High-resolution linkage analysis and physical characterization of the EIX-responding locus in tomato

An ethylene-inducing xylanase (EIX) from Tricohoderma viride is a potent elicitor of ethylene biosynthesis, localized cell death and other defense responses in specific cultivars of tobacco (Nicotiana tabacum) and tomato (Lycopersicon esculentum). Wild species of tomato, such as Lycopersicon cheesmanii and Lycopersicon pennellii, do not respond to EIX treatment. The F₁ progeny of a L. esculentum×L. cheesmanii and a L. esculentum×L. pennellii cross responded to EIX treatment with an increase in ethylene biosynthesis and the induction of localized cell death. The F₂ progeny of the above mentioned crosses segregated 3:1 (responding:non-responding). We mapped the EIX-responding locus (Eix) to the short arm of chromosome 7 using a population of introgression lines (ILs), containing small RFLP-defined chromosome segments of L. pennellii introgressed into L. esculentum. RFLP analysis of 990 F₂ plants that segregated for the introgressed segment mapped the Eix locus 0.1 cM and 0.9 cM from the flanking markers TG61 and TG131, respectively. Using the marker TG61 we isolated a yeast artificial chromosome (YAC) clone that carries 300-kb DNA segments derived from the Eix region. By mapping the ends of this YAC clone we show that it spans the Eix locus. Thus, positional cloning of the Eix locus appears feasible. Received: 20 March 1999 / Accepted: 30 April 1999     

Biomechanical study of the effect of a controlled bending on tomato stem elongation: global mechanical analysis

An experiment was designed to apply a controlled bending to a tomato stem and simultaneously to measure its effect on stem elongation. Stem elongation was measured over 2 d until steady and equal rates were obtained for the control and the treated plants. Thereafter, the basal part of the stem was submitted to a transient controlled bending at constant displacement rate using a motorized dynamometer. After load removal, stem elongation was again measured for 2 d. The tested plants were mature (height visible internodes) and only the basal part of the stem, which had already finished elongation, was loaded (hypocotyl and the first three internodes). A few minutes after the application of bending, elongation stopped completely for 60 min. Thereafter it took 120-1000 min to recover a rate of elongation similar to the control. The growth response was exclusively due to the bending of the basal part of the stem. It was shown that the side mechanical perturbations on the roots and on the stem tissues interacting directly with the clamp were not significantly involved on the elongation response. These results give evidence for mechanical perception and plant signalling from the basal stem to the upper elongating zone. However, none of the variables characterizing the global mechanical state of the bent part of the stem (i.e. the maximal force, bending moment, inclination, mean curvature of the stem, stored mechanical energy) could quantitatively explain the variability of the growth response. A more local mechanical analysis is therefore needed to elucidate how the mechanical stimulus is perceived.     

Environmetric time-series analysis: modelling natural systems from experimental time-series data

Using the modelling of solute transport in flowing media as an example, this paper outlines the main aspects of a systematic approach to the modelling of natural systems from experimental time-series data. The objective of the approach, which exploits sophisticated methods of recursive parameter estimation, is to produce a parametrically efficient, data-based model which is both physically meaningful and statistically well defined. Although the proposed methodology has its origins in systems and control theory and may be unfamiliar to some natural scientists, it has been developed and refined for use with natural environmental systems over the past 20 years, and has wide application potential in areas such as biology and ecology. In this sense, the paper is intended to introduce the more general reader to the topic, in the hope that the tutorial review and practical examples will stimulate interest and encourage reference to the many publications cited in the paper. The practical examples are concerned with the modelling of pollutant dispersion in stream channels: phloem translocation and carbon partitioning in plants: and rainfall-streamflow modelling in a river catchment.     

Delayed leaf senescence in ethylene-deficient ACC-oxidase antisense tomato plants: molecular and physiological analysis

To determine the role of ethylene during tomato (Lycopersicon esculentum Mill. cv. Alisa Craig) leaf senescence, transgenic ACC oxidase antisense plants were analysed. Northern analysis of wild-type plants indicated that ACC oxidase mRNA accumulation normally begins in pre-senescent green leaves but was severely reduced in the antisense plants. Although the levels of ethylene evolved by wild-type and transgenic leaves increased during the progression of senescence, levels were extremely low in transgenic leaves. Leaf senescence, as assessed by colour change from green to yellow, was clearly delayed by 10–14 days in the antisense plants when compared with wild-type plants. Northern analysis of the photosynthesis-associated genes, cab and rbcS, indicated that levels of the corresponding mRNAs were higher in transgenic leaves which were not yet senescing compared with senescing wild-type leaves of exactly the same age. Northern analysis using probes for tomato fruit ripening-related genes expressed during leaf senescence indicated that once senescence was initiated the expression pattern of these mRNAs was similar in transgenic and wild-type leaves. In the antisense plants chlorophyll levels, photosynthetic capacity and chlorophyll fluorescence were higher when compared with senescing wild-type plants of the same age. Photosynthetic capacity and the quantum efficiency of photosystem II were maintained for longer in the transformed plants at values close to those observed in wild-type leaves prior to the visible onset of senescence. These results indicate that inhibiting ACC oxidase expression and ethylene synthesis results in delayed leaf senescence, rather than inducing a stay-green phenotype. Once senescence begins, it progresses normally. Onset of senescence is not, therefore, related to a critical level of ethylene. The correlation between higher levels prior to senescence and early onset, however, suggests that ethylene experienced by the plant may be a significant contributing factor in the timing of senescence.     

High-resolution genetic map of the Lv resistance locus in tomato

 Bulked segregant analysis and high-resolution mapping were used to pinpoint the position of the Lv gene for resistance to Leveillula taurica in tomato. Mapping in an F₂, corresponding to more than 3800 gametes, indicates that Lv is positioned within the 0.84-cM interval defined by the RFLP markers CT121 and CT129, with the closest marker, CT121, being only 0.16 cM from the gene. The tight linkage of these markers demonstrates their usefulness in marker-assisted breeding for Lv, and the high-resolution map provides a starting a starting point for positional cloning of this resistance gene. Received: 25 February 1997 / Accepted: 21 March 1997     

Functional analysis of gene-silencing suppressors from tomato yellow leaf curl disease viruses

Tomato yellow leaf curl disease (TYLCD) is caused by a complex of phylogenetically related Begomovirus spp. that produce similar symptoms when they infect tomato plants but have different host ranges. In this work, we have evaluated the gene-silencing-suppression activity of C2, C4, and V2 viral proteins isolated from the four main TYLCD-causing strains in Spain in Nicotiana benthamiana. We observed varying degrees of local silencing suppression for each viral protein tested, with V2 proteins from all four viruses exhibiting the strongest suppression activity. None of the suppressors were able to avoid the spread of the systemic silencing, although most produced a delay. In order to test the silencing-suppression activity of Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) proteins in a shared (tomato) and nonshared (bean) host, we established novel patch assays. Using these tools, we found that viral proteins from TYLCV were able to suppress silencing in both hosts, whereas TYLCSV proteins were only effective in tomato. This is the first time that viral suppressors from a complex of disease-causing geminiviruses have been subject to a comprehensive analysis using two economically important crop hosts, as well as the established N. benthamiana plant model.     

Effects of soil resistance to root penetration on leaf expansion in wheat (Triticum aestivum L.): kinematic analysis of leaf elongation

Wheat leaves (Triticum aestivum L.) elongated 50% more slowlywhen plants were grown in soils with high mechanical resistanceto penetration (R_s. The profiles of epidermal cell lengths alongthe growth zone of expanding leaves and the locations of newlyformed walls were recorded in order to compare the kineticsof elongation and partitioning of both meristematic and non-meristematiccells. In leaf 5, which completely developed under stress, highR_s, did not affect the flux of mature cells through the elongationzone; leaf elongation was reduced only because these cells wereshorter. This reduced size reflected a reduction in cell lengthat partitioning, associated with shorter cycling time. The relativerates of cell elongation before and after partitioning wereunchanged. Cell fluxes were similar because the population ofmeristematic cells was reduced, offsetting their increased partitioningrate. In contrast, in leaf 1, high R_s, had no effect on thenumber of dividing cells; elongation rate was reduced becauseof slower relative cell expansion rate and slower cell partitioningrate. These differences could reflect differences in the stageat which successive leaves perceived root stress and also time-dependentchanges in the responsiveness of leaf development to stress-inducedroot signals or in the nature of these signals. The data reveal that cell cycling time may in fact be decreasedby unfavourable growth conditions and is not directly relatedto cell expansion rates; they also show that the elongationrate of meristematic cells is partly independently controlledfrom that of non-meristematic cells. Key words: Wheat, kinematics of leaf expansion, cell partitioning, cell elongation, root impedance     

The application of various anatomical techniques for studying the hydraulic network in tomato fruit pedicels

The abscission zone in fruit pedicels plays an important role in affecting not only water uptake in the developing fruit, but also in the transport of chemical signals from root to shoot. In order to characterize the hydraulic network of tomato fruit pedicels, we applied various techniques, including light, fluorescence microscopy, electron microscopy, maceration, tissue clearing, and X-ray computed tomography. Because of significant changes in xylem anatomy, the abscission zone in tomato fruit pedicels is illustrated to show a clear reduction in hydraulic conductance. Based on anatomical measurements, the theoretical axial xylem conductance was calculated via the Hagen–Poiseuille law, suggesting that the hydraulic resistance of the abscission zone increases at least two orders of magnitude compared to the pedicel zone near the stem. The advantages and shortcomings of the microscope techniques applied are discussed.     

High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs

MicroRNAs play a fundamental role in retinal development and function. To characterise the miRNome of the human retina, we carried out deep sequencing analysis on sixteen individuals. We established the catalogue of retina-expressed miRNAs, determined their relative abundance and found that a small number of miRNAs accounts for almost 90% of the retina miRNome. We discovered more than 3000 miRNA variants (isomiRs), encompassing a wide range of sequence variations, which include seed modifications that are predicted to have an impact on miRNA action. We demonstrated that a seed-modifying isomiR of the retina-enriched miR-124-3p was endowed with different targeting properties with respect to the corresponding canonical form. Moreover, we identified 51 putative novel, retina-specific miRNAs and experimentally validated the expression for nine of them. Finally, a parallel analysis of the human Retinal Pigment Epithelium (RPE)/choroid, two tissues that are known to be crucial for retina homeostasis, yielded notably distinct miRNA enrichment patterns compared to the retina. The generated data are accessible through an ad hoc database. This study is the first to reveal the complexity of the human retina miRNome at nucleotide resolution and constitutes a unique resource to assess the contribution of miRNAs to the pathophysiology of the human retina.     

The relationship between leaf growth and ABA accumulation in the grass leaf elongation zone

Detached barley (Hordeum vulgare L.) shoots, maintained at different air temperatures and VPDs, were fed ABA via the sub-crown internode in a leaf elongation assay. Analysis of variance of leaf elongation rate (LER) showed significant effects of temperature (T), fed [ABA] and the interaction T × [ABA]. However, the interaction became non-significant when LER was modelled against the [ABA] of the elongation zone, [EZ-ABA] When detached barley shoots were fed sap from droughted maize (Zea mays L.) plants, sap [ABA] could not explain the growth inhibitory activity. Measurement of [EZ-ABA] accounted for this ‘unexplained’ growth inhibition. The detached shoot experiments indicated that [EZ-ABA], and not xylem sap [ABA], was an appropriate explanatory variable to measure in droughted plants. However, ABA accumulation in the elongation zone could not explain a 35% growth reduction in intact droughted plants; thus we considered an interaction of water status and ABA. Using a coleoptile growth assay, we applied mild osmotic stresses (ψ=0 to ?0.06 MPa) and 10^?4 mol m^?3 ABA. Individually, these treatments did not inhibit growth. However, osmotic stress and ABA applied together significantly reduced growth. This interaction may be an important mechanism in explaining leaf growth inhibition of droughted plants.     

Microsurgical and laser ablation analysis of leaf positioning and dorsoventral patterning in tomato

Leaves are arranged according to regular patterns, a phenomenon referred to as phyllotaxis. Important determinants of phyllotaxis are the divergence angle between successive leaves, and the size of the leaves relative to the shoot axis. Young leaf primordia are thought to provide positional information to the meristem, thereby influencing the positioning of new primordia and hence the divergence angle. On the contrary, the meristem signals to the primordia to establish their dorsoventral polarity, which is a prerequisite for the formation of a leaf blade. These concepts originate from classical microsurgical studies carried out between the 1920s and the 1970s. Even though these techniques have been abandoned in favor of genetic analysis, the resulting insights remain a cornerstone of plant developmental biology. Here, we employ new microsurgical techniques to reassess and extend the classical studies on phyllotaxis and leaf polarity. Previous experiments have indicated that the isolation of an incipient primordium by a tangential incision caused a change of divergence angle between the two subsequent primordia, indicating that pre-existing primordia influence further phyllotaxis. Here, we repeat these experiments and compare them with the results of laser ablation of incipient primordia. Furthermore, we explore to what extent the different pre-existing primordia influence the size and position of new organs, and hence phyllotaxis. We propose that the two youngest primordia (P1 and P2) are sufficient for the approximate positioning of the incipient primordium (I1), and therefore for the perpetuation of the generative spiral, whereas the direct contact neighbours of I1 (P2 and P3) control its delimitation and hence its exact size and position. Finally, we report L1-specific cell ablation experiments suggesting that the meristem L1 layer is essential for the dorsoventral patterning of leaf primordia.     

Short time-series microarray analysis: Methods and challenges

The rapid accumulation of various network-related data from multiple species and conditions (e.g. disease versus normal) provides unprecedented opportunities to study the function and evolution of biological systems. Comparison of biomolecular networks between species or conditions is a promising approach to understanding the essential mechanisms used by living organisms. Computationally, the basic goal of this network comparison or 'querying' is to uncover identical or similar subnetworks by mapping the queried network (e.g. a pathway or functional module) to another network or network database. Such comparative analysis may reveal biologically or clinically important pathways or regulatory networks. In particular, we argue that user-friendly tools for network querying will greatly enhance our ability to study the fundamental properties of biomolecular networks at a system-wide level.     

Life table parameters of the tomato leaf miner Tuta absoluta (Lepidoptera: Gelechiidae) on different tomato cultivars

The tomato leaf miner Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is a devastating pest of tomato plants originating from South America. In this study, the effect of three tomato cultivars on the life table parameters of T. absoluta was investigated. Data were analysed based on age‐stage, two‐sex life table theory. The net reproduction rate (R₀) of T. absoluta on Falkato, Isabella and Grandella cultivars was determined as 15.73 ± 3.35, 17.66 ± 3.33 and 10.03 ± 4.10 eggs, respectively. The intrinsic rate of increase (r) value on those cultivars was 0.09 ± 0.007, 0.095 ± 0.006 and 0.074 ± 0.017 day^?1, respectively. Finite population rates of increase (λ) were 1.095 ± 0.008, 1.099 ± 0.007 and 1.076 ± 0.018 day^?1, and mean generation times (T) on the three cultivars were 30.09 ± 0.29, 30.22 ± 0.27 and 31.12 ± 0.65 days, respectively. The egg incubation period, pre‐adult duration and fecundity on these tomato cultivars was also calculated. The results showed no significant differences between r, R₀, and T on the three tested tomato cultivars. These findings can be useful for developing an integrated pest management strategy against this noxious pest.     

Brassinazole represses tomato hypocotyl elongation via inhibition of cell division

Plant Growth Regulation - Hypocotyl length is determined by cell division and elongation, which are associated with canonical cell cycle and endoreduplication. Plant hormone brassinosteroid (BR) is...     

Dynamic aspects and enhancement of leaf elongation in rice

Some dynamic aspects of leaf elongation in rice were studied. Under both well watered and water-deficient conditions, leaf elongation rates were 15 to 30% greater during the day than during the night. Night temperatures below 27 C limited the rate of elongation at night but when night temperatures exceeded 27 C, night elongation rates exceeded rates during the day. The diurnal pattern of elongation was opposite to the pattern of bulk leaf turgor which was lower during the day than at night.