The plastochron index: still useful after nearly six decades

Heterologous expression of influenza haemagglutinin leads to early and transient activation of the unfolded protein response in Nicotiana benthamiana

The unfolded protein response (UPR) allows cells to cope with endoplasmic reticulum (ER) stress induced by accumulation of misfolded proteins in the ER. Due to its sensitivity to Agrobacterium tumefaciens, the model plant Nicotiana benthamiana is widely employed for transient expression of recombinant proteins of biopharmaceutical interest, including antibodies and virus surface proteins used for vaccine production. As such, study of the plant UPR is of practical significance, since enforced expression of complex secreted proteins often results in ER stress. After 6 days of expression, we recently reported that influenza haemagglutinin H5 induces accumulation of UPR proteins. Since up-regulation of corresponding UPR genes was not detected at this time, accumulation of UPR proteins was hypothesized to be independent of transcriptional induction, or associated with early but transient UPR gene up-regulation. Using time course sampling, we here show that H5 expression does result in early and transient activation of the UPR, as inferred from unconventional splicing of NbbZIP60 transcripts and induction of UPR genes with varied functions. Transient nature of H5-induced UPR suggests that this response was sufficient to cope with ER stress provoked by expression of the secreted protein, as opposed to an antibody that triggered stronger and more sustained UPR activation. As up-regulation of defence genes responding to H5 expression was detected after the peak of UPR activation and correlated with high increase in H5 protein accumulation, we hypothesize that these immune responses, rather than the UPR, were responsible for onset of the necrotic symptoms on H5-expressing leaves.

Molecular responses of agroinfiltrated Nicotiana benthamiana leaves expressing suppressor of silencing P19 and influenza virus-like particles

The production of influenza vaccines in plants is achieved through transient expression of viral hemagglutinins (HAs), a process mediated by the bacterial vector Agrobacterium tumefaciens. HA proteins are then produced and matured through the secretory pathway of plant cells, before being trafficked to the plasma membrane where they induce formation of virus-like particles (VLPs). Production of VLPs unavoidably impacts plant cells, as do viral suppressors of RNA silencing (VSRs) that are co-expressed to increase recombinant protein yields. However, little information is available on host molecular responses to foreign protein expression. This work provides a comprehensive overview of molecular changes occurring in Nicotiana benthamiana leaf cells transiently expressing the VSR P19, or co-expressing P19 and an influenza HA. Our data identifies general responses to Agrobacterium-mediated expression of foreign proteins, including shutdown of chloroplast gene expression, activation of oxidative stress responses and reinforcement of the plant cell wall through lignification. Our results also indicate that P19 expression promotes salicylic acid (SA) signalling, a process dampened by co-expression of the HA protein. While reducing P19 level, HA expression also induces specific signatures, with effects on lipid metabolism, lipid distribution within membranes and oxylipin-related signalling. When producing VLPs, dampening of P19 responses thus likely results from lower expression of the VSR, crosstalk between SA and oxylipin pathways, or a combination of both outcomes. Consistent with the upregulation of oxidative stress responses, we finally show that reduction of oxidative stress damage through exogenous application of ascorbic acid improves plant biomass quality during production of VLPs.

Cellular dynamics in the maize leaf growth zone during recovery from chilling depends on the leaf developmental stage

KEY MESSAGE

A novel non-steady-state kinematic analysis shows differences in cell division and expansion determining a better recovery from a 3-day cold spell in emerged compared to non-emerged maize leaves. Zea mays is highly sensitive to chilling which frequently occurs during its seedling stage. Although the direct effect of chilling is well studied, the mechanisms determining the subsequent recovery are still unknown. Our goal is to determine the cellular basis of the leaf growth response to chilling and during recovery of leaves exposed before or after their emergence. We first studied the effect of a 3-day cold spell on leaf growth at the plant level. Then, we performed a kinematic analysis to analyse the dynamics of cell division and elongation during recovery of the 4th leaf after exposure to cold before or after emergence. Our results demonstrated cold more strongly reduced the final length of non-emerged than emerged leaves (- 13 vs. - 18%). This was not related to growth differences during cold, but a faster and more complete recovery of the growth of emerged leaves. This difference was due to a higher cell division rate on the 1st and a higher cell elongation rate on the 2nd day of recovery, respectively. The dynamics of cell division and expansion during recovery determines developmental stage-specific differences in cold tolerance of maize leaves.

Model-based reconstruction of whole organ growth dynamics reveals invariant patterns in leaf morphogenesis

Plant organ morphogenesis spans several orders of magnitude in time and space. Because of limitations in live-imaging, analysing whole organ growth from initiation to mature stages typically rely on static data sampled from different timepoints and individuals. We introduce a new model-based strategy for dating organs and for reconstructing morphogenetic trajectories over unlimited time windows based on static data. Using this approach, we show that Arabidopsis thaliana leaves are initiated at regular 1-day intervals. Despite contrasted adult morphologies, leaves of different ranks exhibited shared growth dynamics, with linear gradations of growth parameters according to leaf rank. At the sub-organ scale, successive serrations from same or different leaves also followed shared growth dynamics, suggesting that global and local leaf growth patterns are decoupled. Analysing mutants leaves with altered morphology highlighted the decorrelation between adult shapes and morphogenetic trajectories, thus stressing the benefits of our approach in identifying determinants and critical timepoints during organ morphogenesis.

Late-day measurement of excised branches results in uncertainty in the estimation of two stomatal parameters derived from response curves in Populus deltoides Bartr. × Populus nigra L

Many terrestrial biosphere models depend on an understanding of the relationship between stomatal conductance and photosynthesis. However, unlike the measurement of photosynthetic parameters, such as the maximum carboxylation capacity, where standard methods (e.g., CO2 response or ACi curves) are widely accepted, a consensus method for empirically measuring parameters representing stomatal response has not yet emerged. Most models of stomatal response to environment represent stomatal conductance as being bounded by a lower intercept parameter (g0), and linearly scaled based on a multivariate term described by the stomatal slope parameter (g1). Here we employ the widely used Unified Stomatal Optimization model, to test whether g1 and g0 parameters are impacted by the choice of measurement method, either on an intact branch or a cut branch segment stored in water. We measured paired stomatal response curves on intact and excised branches of a hybrid poplar clone (Populus deltoides Bartr. × Populus nigra L. OP367), measured twice over a diurnal period. We found that predawn branch excision did not significantly affect measured g0 and g1 when measured within 4 h of excision. Measurement in the afternoon resulted in significantly higher values of g1 and lower values of g0, with values changing by 55% and 56%, respectively. Excision combined with afternoon measurement resulted in a marked effect on parameter estimates, with g1 increasing 89% from morning to afternoon and a 25% lower g1 for cut branches than those measured in situ. We also show that in hybrid poplar the differences in parameter estimates obtained from plants measured under different conditions can directly impact models of canopy function, reducing modeled transpiration by 18% over a simulated 12.5-h period. Although these results are only for a single isohydric woody species, our findings suggest that stomatal optimality parameters may not remain constant throughout the day.

The PagKNAT2/6b-PagBOP1/2a Regulatory Module Controls Leaf Morphogenesis in Populus

Leaf morphogenesis requires precise regulation of gene expression to achieve organ separation and flat-leaf form. The poplar KNOTTED-like homeobox gene PagKNAT2/6b could change plant architecture, especially leaf shape, in response to drought stress. However, its regulatory mechanism in leaf development remains unclear. In this work, gene expression analyses of PagKNAT2/6b suggested that PagKNAT2/6b was highly expressed during leaf development. Moreover, the leaf shape changes along the adaxial-abaxial, medial-lateral, and proximal-distal axes caused by the mis-expression of PagKNAT2/6b demonstrated that its overexpression (PagKNAT2/6b OE) and SRDX dominant repression (PagKNAT2/6b SRDX) poplars had an impact on the leaf axial development. The crinkle leaf of PagKNAT2/6b OE was consistent with the differential expression gene PagBOP1/2a (BLADE-ON-PETIOLE), which was the critical gene for regulating leaf development. Further study showed that PagBOP1/2a was directly activated by PagKNAT2/6b through a novel cis-acting element "CTCTT". Together, the PagKNAT2/6b-PagBOP1/2a module regulates poplar leaf morphology by affecting axial development, which provides insights aimed at leaf shape modification for further improving the drought tolerance of woody plants.

Understanding Willow Transcriptional Response in the Context of Oil Sands Tailings Reclamation

One of the reclamation objectives for treated oil sands tailings (OST) is to establish boreal forest communities that can integrate with the surrounding area. Hence, selection of appropriate soil reclamation cover designs and plant species for revegetation are important aspects of tailings landform reclamation and closure. Research and monitoring of the long term and immediate impacts of capped OST on the growth and survival of native boreal plant species are currently underway. However, plant responses to OST-associated toxicity are not well known at the molecular level. Using RNA sequencing, we examined the effects of three types of OST on the willow transcriptome under different capping strategies. The transcriptomic data showed that some genes respond universally and others in a specific manner to different types of OST. Among the dominant and shared upregulated genes, we found some encoding protein detoxification (PD), Cytochrome P450 (CYPs), glutathione S-transferase regulatory process (GST), UDP-glycosyltransferase (UGT), and ABC transporter and regulatory process associated proteins. Moreover, genes encoding several stress-responsive transcription factors (bZIP, BHLH, ERF, MYB, NAC, WRKY) were upregulated with OST-exposure, while high numbers of transcripts related to photosynthetic activity and chloroplast structure and function were downregulated. Overall, the expression of 40 genes was found consistent across all tailings types and capping strategies. The qPCR analysis of a subset of these shared genes suggested that they could reliably distinguish plants exposed to different OST associated stress. Our results indicated that it is possible to develop OST stress exposure biosensors merely based on changes in the level of expression of a relatively small set of genes. The outcomes of this study will further guide optimization of OST capping and revegetation technology by using knowledge based plant stress adaptation strategies.

Towards a Stochastic Model to Simulate Grapevine Architecture: A Case Study on Digitized Riesling Vines Considering Effects of Elevated CO2

Modeling plant growth, in particular with functional-structural plant models, can provide tools to study impacts of changing environments in silico. Simulation studies can be used as pilot studies for reducing the on-field experimental effort when predictive capabilities are given. Robust model calibration leads to less fragile predictions, while introducing uncertainties in predictions allows accounting for natural variability, resulting in stochastic plant growth models. In this study, stochastic model components that can be implemented into the functional-structural plant model Virtual Riesling are developed relying on Bayesian model calibration with the goal to enhance the model towards a fully stochastic model. In this first step, model development targeting phenology, in particular budburst variability, phytomer development rate and internode growth are presented in detail. Multi-objective optimization is applied to estimate a single set of cardinal temperatures, which is used in phenology and growth modeling based on a development days approach. Measurements from two seasons of grapevines grown in a vineyard with free-air carbon dioxide enrichment (FACE) are used; thus, model building and selection are coupled with an investigation as to whether including effects of elevated CO2 conditions to be expected in 2050 would improve the models. The results show how natural variability complicates the detection of possible treatment effects, but demonstrate that Bayesian calibration in combination with mixed models can realistically recover natural shoot growth variability in predictions. We expect these and further stochastic model extensions to result in more realistic virtual plant simulations to study effects, which are used to conduct in silico studies of canopy microclimate and its effects on grape health and quality.

An improved and efficient method of Agrobacterium syringe infiltration for transient transformation and its application in the elucidation of gene function in poplar

BACKGROUND

Forest trees have important economic and ecological value. As a model tree, poplar has played a significant role in elucidating the molecular mechanisms underlying tree biology. However, a lack of mutant libraries and time-consuming stable genetic transformation processes severely limit progress into the functional characterization of poplar genes. A convenient and fast transient transformation method is therefore needed to enhance progress on functional genomics in poplar.

METHODS

A total of 11 poplar clones were screened for amenability to syringe infiltration. Syringe infiltration was performed on the lower side of the leaves of young soil-grown plants. Transient expression was evaluated by visualizing the reporters β-glucuronidase (GUS) and green fluorescent protein (GFP). The experimental parameters of the syringe agroinfiltration were optimized based on the expression levels of the reporter luciferase (LUC). Stably transformed plants were regenerated from transiently transformed leaf explants through callus-induced organogenesis. The functions of Populus genes in secondary cell wall-thickening were characterized by visualizing lignin deposition therein after staining with basic fuchsin.

RESULTS

We greatly improved the transient transformation efficiency of syringe Agrobacterium infiltration in poplar through screening for a suitable poplar clone from a variety of clones and optimizing the syringe infiltration procedure. The selected poplar clone, Populus davidiana × P. bolleana, is amenable to Agrobacterium syringe infiltration, as indicated by the easy diffusion of the bacterial suspension inside the leaf tissues. Using this technique, we localized a variety of poplar proteins in specific intracellular organelles and illustrated the protein-protein and protein-DNA interactions. The transiently transformed leaves could be used to generate stably transformed plants with high efficiency through callus induction and differentiation processes. Furthermore, transdifferentiation of the protoxylem-like vessel element and ectopic secondary wall thickening were induced in the agroinfiltrated leaves via the transient overexpression of genes associated with secondary wall formation.

CONCLUSIONS

The application of P. davidiana × P. bolleana in Agrobacterium syringe infiltration provides a foundation for the rapid and high-throughput functional characterization of Populus genes in intact poplar plants, including those involved in wood formation, and provides an effective alternative to Populus stable genetic transformation.

Leaf shape in Populus tremula is a complex, omnigenic trait

Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome-wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA-Seq data that we used to perform gene co-expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.

Temporal Distinction between Male and Female Floral Organ Development in Nicotiana tabacum cv. Xanthi (Solanaceae)

Early floral developmental investigations provide crucial evidence for phylogenetic and molecular studies of plants. The developmental and evolutionary mechanisms underlying the variations in floral organs are critical for a thorough understanding of the diversification of flowers. Ontogenetic comparisons between anthers and pistil within single flowers were characterized over time in Nicotiana tabacum cv. Xanthi. The ages of 42 tobacco flower or flower primordia were estimated using corolla growth analysis. Results showed that the protodermal layer in carpel primordia contributes to carpel development by both anticlinal and periclinal divisions. Periclinal divisions in the hypodermal layer of the placenta were observed around 4.8 ± 1.3 days after the formation of early carpel primordia (ECP) and ovule initiation occurred 10.0 ± 0.5 days after ECP. Meiosis in anthers and ovules began about 8.9 ± 1.1 days and 14.4 ± 1.3 days after ECP, respectively. Results showed an evident temporal distinction between megasporogenesis and microsporogenesis. Flower ages spanned a 17-day interval, starting with flower primordia containing the ECP and anther primordia to the tetrad stage of meiosis in megasporocytes and the bicellular stage in pollen grains. These results establish a solid foundation for future studies in order to identify the developmental and molecular mechanisms responsible for the mating system in tobacco.

Protocols for Investigating the Leaf Mycobiome Using High-Throughput DNA Sequencing

High-throughput sequencing of taxon-specific loci, or DNA metabarcoding, has become an invaluable tool for investigating the composition of plant-associated fungal communities and for elucidating plant-fungal interactions. While sequencing fungal communities has become routine, there remain numerous potential sources of systematic error that can introduce biases and compromise metabarcoding data. This chapter presents a protocol for DNA metabarcoding of the leaf mycobiome based on current best practices to minimize errors through careful laboratory practices and validation.

Phytohormone inhibitor treatments phenocopy brassinosteroid-gibberellin dwarf mutant interactions in maize

Phytohormone biosynthesis produces metabolites with profound effects on plant growth and development. Modulation of hormone levels during developmental events, in response to the environment, by genetic polymorphism, or by chemical application, can reveal the plant processes most responsive to a phytohormone. Applications of chemical inhibitors and subsequent measurements of specific phytohormones can determine whether, and which, phytohormone is affected by a molecule. In many cases, the sensitivity of biochemical testing has determined multiple pathways affected by a single inhibitor. Genetic studies are not subject to this problem, and a wealth of data about the morphological impacts of hormone biosynthetic inhibition have accumulated through the study of enzyme mutants. In this work, we sought to assess the specificity of three triazole inhibitors of cytochrome P450s by determining their abilities to recapitulate the phenotypes of single and double mutants affected in the production of brassinosteroid (BR) and gibberellin (GA) biosynthesis. The GA biosynthetic inhibitors uniconazole (UCZ) and paclobutrazol (PAC) were applied to the BR biosynthetic mutant nana plant2 (na2), and all double-mutant phenotypes were recovered in the UCZ treatment. PAC was unable to suppress the retention of pistils in the tassels of na2 mutant plants. The BR biosynthetic inhibitor propiconazole (PCZ) suppressed tiller outgrowth in the GA biosynthetic mutant dwarf5 (d5). All treatments were additive with genetic mutants for effects on plant height. Due to additional measurements performed here but not in previous studies of the double mutants, we detected new interactions between GA and BR biosynthesis affecting the days to tassel emergence and tassel branching. These experiments, a refinement of our previous model, and a discussion of the extension of this type of work are presented.

Convergence in relationships between leaf traits, spectra and age across diverse canopy environments and two contrasting tropical forests

Leaf age structures the phenology and development of plants, as well as the evolution of leaf traits over life histories. However, a general method for efficiently estimating leaf age across forests and canopy environments is lacking. Here, we explored the potential for a statistical model, previously developed for Peruvian sunlit leaves, to consistently predict leaf ages from leaf reflectance spectra across two contrasting forests in Peru and Brazil and across diverse canopy environments. The model performed well for independent Brazilian sunlit and shade canopy leaves (R²  = 0.75-0.78), suggesting that canopy leaves (and their associated spectra) follow constrained developmental trajectories even in contrasting forests. The model did not perform as well for mid-canopy and understory leaves (R²  = 0.27-0.29), because leaves in different environments have distinct traits and trait developmental trajectories. When we accounted for distinct environment-trait linkages - either by explicitly including traits and environments in the model, or, even better, by re-parameterizing the spectra-only model to implicitly capture distinct trait-trajectories in different environments - we achieved a more general model that well-predicted leaf age across forests and environments (R²  = 0.79). Fundamental rules, linked to leaf environments, constrain the development of leaf traits and allow for general prediction of leaf age from spectra across species, sites and canopy environments.

Genome-wide DNA-(de)methylation is associated with Noninfectious Bud-failure exhibition in Almond (Prunus dulcis [Mill.] D.A.Webb)

Noninfectious bud-failure (BF) remains a major threat to almond production in California, particularly with the recent rapid expansion of acreage and as more intensive cultural practices and modern cultivars are adopted. BF has been shown to be inherited in both vegetative and sexual progeny, with exhibition related to the age and propagation history of scion clonal sources. These characteristics suggest an epigenetic influence, such as the loss of juvenility mediated by DNA-(de)methylation. Various degrees of BF have been reported among cultivars as well as within sources of clonal propagation of the same cultivar. Genome-wide methylation profiles for different clones within almond genotypes were developed to examine their association with BF levels and association with the chronological time from initial propagation. The degree of BF exhibition was found to be associated with DNA-(de)methylation and clonal age, which suggests that epigenetic changes associated with ageing may be involved in the differential exhibition of BF within and among almond clones. Research is needed to investigate the potential of DNA-(de)methylation status as a predictor for BF as well as for effective strategies to improve clonal selection against age related deterioration. This is the first report of an epigenetic-related disorder threatening a major tree crop.