs in leaves with irregular shape, a reticulated cytosol, and fragmented vacuoles as GCs from roots. Leaf cells around the nematode enter G2-M shown by ProCycB1;1:CycB1;1(NT)-GUS expression, consistent to multinucleated GCs. In addition, GCs nuclei present irregular and varied sizes. All these characteristics mentioned, being equivalent to GCs in root-galls. RKNs complete their life cycle forming a gall/callus-like structure in the leaf vascular tissues resembling auxin-induced callus with an auxin-response maxima, indicated by high expression of DR5::GUS that is dependent on leaf auxin-transport. Notably, induction of leaves calli/GCs requires molecular components from roots crucial for lateral roots (LRs), auxin-induced callus and root-gall formation, i.e., LBD16. Hence, LBD16 is a xylem pole pericycle specific and local marker in LR primordia unexpectedly induced locally in the vascular tissue of leaves after RKN infection. LBD16 is also fundamental for feeding site formation as RKNs could not stablish in 35S::LBD16-SRDX leaves, and likely it is also a conserved molecular hub between biotic and developmental signals in Arabidopsis either in roots or leaves. Moreover, RKNs induce the ectopic development of roots from leaf and root-galls, also formed in mutants compromised in LR formation, arf7/arf19, slr, and alf4. Therefore, nematodes must target molecular signatures to induce post-embryogenic de novo organogenesis through the LBD16 callus formation pathway partially different from those prevalent during normal LR development.

A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

What determines a leaf's shape?

The independent origin and evolution of leaves as small, simple microphylls or larger, more complex megaphylls in plants has shaped and influenced the natural composition of the environment. Significant contributions have come from megaphyllous leaves, characterized usually as flat, thin lamina entrenched with photosynthetic organelles and stomata, which serve as the basis of primary productivity. During the course of evolution, the megaphylls have attained complexity not only in size or venation patterns but also in shape. This has fascinated scientists worldwide, and research has progressed tremendously in understanding the concept of leaf shape determination. Here, we review these studies and discuss the various factors that contributed towards shaping the leaf; initiated as a small bulge on the periphery of the shoot apical meristem (SAM) followed by asymmetric outgrowth, expansion and maturation until final shape is achieved. We found that the underlying factors governing these processes are inherently genetic: PIN1 and KNOX1 are indicators of leaf initiation, HD-ZIPIII, KANADI, and YABBY specify leaf outgrowth while ANGUSTIFOLIA3 and GROWTH-REGULATING FACTOR5 control leaf expansion and maturation; besides, recent research has identified new players such as APUM23, known to specify leaf polarity. In addition to genetic control, environmental factors also play an important role during the final adjustment of leaf shape. This immense amount of information available will serve as the basis for studying and understanding innovative leaf morphologies viz. the pitchers of the carnivorous plant Nepenthes which have evolved to provide additional support to the plant survival in its nutrient-deficient habitat. In hindsight, formation of the pitcher tube in Nepenthes might involve the recruitment of similar genetic mechanisms that occur during sympetaly in Petunia.

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

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

NbPHAN, a MYB transcriptional factor, regulates leaf development and affects drought tolerance in Nicotiana benthamiana

MYB transcriptional factors, characterized by the presence of conserved DNA-binding domains (BDs) (MYB domain), are involved in diverse processes including plant growth, development, metabolic and stress responses. In this study, a new R2R3-type MYB gene, NbPHAN (Nicotiana benthamiana PHANTASTICA), was identified in N. benthamiana. The NbPHAN encodes a protein of 362 amino acids and shares high sequence identities with the AS1-RS2-PHANs (ARPs) from other plant species. The NbPHAN protein targets to and forms homodimers in the nucleus. The MYB domain and C-terminal region of NbPHAN determine its subcellular localization and homodimerization, respectively. Using virus-induced gene silencing, we showed that the NbPHAN-silenced leaves exhibited severe downward curling and abnormal growth of blades along the main veins through suppressing the expression of the NTH20 gene. In addition, we found NbPHAN plays an important role in drought tolerance. The NbPHAN-silenced plants exhibited severe wilting and increased rate of water loss than that found in the non-silenced plants when growing under the water deficit condition. Although abscisic acid accumulation was not altered in the NbPHAN-silenced plants as compared with that in the non-silenced plants, several other stress-inducible genes were clearly repressed under the water deficit condition. Our results provide strong evidence that other than controlling leaf development, the ARP genes can also regulate plant tolerance to drought stress.

Distinct and conserved transcriptomic changes during nematode-induced giant cell development in tomato compared with Arabidopsis: a functional role for gene repression

Root-knot nematodes (RKNs) induce giant cells (GCs) from root vascular cells inside the galls. Accompanying molecular changes as a function of infection time and across different species, and their functional impact, are still poorly understood. Thus, the transcriptomes of tomato galls and laser capture microdissected (LCM) GCs over the course of parasitism were compared with those of Arabidopsis, and functional analysis of a repressed gene was performed. Microarray hybridization with RNA from galls and LCM GCs, infection-reproduction tests and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) transcriptional profiles in susceptible and resistant (Mi-1) lines were performed in tomato. Tomato GC-induced genes include some possibly contributing to the epigenetic control of GC identity. GC-repressed genes are conserved between tomato and Arabidopsis, notably those involved in lignin deposition. However, genes related to the regulation of gene expression diverge, suggesting that diverse transcriptional regulators mediate common responses leading to GC formation in different plant species. TPX1, a cell wall peroxidase specifically involved in lignification, was strongly repressed in GCs/galls, but induced in a nearly isogenic Mi-1 resistant line on nematode infection. TPX1 overexpression in susceptible plants hindered nematode reproduction and GC expansion. Time-course and cross-species comparisons of gall and GC transcriptomes provide novel insights pointing to the relevance of gene repression during RKN establishment.

The tomato leaf as a model system for organogenesis

Compound tomato leaves are composed of multiple leaflets that are generated gradually during leaf development, and each resembles a simple leaf. The elaboration of a compound leaf form requires the maintenance of transient organogenic activity at the leaf margin. The developmental window of organogenic activity is defined by the antagonistic activities of factors that promote maturation, such as TCP transcription factors, SFT and gibberellin, and factors that delay maturation, such as KNOX transcription factors and cytokinin. Leaflet initiation sites are specified spatially and temporally by spaced and specific activities of CUCs, auxin and ENTIRE, as well as additional factors. The partially indeterminate growth of the compound tomato leaf makes it a useful model to understand the balance between determinate and indeterminate growth, and the mechanisms of organogenesis, some of which are common to many developmental processes in 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 R2R3-MYB transcription factor gene family in maize

MYB proteins comprise a large family of plant transcription factors, members of which perform a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). In the present study, we performed a comprehensive computational analysis, to yield a complete overview of the R2R3-MYB gene family in maize, including the phylogeny, expression patterns, and also its structural and functional characteristics. The MYB gene structure in maize and Arabidopsis were highly conserved, indicating that they were originally compact in size. Subgroup-specific conserved motifs outside the MYB domain may reflect functional conservation. The genome distribution strongly supports the hypothesis that segmental and tandem duplication contribute to the expansion of maize MYB genes. We also performed an updated and comprehensive classification of the R2R3-MYB gene families in maize and other plant species. The result revealed that the functions were conserved between maize MYB genes and their putative orthologs, demonstrating the origin and evolutionary diversification of plant MYB genes. Species-specific groups/subgroups may evolve or be lost during evolution, resulting in functional divergence. Expression profile study indicated that maize R2R3-MYB genes exhibit a variety of expression patterns, suggesting diverse functions. Furthermore, computational prediction potential targets of maize microRNAs (miRNAs) revealed that miR159, miR319, and miR160 may be implicated in regulating maize R2R3-MYB genes, suggesting roles of these miRNAs in post-transcriptional regulation and transcription networks. Our comparative analysis of R2R3-MYB genes in maize confirm and extend the sequence and functional characteristics of this gene family, and will facilitate future functional analysis of the MYB gene family in maize.

Genetic interaction and mapping studies on the leaflet development (lld) mutant in Pisum sativum

In Pisum sativum, the completely penetrant leaflet development (lld) mutation is known to sporadically abort pinnae suborgans in the unipinnate compound leaf. Here, the frequency and morphology of abortion was studied in each of the leaf suborgans in 36 genotypes and in presence of auxin and gibberellin, and their antagonists. Various lld genotypes were constructed by multifariously recombining lld with a coch homeotic stipule mutation and with af, ins, mare, mfp, tl and uni-tac leaf morphology mutations. It was observed that the suborgans at all levels of pinna subdivisions underwent lld-led abortion events at different stages of development. As in leafblades, lld aborted the pinnae in leaf-like compound coch stipules. The lld mutation interacted with mfp synergistically and with other leaf mutations additively. The rod-shaped and trumpet-shaped aborted pea leaf suborgans mimicked the phenotype of aborted leaves in HD-ZIP-III-deficient Arabidopsis thaliana mutants. Suborganwise aborted morphologies in lld gnotypes were in agreement with basipetal differentiation of leaflets and acropetal differentiation in tendrils. Altogether, the observations suggested that LLD was the master regulator of pinna development. On the basis of molecular markers found linked to lld, its locus was positioned on the linkage group III of the P. sativum genetic map.

A complex case of simple leaves: indeterminate leaves co-express ARP and KNOX1 genes

The mutually exclusive relationship between ARP and KNOX1 genes in the shoot apical meristem and leaf primordia in simple leaved plants such as Arabidopsis has been well characterized. Overlapping expression domains of these genes in leaf primordia have been described for many compound leaved plants such as Solanum lycopersicum and Cardamine hirsuta and are regarded as a characteristic of compound leaved plants. Here, we present several datasets illustrating the co-expression of ARP and KNOX1 genes in the shoot apical meristem, leaf primordia, and developing leaves in plants with simple leaves and simple primordia. Streptocarpus plants produce unequal cotyledons due to the continued activity of a basal meristem and produce foliar leaves termed "phyllomorphs" from the groove meristem in the acaulescent species Streptocarpus rexii and leaves from a shoot apical meristem in the caulescent Streptocarpus glandulosissimus. We demonstrate that the simple leaves in both species possess a greatly extended basal meristematic activity that persists over most of the leaf's growth. The area of basal meristem activity coincides with the co-expression domain of ARP and KNOX1 genes. We suggest that the co-expression of ARP and KNOX1 genes is not exclusive to compound leaved plants but is associated with foci of meristematic activity in leaves.

Morphogenesis of simple and compound leaves: a critical review

The leaves of seed plants evolved from a primitive shoot system and are generated as determinate dorsiventral appendages at the flanks of radial indeterminate shoots. The remarkable variation of leaves has remained a constant source of fascination, and their developmental versatility has provided an advantageous platform to study genetic regulation of subtle, and sometimes transient, morphological changes. Here, we describe how eudicot plants recruited conserved shoot meristematic factors to regulate growth of the basic simple leaf blade and how subsets of these factors are subsequently re-employed to promote and maintain further organogenic potential. By comparing tractable genetic programs of species with different leaf types and evaluating the pros and cons of phylogenetic experimental procedures, we suggest that simple and compound leaves, and, by the same token, leaflets and serrations, are regulated by distinct ontogenetic programs. Finally, florigen, in its capacity as a general growth regulator, is presented as a new upper-tier systemic modulator in the patterning of compound leaves.

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

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

Comprehensive transcriptome profiling in tomato reveals a role for glycosyltransferase in Mi-mediated nematode resistance

Root-knot nematode (RKN; Meloidogyne spp.) is a major crop pathogen worldwide. Effective resistance exists for a few plant species, including that conditioned by Mi in tomato (Solanum lycopersicum). We interrogated the root transcriptome of the resistant (Mi+) and susceptible (Mi-) cultivars 'Motelle' and 'Moneymaker,' respectively, during a time-course infection by the Mi-susceptible RKN species Meloidogyne incognita and the Mi-resistant species Meloidogyne hapla. In the absence of RKN infection, only a single significantly regulated gene, encoding a glycosyltransferase, was detected. However, RKN infection influenced the expression of broad suites of genes; more than half of the probes on the array identified differential gene regulation between infected and uninfected root tissue at some stage of RKN infection. We discovered 217 genes regulated during the time of RKN infection corresponding to establishment of feeding sites, and 58 genes that exhibited differential regulation in resistant roots compared to uninfected roots, including the glycosyltransferase. Using virus-induced gene silencing to silence the expression of this gene restored susceptibility to M. incognita in 'Motelle,' indicating that this gene is necessary for resistance to RKN. Collectively, our data provide a picture of global gene expression changes in roots during compatible and incompatible associations with RKN, and point to candidates for further investigation.

Different expression patterns of duplicated PHANTASTICA-like genes in Lotus japonicus suggest their divergent functions during compound leaf development

Recent studies on leaf development demonstrate that the mechanism on the adaxial-abaxial polarity pattern formation could be well conserved among the far-related species, in which PHANTASTICA (PAHN)-like genes play important roles. In this study, we explored the conservation and diversity on functions of PHAN-like genes during the compound leaf development in Lotus japonicus, a papilionoid legume. Two PHAN-like genes in L. japonicus, LjPHANa and LjPHANb, were found to originate from a gene duplication event and displayed different expression patterns during compound leaf development. Two mutants, reduced leaflets1 (rel1) and reduced leaflets3 (rel3), which exhibited decreased adaxial identity of leaflets and reduced leaflet initiation, were identified and investigated. The expression patterns of both LjPHANs in rel mutants were altered and correlated with abnormalities of compound leaves. Our data suggest that LjPHANa and LjPHANb play important but divergent roles in regulating adaxial-abaxial polarity of compound leaves in L. japonicus.

Expression patterns of STM-like KNOX and Histone H4 genes in shoot development of the dissected-leaved basal eudicot plants Chelidonium majus and Eschscholzia californica (Papaveraceae)

Knotted-like homeobox (KNOX) genes encode important regulators of shoot development in flowering plants. In Arabidopsis, class I KNOX genes are part of a regulatory system that contributes to indeterminacy of shoot development, delimitation of leaf primordia and internode development. In other species, class I KNOX genes have also been recruited in the control of marginal blastozone fractionation during dissected leaf development. Here we report the isolation of class I KNOX genes from two species of the basal eudicot family Papaveraceae, Chelidonium majus and Eschscholzia californica. Sequence comparisons and expression patterns indicate that these genes are orthologs of SHOOTMERISTEMLESS (STM), a class I KNOX gene from Arabidopsis. Both genes are expressed in the center of vegetative and floral shoot apical meristems (SAM), but downregulated at leaf or floral organ initiating sites. While Eschscholzia californica STM (EcSTM) is again upregulated during acropetal pinna formation, in situ hybridization could not detect Chelidonium majus STM (CmSTM) transcripts at any stage of basipetal leaf development, indicating divergent evolution of STM gene function in leaves within Papaveraceae. Immunolocalization of KNOX proteins indicate that other gene family members may control leaf dissection in both species. The contrasting direction of pinna initiation in the two species was also investigated using Histone H4 expression. Leaves at early stages of development did not reveal notable differences in cell division activity of the elongating leaf axis, suggesting that differential meristematic growth may not play a role in determining the observed dissection patterns.

Differences in Feeding Sites Induced by Root-Knot Nematodes, Meloidogyne spp., in Chickpea

ABSTRACT Root-knot nematodes (Meloidogyne spp.) are sedentary, obligate endoparasites in plants, where they induce specialized feeding sites. The feeding sites act as strong metabolic sinks to which photosynthates are mobilized. The histopathological modifications in the nematode-induced feeding sites of artificially inoculated chickpea cv. UC 27 were qualitatively and quantitatively compared using five isolates of M. artiellia and one isolate each of M. arenaria, M. incognita, and M. javanica. All Meloidogyne isolates infected chickpea plants, but root gall thickening was significantly less for M. artiellia isolates than for the other Meloidogyne species. Nevertheless, neither the number of giant cells in the feeding site (averaging four to six) nor the area of individual giant cells was influenced by nematode species or isolate. However, the number of nuclei per giant cell was significantly smaller, and the maximum diameters of nuclei and nucleoli were significantly greater, in giant cells induced by M. artiellia isolates than in those induced by M. arenaria, M. incognita, or M. javanica. In a second experiment, M. artiellia-induced giant cells in faba bean and rapeseed also contained a small number of large nuclei.

The mutant crispa reveals multiple roles for PHANTASTICA in pea compound leaf development

Pinnate compound leaves have laminae called leaflets distributed at intervals along an axis, the rachis, whereas simple leaves have a single lamina. In simple- and compound-leaved species, the PHANTASTICA (PHAN) gene is required for lamina formation. Antirrhinum majus mutants lacking a functional gene develop abaxialized, bladeless adult leaves. Transgenic downregulation of PHAN in the compound tomato (Solanum lycopersicum) leaf results in an abaxialized rachis without leaflets. The extent of PHAN gene expression was found to be correlated with leaf morphology in diverse compound-leaved species; pinnate leaves had a complete adaxial domain of PHAN gene expression, and peltate leaves had a diminished domain. These previous studies predict the form of a compound-leaved phan mutant to be either peltate or an abaxialized rachis. Here, we characterize crispa, a phan mutant in pea (Pisum sativum), and find that the compound leaf remains pinnate, with individual leaflets abaxialized, rather than the whole leaf. The mutant develops ectopic stipules on the petiole-rachis axis, which are associated with ectopic class 1 KNOTTED1-like homeobox (KNOX) gene expression, showing that the interaction between CRISPA and the KNOX gene PISUM SATIVUM KNOTTED2 specifies stipule boundaries. KNOX and CRISPA gene expression patterns indicate that the mechanism of pea leaf initiation is more like Arabidopsis thaliana than tomato.

Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in Lotus japonicus

The symbiosis responsible for nitrogen fixation in legume root nodules is initiated by rhizobial signaling molecules [Nod factors (NF)]. Using transgenically tagged microtubules and actin, we dynamically profiled the spatiotemporal changes in the cytoskeleton of living Lotus japonicus root hairs, which precede root-hair deformation and reflect one of the earliest host responses to NF. Remarkably, plant-parasitic root-knot nematodes (RKN) invoke a cytoskeletal response identical to that seen in response to NF and induce root-hair waviness and branching in legume root hairs via a signal able to function at a distance. Azide-killed nematodes do not produce this signal. A similar response to RKN was seen in tomato. Aspects of the host responses to RKN were altered or abolished by mutations in the NF receptor genes nfr1, nfr5, and symRK, suggesting that RKN produce a molecule with functional equivalence to NF, which we name NemF. Because the ability of RKN to establish feeding sites and reproduce was markedly reduced in the mutant lines, we propose that RKN have adapted at least part of the symbiont-response pathway to enhance their parasitic ability.

Compound leaves: equal to the sum of their parts?

The leaves of seed plants can be classified as being either simple or compound according to their shape. Two hypotheses address the homology between simple and compound leaves, which equate either individual leaflets of compound leaves with simple leaves or the entire compound leaf with a simple leaf. Here we discuss the genes that function in simple and compound leaf development, such as KNOX1 genes, including how they interact with growth hormones to link growth regulation and development to cause changes in leaf complexity. Studies of transcription factors that control leaf development, their downstream targets, and how these targets are regulated are areas of inquiry that should increase our understanding of how leaf complexity is regulated and how it evolved through time.

Signaling between nematodes and plants

After hatching in the soil, root-knot nematodes must locate and penetrate a root, migrate into the vascular cylinder, and establish a permanent feeding site. Presumably, these events are accompanied by extensive signaling between the nematode parasite and the host. Hence, much emphasis has been placed on identifying proteins that are secreted by the nematode during the migratory phase. Further progress in understanding the signaling events has been made recently by studying the host response. Striking parallels can be drawn between the nematode-plant interaction and plant symbioses with other microorganisms, and evidence is emerging to suggest that nematodes acquired components of their parasitic armory from those microbes.

Quantitative Trait Locus Analysis of Leaf Dissection in Tomato Using Lycopersicon pennellii Segmental Introgression Lines

Leaves are one of the most conspicuous and important organs of all seed plants. A fundamental source of morphological diversity in leaves is the degree to which the leaf is dissected by lobes and leaflets. We used publicly available segmental introgression lines to describe the quantitative trait loci (QTL) controlling the difference in leaf dissection seen between two tomato species, Lycopersicon esculentum and L. pennellii. We define eight morphological characteristics that comprise the mature tomato leaf and describe loci that affect each of these characters. We found 30 QTL that contribute one or more of these characters. Of these 30 QTL, 22 primarily affect leaf dissection and 8 primarily affect leaf size. On the basis of which characters are affected, four classes of loci emerge that affect leaf dissection. The majority of the QTL produce phenotypes intermediate to the two parent lines, while 5 QTL result in transgression with drastically increased dissection relative to both parent lines.

Reduced leaf complexity in tomato wiry mutants suggests a role for PHAN and KNOX genes in generating compound leaves

Recent work on species with simple leaves suggests that the juxtaposition of abaxial (lower) and adaxial (upper) cell fates (dorsiventrality) in leaf primordia is necessary for lamina outgrowth. However, how leaf dorsiventral symmetry affects leaflet formation in species with compound leaves is largely unknown. In four non-allelic dorsiventrality-defective mutants in tomato, wiry, wiry3, wiry4 and wiry6, partial or complete loss of ab-adaxiality was observed in leaves as well as in lateral organs in the flower, and the number of leaflets in leaves was reduced significantly. Morphological analyses and expression patterns of molecular markers for ab-adaxiality [LePHANTASTICA (LePHAN) and LeYABBY B (LeYAB B)] indicated that ab-adaxial cell fates were altered in mutant leaves. Reduction in expression of both LeT6 (a tomato KNOX gene) and LePHAN during post-primordial leaf development was correlated with a reduction in leaflet formation in the wiry mutants. LePHAN expression in LeT6 overexpression mutants suggests that LeT6 is a negative regulator of LePHAN. KNOX expression is known to be correlated with leaflet formation and we show that LeT6 requires LePHAN activity to form leaflets. These phenotypes and gene expression patterns suggest that the abaxial and adaxial domains of leaf primordia are important for leaflet primordia formation, and thus also important for compound leaf development. Furthermore, the regulatory relationship between LePHAN and KNOX genes is different from that proposed for simple-leafed species. We propose that this change in the regulatory relationship between KNOX genes and LePHAN plays a role in compound leaf development and is an important feature that distinguishes simple leaves from compound leaves.

The expression domain of PHANTASTICA determines leaflet placement in compound leaves

Diverse leaf forms in nature can be categorized as simple or compound. Simple leaves, such as those of petunia, have a single unit of blade, whereas compound leaves, such as those of tomato, have several units of blades called leaflets. Compound leaves can be pinnate, with leaflets arranged in succession on a rachis, or palmate, with leaflets clustered together at the leaf tip. The mechanisms that generate these various leaf forms are largely unknown. The upper (adaxial) surface is usually different from the bottom (abaxial) surface in both simple and compound leaves. In species with simple leaves, the specification of adaxial and abaxial cells is important for formation of the leaf blade, and the MYB transcription factor gene PHANTASTICA (PHAN) is involved in maintaining the leaf adaxial (upper) domain. Here we show that downregulation of PHAN is sufficient to reduce the adaxial domain of leaf primordia and to change pinnate compound leaves into palmate compound leaves. Furthermore, this mechanism seems to be shared among compound leaves that arose independently.

Interpretation of mutants in leaf morphology: genetic evidence for a compensatory system in leaf morphogenesis that provides a new link between cell and organismal theories

On the basis of "cell theory," we tend to think that some changes in cellular behavior must be responsible for mutant morphology. According to the cell theory, the unit of morphogenesis of a multicellular organism is the cell. Another interpretation of morphogenesis of plants is the "organismal theory," which postulates that the individual cell is not the basic unit of morphogenesis. Here we examine the validity of the cell and organismal theories, with particular emphasis on the phenotypes of mutant or transgenic Arabidopsis plants with altered leaf morphology. Genetic evidence shows that a compensatory system(s) is involved in leaf morphogenesis, and an increase in cell volume might be triggered by a decrease in cell number. Such evidence provides a new link between cell and organismal theories. In conclusion, the size and number of leaf cells affect the dimensions and sizes of leaves. Moreover, the leaf size is, at least to some extent, uncoupled from the size and number of cells by the compensatory system(s).

Coordination of cell proliferation and cell fate decisions in the angiosperm shoot apical meristem

A unique feature of flowering plants is their ability to produce organs continuously, for hundreds of years in some species, from actively growing tips called apical meristems. All plants possess at least one form of apical meristem, whose cells are functionally analogous to animal stem cells because they can generate specialized organs and tissues. The shoot apical meristem of angiosperm plants acts as a continuous source of pluripotent stem cells, whose descendents become incorporated into organ primordia and acquire different fates. Recent studies are unveiling some of the molecular pathways that specify stem cell fate in the center of the shoot apical meristem, that confer organ founder cell fate on the periphery, and that connect meristem patterning elements with events at the cellular level. The results are providing important insights into the mechanisms through which shoot apical meristems integrate cell fate decisions with cellular proliferation and global regulation of growth and development.

Gene expression in nematode feeding sites

The feeding sites induced by sedentary root-endoparasitic nematodes have long fascinated researchers. Nematode feeding sites are constructed from plant cells, modified by the nematode to feed itself. Powerful new techniques are allowing us to begin to elucidate the molecular mechanisms that produce the ultrastructural features in nematode feeding cells. Many plant genes that are expressed in feeding sites produced by different nematodes have been identified in several plant species. Nematode-responsive plant genes can now be grouped in categories related to plant developmental pathways and their roles in the making of a feeding site can be illuminated. The black box of how nematodes bring about such elaborate cell differentiation in the plant is also starting to open. Although the information is far from complete, the groundwork is set so that the functions of the plant and nematode genes in feeding site development can begin to be assessed.

Overlapping plant signal transduction pathways induced by a parasitic nematode and a rhizobial endosymbiont

Root-knot nematodes and rhizobia establish interactions with roots characterized by the de novo induction of host structures, termed giant cells and nodules, respectively. Two transcription regulators, PHAN and KNOX, required for the establishment of meristems were previously shown to be expressed in tomato giant cells. We isolated the orthologues of PHAN and KNOX (Mt-phan and Mt-knox-1) from the model legume Medicago truncatula, and established the spatial distribution of their expression in situ. We confirmed that Mt-phan and Mt-knox-1 are expressed in lateral root initials and in nematode-induced giant cells and showed that they are expressed in nodules induced by Sinorhizobium meliloti. Expression of both genes becomes spatially restricted as the nodules develop. We further examined nematode feeding sites for the expression of two genes involved in nodule formation, ccs52 (encodes a mitotic inhibitor) and ENOD40 (encodes an early, nodulation mitogen), and found transcripts of both genes to be present in and around giant cells induced in Medicago. Collectively, these results reveal common elements of host responses to mutualistic and parasitic plant endosymbionts and imply that overlapping regulatory pathways lead to giant cells and nodules. We discuss these pathways in the context of phytohormones and parallels between beneficial symbiosis and disease.

Patterns and symmetries in leaf development

The leaf is a coordinated mosaic of developmental domains, which are evident from leaf inception on the flanks of the apical meristem. The subdivision of the meristem into molecularly defined domains is regulated by the interactions of a number of gene products and by receptor kinase-mediated signals. The acquisition of symmetry axes in the emerging leaf is a process coordinated by hormones (such as auxin and cytokinins) and the expression of classes of genes (such as the knox and the ARP, as1/rs2/phan, genes). As with simple leaves, the architecture of compound leaves is defined by spatial/temporal gradients of regulatory gene functions: complexity results from the interplay between leaf differentiation processes and genes maintaining a partial level of indeterminacy in the developing primordium. Boundaries between regions with different molecular 'addresses' are considered, in plants as in Drosophila, as organizing centres for lateral organ development.

Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein

The Arabidopsis thaliana PROTODERMAL FACTOR1 (PDF1) gene encoding a putative extracellular proline-rich protein is exclusively expressed in the L1 layer of shoot apices and the protoderm of organ primordia. In order to identify essential cis-regulatory sequences required for the L1 layer-specific expression, a series of 5' deletions of the PDF1 promoter were fused to the beta-glucronidase (GUS) gene and introduced into Arabidopsis plants. Our analysis revealed that the minimum region necessary to confer L1-specific expression of PDF1 is confined within a 260-bp fragment upstream of the transcription start site. We identified an 8-bp motif in this region that is conserved between promoter regions of all the L1-specific genes so far cloned, and we designated it the L1 box. Electrophoretic mobility shift assays demonstrated that the L1-specific homeodomain protein ATML1 can bind to the L1 box sequence in vitro. The GUS expression in transgenic plants disappeared when a mutation that abolishes binding of ATML1 was introduced into the PDF1 l1 box sequence of the construct. These results suggest that the L1 box plays a crucial role in the regulation of PDF1 expression in L1 cells and that ATML1 could cooperate to drive L1-specific expression.

Novel marker genes for early leaf development indicate spatial regulation of carbohydrate metabolism within the apical meristem

To identify genes expressed at the earliest stages of leaf development, we have performed a differential display analysis using portions of meristems destined to form leaves. Our analysis led to the identification of five genes showing an asymmetric pattern of gene expression within the meristem associated with leaf formation. Surprisingly, three of these genes encoded enzymes involved in carbohydrate metabolism (ADPglucose pyrophosphorylase, sucrose synthase and an SNF1-like kinase). Furthermore, specific transcript patterns were responsive to specific sugar and hormonal treatments. The other two genes identified encoded a Phantastica-like myb transcription factor (associated with the acquisition of leaf dorsiventrality) and CYP85 (a cytochrome P450, which plays a pivotal role in brassinolide metabolism). These data, firstly, identify a novel set of marker genes for the analysis of the earliest stages of leaf formation. Secondly, the function of the proteins encoded by these genes and their expression patterns within the meristem indicate that carbohydrate metabolism is spatially regulated within a tissue involved in key developmental processes. Finally, our data provide the first indication of an asymmetry in gene expression related to hormone biosynthesis in the meristem.

Development of leaf shape

Variation among vascular plants in the initiation and patterning of leaves results in a diverse array of leaf shape, including the strap-like leaf of many grasses and the broad lamina of most eudicots. Recent findings highlight the importance of interactions between the shoot apical meristem (SAM) and developing leaf primordia in axis specification and the establishment of leaf shape. Global regulators of epigenetic states have been implicated in these interactions and may play a role in distinguishing founder cells and stem cells within the SAM.

High throughput cellular localization of specific plant mRNAs by liquid-phase in situ reverse transcription-polymerase chain reaction of tissue sections

Advances in high throughput DNA sequencing and bioinformatic gene discovery far outpace our ability to analyze gene function, necessitating development of more efficient means to examine expression at the cellular level. Here we present a polymerase chain reaction-based method to detect mRNA species in situ in which essentially all of the steps are carried out in liquid phase in a 96-well microtiter tray and only the final signal detection is performed on a microscope slide. We demonstrate the sensitivity of the method by the cellular localization of mRNA for the Tkn2 transcription factor in a wide variety of plant tissues, and its selectivity in discriminating a single gene family member by the in situ localization of rbcs3 transcripts. Furthermore, we demonstrate the utility of the in-well in situ method in detecting FDL and IFL1 transcripts in Arabidopsis sections, thus establishing the method as a tool to determine spatial expression pattern of sequences obtained from genomic sequencing projects. Being amenable to robotic processing, in-well in situ reverse transcription-polymerase chain reaction permits a great enhancement in the number of tissue samples that can be processed. Consequently, this method may become a powerful tool for functional genomics studies, permitting the cellular site of transcription of large numbers of sequences obtained from databases to be rapidly established.