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Results for “Plant Biology”

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At least 109 records · Page 6Linked to original sources

bioRxiv2015

Auxin signaling is a common factor underlying natural variation in tomato shade avoidance

Light is an essential resource for photosynthesis. Limitation of light by shade from plant neighbors can induce a light competition program known as the shade avoidance response (SAR), thereby altering plant growth and development for the sake of survival. Natural genetic variation in SAR is found in plants adapted to distinct environments, including domesticated tomato Solanum lycopersicum and its wild relative Solanum pennellii. QTL mapping was used to examine variation of the SAR between these two species. We found organ specific responses in the elongation of the stem and petiole, including developmental acceleration of growth. Through RNAseq analysis we identified a number of ILs with reduced expression of auxin-related genes in shade treatment. These same ILs display a shade tolerant phenotype in stem growth and overall height. We also identified ILs with altered SAR expression of cell wall expansion genes, although these genotypes had no accompanying alteration in phenotype. Examination of weighted gene co-expression Connectivity networks in sun- and shade-treated plants revealed Connectivity changes in auxin and light signaling genes; this result was supported by the Identification of motifs within the promoters of a subset of shade-responsive genes that were enriched in light signaling, developmental pathways, and auxin responsive transcriptional domains. The Identification ofboth systemic and organ-specific shade tolerance in the ILs, as well as associated changes in the transcriptome, has the potential to inform future studies for breeding plants able to be grown closely (while neighbor-shaded), yet still maintaining high yield.\n\nSummaryGrowth plasticity in response to shade involves expression of specific auxin signaling and cell wall expansion genes, and shade avoidance QTL affect both stem elongation and developmental rate.

Plant Biology↗

bioRxiv2015

Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in Arabidopsis thaliana

BackgroundPlant meristems are analogous to animal stem cell niches as they maintain a pool of undifferentiated cells that divide and differentiate to give rise to organs. The carpel margin meristem is a vital, multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development.\n\nResultsUsing a floral synchronization system and a SHATTERPROOF2 domain-specific reporter, paired with fluorescence-activated cell sorting and RNA sequencing, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. This analysis reveals a set of genes that are differentially expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members including differentially expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development. Members of the REPRODUCTIVE MERISTEM (REM) family of transcriptional regulators were enriched in the SHATTERPROOF2-expressing cell population including a previously unrecognized REM family member. Finally, the analysis transcriptional isoforms in the medial domain identified genes that may exhibit \"isoform switching\" behavior during gynoecial development.\n\nConclusionsThis data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, a vital reproductive structure that gives rise to the ovules in Arabidopsis thaliana.

Plant Biology↗

bioRxiv2015

Segmental interpolation surface: a tool to dissect environmental effects on plant water-use efficiency in drought prone scenarios

Water use efficiency (WUE), defined as the ratio of biomass (B) produced per unit of water transpired (E) by plants, is an important determinant of plant productivity. A mathematical approach was developed with the purpose explaining the WUE of two forage legumes (clover and birdsfoot trefoil). The approach applied involved an interpolation method by cubic spline which results in the smoothest curve that fits the set of data points obtained experimentally. The results obtained show the importance of recognizing the WUE as a function of two variables, one represents the supply ({theta}) and the other represents the demand (D). It is important to note that these surfaces generated by the model allowed the estimation of the WUE value for any value of {theta} and any value of D, showing it is able to dissect the effect of both environmental variables on WUE. From the surface generated by the model, a scalar field plot (SFP) was created. Analysis of these SFPs allowed decomposing the environmental effect on B and E parameters defining WUE. The SFPs allow identify, in one picture, what are the environmental conditions and what variable are explaining a high WUE in both species. Spline application for generating SFP could have a significant impact on the quantitative understanding of the WUE and our study represents a first step towards an analytical and integrated view of this parameters.\n\nMathematics Subject Classification 92B05 65D05 65D07 65D10

Plant Biology↗

bioRxiv2015

SLTAB2 is the paramutated SULFUREA locus in tomato

The sulfurea (sulf) allele is a silent epigenetic variant of a tomato gene (Solanum lycopersicum) affecting pigment production. It is homozygous lethal but, in a heterozygote sulf/+, the wild type allele undergoes silencing so that the plants exhibit chlorotic sectors. This transfer of the silenced state between alleles resembles the process of paramutation that is best characterised in maize. To understand the mechanism of paramutation we mapped SULF to the ortholog SLTAB2 of an Arabidopsis gene that, consistent with the pigment deficiency, is involved in the translation of photosystem I. Paramutation of SLTAB2 is linked to an increase in DNA methylation and production of small interfering RNAs at its promoter. Virus-induced gene silencing of SLTAB2 phenocopies sulf consistent with the possibility that siRNAs mediate the paramutation of SULFUREA. Unlike the maize systems the paramutagenicity of sulf is not, however, associated with repeated sequences at the region of siRNA production or DNA methylation.

Plant Biology↗

bioRxiv2015

Genomic and Chemical Diversity in Cannabis

Plants of the Cannabis genus are the only producers of phytocannabinoids, terpenoid compounds that strongly interact with evolutionarily ancient endocannabinoid receptors shared by most bilaterian taxa. For millennia, the plant has been cultivated for these compounds, but also for food, rope, paper, and clothing. Today, specialized varieties yielding high-quality textile fibers, nutritional seed oil or high cannabinoid content are cultivated across the globe. However, the genetic identities and histories of these diverse populations remain largely obscured. We analyzed the nuclear genomic diversity among 340 Cannabis varieties, including fiber and seed oil hemp, high cannabinoid drug-types and feral populations. These analyses demonstrate the existence of at least three major groups of diversity, with European hemp varieties more closely related to narrow leaflet drug-types (NLDT) than to broad leaflet drug-types (BLDT). The BLDT group appears to encompass less diversity than the NLDT, which reflects the larger geographic range of NLDTs, and suggests a more recent origin of domestication of the BLDTs. As well as being genetically distinct, hemp, NLDT and BLDT genetic groups each produce unique cannabinoid and terpenoid content profiles. This combined analysis of population genomic and trait variation informs our understanding of the potential uses of different genetic variants for medicine and agriculture, providing valuable insights and tools for a rapidly emerging, valuable legal industry.

Plant Biology↗

bioRxiv2015

The Arabidopsis Auxin F-box proteins AFB4 and AFB5 are Required for Response to the Synthetic Auxin Picloram

The plant hormone auxin is perceived by a family of F-box proteins called the TIR1/AFBs. Phylogenetic studies reveal that these proteins fall into four clades in flowering plants called TIR1, AFB2, AFB4, and AFB6 (Parry et al. 2009). Genetic studies indicate that members of the TIR1 and AFB2 groups act as positive regulators of auxin signaling by promoting the degradation of the Aux/IAA transcriptional repressors (Dharmasiri et al. 2005; Parry et al. 2009). In this report, we demonstrate that both AFB4 and AFB5 also function as auxin receptors based on in vitro assays. We also provide genetic evidence that both AFB4 and AFB5 are targets of the picloram family of auxinic herbicides. In contrast to previous studies we find that null afb4 alleles do not exhibit obvious defects in seedling morphology or auxin hypersensitivity. We conclude that AFB4 and AFB5 act in a similar fashion to other members of the family but exhibit a distinct auxin specificity.

Plant Biology↗

bioRxiv2015

Arabidopsis late blight: Infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans

The oomycete pathogen Phytophthora infestans causes potato late blight, and as a potato and tomato specialist pathogen, is seemingly poorly adapted to infect plants outside the Solanaceae. Here, we report the unexpected finding that P. infestans can infect Arabidopsis thaliana when another oomycete pathogen, Albugo laibachii, has colonized the host plant. The behaviour and speed of P. infestans infection in Arabidopsis pre-infected with A. laibachii resemble P. infestans infection of susceptible potato plants. Transcriptional profiling of P. infestans genes during infection revealed a significant overlap in the sets of secreted-protein genes that are induced in P. infestans upon colonisation of potato and susceptible Arabidopsis, suggesting major similarities in P. infestans gene expression dynamics on the two plant species. Furthermore, we found haustoria of A. laibachii and P. infestans within the same Arabidopsis cells. This Arabidopsis - A. laibachii - P. infestans tripartite interaction opens up various possibilities to dissect the molecular mechanisms of P. infestans infection and the processes occurring in co-infected Arabidopsis cells.

Plant Biology↗

bioRxiv2015

Post-embryonic hourglass patterns mark ontogenetic transitions in plant development

The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found post-embryonically. We found that the two main phase changes during the life cycle of Arabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints.

Plant Biology↗

bioRxiv2016

Canopy position has a profound effect on soybean seed composition

Although soybean seeds appear homogeneous, their composition (protein, oil and mineral concentrations) can vary significantly with the canopy position where they were produced. In studies with 10 cultivars grown over a 3-yr period, we found that seeds produced at the top of the canopy have higher concentrations of protein but less oil and lower concentrations of minerals such as Mg, Fe, and Cu compared to seeds produced at the bottom of the canopy. Among cultivars, mean protein concentration (average of different positions) correlated positively with mean concentrations of S, Zn and Fe, but not other minerals. Therefore, on a whole plant basis, the uptake and allocation of S, Zn and Fe to seeds correlated with the production and allocation of reduced N to seed protein; however, the reduced N and correlated minerals (S, Zn and Fe) showed different patterns of allocation among node positions. For example, while mean concentrations of protein and Fe correlated positively, the two parameters correlated negatively in terms of variation with canopy position. Altering the microenvironment within the soybean canopy by removing neighboring plants at flowering increased protein concentration in particular at lower node positions and thus altered the node-position gradient in protein (and oil) without altering the distribution of Mg, Fe and Cu, suggesting different underlying control mechanisms. Metabolomic analysis of developing seeds at different positions in the canopy suggests that availability of free asparagine may be a positive determinant of storage protein accumulation in seeds and may explain the increased protein accumulation in seeds produced at the top of the canopy. Our results establish node-position variation in seed constituents and provide a new experimental system to identify genes controlling key aspects of seed composition. In addition, our results provide an unexpected and simple approach to link agronomic practices to improve human nutrition and health in developing countries because food products produced from seeds at the bottom of the canopy contained higher Fe concentrations than products from the top of the canopy. Therefore, using seeds produced in the lower canopy for production of iron-rich soy foods for human consumption could be important when plants are the major source of protein and human diets can be chronically deficient in Fe and other minerals.

Plant Biology↗

bioRxiv2016

A bacterial parasite effector mediates insect vector attraction in host plants independently of developmental changes

Parasites can take over their hosts and trigger dramatic changes in host appearance and behaviour that are typically interpreted as extended phenotypes to promote parasite survival and fitness1. For example, Toxoplasma gondii manipulates the behaviour of infected rodents to aid transmission to cats2 and parasitic trematodes of the genus Ribeiroia alter limb development in their amphibian hosts to facilitate predation by birds3. Plant parasites and pathogens also reprogram host development and morphology4. Phytoplasma parasites of plants induce extensive leaf-like flower phenotype (phyllody) in their host plants, presumably to attract insect vectors on which these bacteria depend for transmission5,6. However, it remains debatable whether morphological phenotypes, such as phyllody, are directly beneficial to the parasites or are side-products of parasite infection7,8. Previously, we found that phytoplasma virulence protein (effector) SAP54 binds and mediates degradation of host MADS-box transcription factors 26 (MTFs), regulatory hubs of plant development and hormone physiology, to induce phyllody and promote insect vector colonisation5. Here we show that plants heterologously expressing SAP54 are strongly attractive to insects, but surprisingly, insect attraction was independent of the presence of leaf-like flowers. Moreover, plants that produce leaf-like flowers in the absence of SAP54 did not attract insects. We conclude that the SAP54 effector mediates insect vector attraction in host plants by exploiting the role of its MTF targets in insect defence and that perturbation of floral development may be a secondary effect of the effector activity.

Plant Biology↗

bioRxiv2016

Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana

Molecular data concerning the involvement of the roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutation was reported to alter flowering time are expressed in the roots but only few flowering integrators were found. Transcriptomic analysis of the roots during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. A delay in clock gene expression was observed upon extension of the photoperiod. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories and cis-regulatory elements converged towards sugar signaling. We inferred that roots are integrated in systemic signaling whereby carbon supply coordinates growth at the whole plant level during the induction of flowering.

Plant Biology↗

bioRxiv2016

Changes in bioactive components of Aristolochia tagala .Cham, a rare species of medicinal importance during its in vitro development through direct regeneration

Tissue culture propagation system was developed for Aristolochia tagala, a threatened medicinal plant, using apical bud explants. The most effective medium was found to be MS medium supplemented with BAP (3 M), KIN (0.5 M) and activated charcoal (0.1%). The addition of activated charcoal helped in circumventing the problem of polyphenol exudation from the explants which hampered the regeneration of adventitious shoots. A maximum of 12.6 shoots were obtained on average from the apical bud explants after 25 days of inoculation. Well developed shoots were rooted on MS medium supplemented with indole acetic acid (1.5 M), Kinetin (1.5 M) and 6-benzylaminopurine (0.5 M). Regenerated shoots from the apical buds were successfully rooted and acclimated to greenhouse conditions. Qualitative and quantitative analysis of bioactive compounds was done at various stages of development, so as establish the effect of culture conditions on the production of bioactive components. Comparisons were made between three types of plant material from the same clone: leaves from field-grown plant, leaves from in vitro apical bud cultures and leaf derived callus. It was observed that the leaf derived callus showed the presence of components which were not there in the in vivo leaves, suggesting the influence of in vitro developmental conditions.\n\nTagalaSummary Statement\n\nThis is the first report on direct regeneration of Aristolochia tagala, (a threatened yet important medicinal plant) using apical bud explants derived from mature plants. Also, for the very first time we report the results of analysis of secondary metabolites during its various stages of in vitro development.\n\nAbbreviationsAC - activated charcoal; BAP - 6-benzylaminopurine; 2,4-D - 2,4- dichloro phenoxyacetic acid, IAA - indole acetic acid, IBA - indolebutyric acid, KIN- kinetin, MS- Murashige and Skoog (1962); NAA- -naphthaleneacetic acid.

Plant Biology↗

bioRxiv2016

Plastid degeneration in Tillandsia (Bromeliaceae) provides evidence about the origin of multilamellar bodies in plants

Vesicle-like structures containing several to numerous concentric membranes, called multilamellar bodies (MLBs), are present both in animal and plant cells. The origin of MLBs in animal cells has been elucidated partially, while that of plant MLBs is unknown. MLBs in plant cells are present in the cytoplasm, at the interface of cytoplasm and vacuole, and inside vacuoles. This suggests that they become transported from the cytoplasm to the vacuole. The function of plant MLBs thus seems transfer of cellular membranes to the vacuole. Although it is often impossible to discern whether they have a single or a double outer membrane, in some examples a double outer membrane is present. This might suggest autophagic/mitochondrial/plastidial origin. Membrane structures similar to those in MLBs have not been described, apparently, in mitochondria. By contrast, structures similar to MLBs are found in autophagous structures and in degenerating chloroplasts and other plastids. The data might suggest the hypothesis that plant MLBs derive from autophagous structures and/or from plastids.

Plant Biology↗

bioRxiv2016

Cell re-entry assays do not support models of pathogen- independent translocation of AvrM and AVR3a effectors into plant cells

The cell re-entry assay is widely used to evaluate pathogen effector protein uptake into plant cells. The assay is based on the premise that effector proteins secreted out of a leaf cell would translocate back into the cytosol of the same cell via a yet unknown host-derived uptake mechanism. Here, we critically assess this assay by expressing domains of the effector proteins AvrM-A of Melampsora lini and AVR3a of Phytophthora infestans fused to a signal peptide and fluorescent proteins in Nicotiana benthamiana. We found that the secreted fusion proteins do not re-enter plant cells from the apoplast and that the assay is prone to false-positives. We therefore emit a cautionary note on the use of the cell re-entry assay for protein trafficking studies.

Plant Biology↗

bioRxiv2016

ELF3 polyQ variation in Arabidopsis thaliana reveals a PIF4-independent role in thermoresponsive flowering.

Plants have evolved elaborate mechanisms controlling developmental responses to environmental stimuli. A particularly important stimulus is temperature. Previous work has identified the interplay of PIF4 and ELF3 as a central circuit underlying thermal responses in Arabidopsis thaliana. However, thermal responses vary widely among strains, possibly offering mechanistic insights into the wiring of this circuit. ELF3 contains a polyglutamine (polyQ) tract that is crucial for ELF3 function and varies in length across strains. Here, we use transgenic analysis to test the hypothesis that natural polyQ variation in ELF3 is associated with the observed natural variation in thermomorphogenesis. We found little evidence that the polyQ tract plays a specific role in thermal responses beyond modulating general ELF3 function. Instead, we made the serendipitous discovery that ELF3 plays a crucial, PIF4-independent role in thermoresponsive flowering under conditions more likely to reflect field conditions. We present evidence that ELF3 acts through the photoperiodic pathway, pointing to a previously unknown symmetry between low and high ambient temperature responses. Moreover, in analyzing two strain backgrounds with vastly different thermal responses, we demonstrate that responses may be shifted rather than fundamentally rewired across strains. Our findings tie together disparate observations into a coherent framework in which multiple pathways converge in accelerating flowering in response to temperature, with some such pathways modulated by photoperiod.

Plant Biology↗

bioRxiv2016

PLASTID OSMOTIC STRESS INFLUENCES CELL DIFFERENTIATION AT THE PLANT SHOOT APEX

The balance between proliferation and differentiation in the plant shoot apical meristem is controlled by regulatory loops involving the phytohormone cytokinin and stem cell identity genes. Concurrently, cellular differentiation in the developing shoot is coordinated with the environmental and developmental status of plastids within those cells. Here we employ an Arabidopsis thaliana mutant exhibiting constitutive plastid osmotic stress to investigate the molecular and genetic pathways connecting plastid osmotic stress with cell differentiation at the shoot apex. msl2 msl3 mutants exhibit dramatically enlarged and deformed plastids in the shoot apical meristem, and develop a mass of callus tissue at the shoot apex. Callus production in this mutant requires the cytokinin receptor AHK2 and is characterized by increased cytokinin levels, down-regulation of cytokinin signaling inhibitors ARR7 and ARR15, and induction of the stem cell identity gene WUSCHEL. Furthermore, plastid stress-induced apical callus production requires elevated plastidic ROS, ABA biosynthesis, the retrograde signaling protein GUN1, and ABI4. These results are consistent with a model wherein the cytokinin/WUS pathway and retrograde signaling control cell differentiation at the shoot apex.\n\nSUMMARY STATEMENTPlastid osmotic stress influences differentiation at the plant shoot apex. Two established mechanisms that control proliferation, the cytokinin/WUSCHEL stem cell identity loop and a plastid-to-nucleus signaling pathway, are implicated.

Plant Biology↗

bioRxiv2016

Assessing the relationship between height growth and molecular genetic variation in Douglas-fir (Pseudotsuga menziesii) provenances

Douglas-fir (Pseudotsuga menziesii) is a conifer tree native to western North America. In central Europe, it shows superior growth performance and is considered a suitable substitute for tree species impaired in vitality due to climate change. Maintenance and improvement of growth performance in a changing environment is a main challenge for forest tree breeders. In this context, genetic variation as a factor underlying phenotypic variation, but also as the basis for future adaptation, is of particular interest. The aims of this study were to analyse (i) genetic diversity of selected Douglas-fir provenances, (ii) variation in height growth among provenances, and (iii) to assess the link between genetic and phenotypic variation height growth. Genotyping was done on microsatellite loci. Effects of provenance, genotype, and site on height growth were assessed by fitting mixed linear models. The most significant genetic differentiation was observed between provenances of the coastal variety, versus a provenance of the interior variety originating from British Columbia. Although genetic differentiation among provenances of the coastal variety was lower, genetic structures within this variety were identified. Moreover, genetic diversity showed a latitudinal gradient with the southernmost provenances being more diverse, probably reflecting the species' evolutionary history. The modelling approach revealed that height growth differed significantly by provenance, site, and the interaction between site and provenance, demonstrating that height growth is under strong genetic control. Additionally, this analysis showed that genetic variation captured by the genotyped microsatellite loci was significantly related to variation in height growth, providing statistical evidence for a genetic component in the observed phenotypic variation.

Plant Biology↗

bioRxiv2016

Arabidopsis ATHB17 coordinates nuclear and plastidic photosynthesis gene expression in response to abiotic stress

Photosynthesis is sensitive to environmental stresses. How nuclear and plastid genome coordinate to cope with abiotic stress is not well understood. Here we report that ATHB17, an Arabidopsis HD-Zip transcription factor, coordinates the expression of nuclear encoded photosynthetic genes (NEPGs) and plastid encoded genes (PEGs) in response to abiotic stress. ATHB17-overexpressing plants display enhanced stress tolerance, whereas its knockout mutant is more sensitive compared to the wild type. Through RNA-seq analysis, we found that ATHB17 down-regulated many NEPGs while up-regulated a number of PEGs. ATHB17 could directly modulate the expression of several NEPGs by binding to their promoters. Furthermore, we identified ATSIG5, encoding a plastid sigma factor, as one of the target genes of ATHB17. Loss of ATSIG5 reduced salt tolerance while overexpression of ATSIG5 enhanced salt tolerance, similar to that of ATHB17. Taken together, our results reveal that ATHB17 is an important coordinator between NEPGs and PEGs partially through ATSIG5 to protect photosynthesis machinery in response to abiotic stresses.

Plant Biology↗