Journal of Experimental Botany最新文献

Cotton fiber derived from the ovule epidermis provides a natural source for the textile industry. Transcriptional features of the ovule epidermis contribute critical signals and guide fiber development. This study applied 10× Genomics Visium spatial transcriptome platform to cotton ovules at one day post-anthesis, generating high-resolution, tissue-specific gene expression profiles during early ovule development. Following data normalization, dimensionality reduction, and clustering with Seurat, ovule cross-sections were segmented into seven distinct tissue groups based on anatomical features: nucellus/embryo sac, inner integument micropylar end, inner integument chalaza, outer integument chalazal end, outer integument chalaza, outer integument micropylar end, and funicle. These clusters reveal unique transcriptional signatures that closely correspond with the developmental functions of each tissue region. The cotton fiber condensation region on outer integument chalazal end is characterized by primary cell biosynthesis while the outer integument micropylar end is enriched with lipid transportation associated with fiber yield. The resulting 1-DPA cotton ovule spatial transcriptome atlas (1-COSTA) captures key gene expression patterns linked to fiber and lint yield regulation. To facilitate data exploration, the 1-COSTA database was established with a user-friendly web interface built on R Shiny Server, enabling researchers to access core Seurat visualization and analysis tools including 3D expression visualization of genes in a code-free manner. This resource offers an invaluable reference for understanding spatial gene regulation in cotton fiber development and seed yield.

Genetics studies based on end-of-season measurements focus only on the outcome of a complex and dynamic process. Uncovering the genetic basis underlying the temporal dynamics of plant height will enhance our understanding of the genotype-to-phenotype relationship. Here, we conducted functional mapping to investigate the temporal dynamics of plant height using the time-series data extracted from UAV-based RGB imagery from two sorghum populations. Significant correlations were found between the UAV-derived measurements and manual measurements. We modeled the growth trajectory using a logistic function. Among QTLs identified by mapping with the growth curve parameters as derived traits, several were co-localized with known genes controlling plant height. To further visualize the temporal patterns of genetic effects, we used the logistic function to estimate each genotype's height at a five-day interval. Genome scans of the model-estimated heights detected QTLs with dynamic effect changes across development. Persistent QTLs, co-localizing with Dw1, Dw2, Dw3, and qHT7.1, were detectable starting from 40 days after planting, whereas several transient QTLs were only detectable within specific shorter periods or at some growing seasons. These findings enabled us to generate a conceptual figure to depict six potential dynamic patterns of persistent and transient QTLs underlying growth trajectories.

Root-exuded organic acids are crucial in mitigating iron (Fe) and phosphorus (P) deficiencies. Their biosynthesis and secretion require significant metabolic investment. Recent studies have shown that roots can also uptake exudates. We hypothesized that citric acid uptake increases under Fe and P deficiencies, declines over time, and contributes to primary metabolism. We investigated citric acid uptake, translocation, and metabolization in Fe- and P-deficient in hydroponically-grown tomato plants. We applied 13C-labeled citric acid analysed through bulk stable isotope and compound-specific stable isotope analysis. Physiological parameters, root morphology, and elemental composition were also assessed. Deficient plants showed reduced P and Fe content, reduced photosynthesis, altered root morphology and an altered citric acid uptake, which could not be attributed to morphological differences. Iron deficiency reduced citric acid uptake, indicating its role in rhizospheric Fe mobilization, while P deficiency increased the uptake emphasizing resource use efficiency. Unexpectedly, citric acid uptake increased with plant development. In Fe deficiency, citric acid-derived carbon is allocated to secondary metabolites, while in P deficiency, it supports the TCA and GS-GOGAT cycles. This study is the first to demonstrate citric acid uptake as a multifunctional process, underscoring its critical role in plant responses to nutrient starvation, especially under P deficiency.

Isoprenoids (also called terpenoids) are a large group of natural chemical compounds. Some isoprenoids are specialized metabolites that give smell and taste to plants and provide protection against herbivores and pathogens. Production of these particular substances is specific to certain species and plant families and hence is classified as secondary metabolism. In addition, numerous isoprenoids perform essential cellular functions for example chloroplast isoprenoids give rise to photosynthetic pigments, electron transporters, and membrane modifiers in the thylakoid membrane to adjust the correct level of photosynthetic performance and prevent oxidative damage in the chloroplasts. Similarly, some cytoplasmic isoprenoids serve a key role in the primary cell metabolism of all eukaryotic cells, forming membrane microdomains (sterols), serving as lipid anchors for prenylated proteins (geranylgeranyl and farnesyl groups), and co-factors of protein glycosylation (dolichols). The non-steroid isoprenoids (prenyl groups of proteins and ubiquinone, dolichols) and their role in the plants are far less described than sterols. In this review, we present a summary of the knowledge on protein prenylation but also farnesol and geranylgeraniol turnover in cytoplasm in the context of membrane structure, biochemistry, plant physiology, and development in Arabidopsis model plant and other species.

A considerable quantity of locally respired CO2 in stems can be assimilated via woody tissue photosynthesis (Pwt). Hence, Pwt locally provides carbon fueling radial stem growth and therefore plays a major role in the stem carbon balance. It is, however, not straightforward to quantify or visualize its dynamic behavior, especially on small spatial scales. To assess Pwt we traced xylem-transported 11CO2 in detached branches of Populus tremula L. and used positron autoradiography to visualize and quantify its dynamics on a submillimeter scale, while manipulating light exposure to the branch. Experiments using 18F-fluoride were conducted to study water transport. In light-exposed branch segments 11C was found to be highly retained whereas light-excluded parts solely indicated transport of 11CO2 by the sap. The latter results were confirmed by visualizing sap transport through 18F-labelling. Analogue experiments with 13CO2 unambiguously revealed assimilation of xylem-transported CO2 into fructose and glucose, and also suggest light-independent fixation in light-excluded parts. The combination of stable and unstable isotope experiments highlight that (i) Pwt is highly light-responsive in young branches; and (ii) xylem-transported CO2 is fixed by photosynthetic cells in bark and locally provides sugars for growth and energy to woody tissues.

Plant development is a sequence of precisely timed and spatially coordinated events that produce organs such as leaves and flowers. In Arabidopsis thaliana, for example, the development of leaves (called bracts in the inflorescence) halts once the first flower forms. Understanding how this transition is regulated is key for decoding how developmental programmes are coordinated during the floral transition. In this study, we investigated a natural phenotypic variation that uncouples bract repression from flower initiation. We discovered that the continued formation of bracts after the floral transition involves complex genetic interactions across at least four loci. Interestingly, none of these loci included known floral identity genes previously linked to bract repression, pointing to novel regulators in the coordination of bract and flower development. Using time-series transcriptomics and curve registration, we found that differences in gene expression levels when bracts persist are mainly driven by a massive desynchronization of gene dynamics. This affects a wide range of biological processes beyond those associated with leaf identity. These findings align with the 'inverse hourglass' model, which proposes that transcriptomic divergence at transitional stages contributes to morphological variation. Our results suggest that this model may also explain trait variability within species, highlighting how transcriptome dynamics shape phenotypic robustness during developmental transitions.

Sulfur (S) assimilation directly or indirectly affects the uptake, translocation, and homeostasis of essential and beneficial micronutrients, as well as detoxification of toxic metal(loid)s in plants. This review synthesizes the multifaceted roles of S assimilation and metabolites in trace element dynamics. Sulfate transporters mediate the uptake of structurally similar oxyanions such as selenate, molybdate and chromate, while S availability modulates the biosynthesis and secretion of phytosiderophores required for iron (Fe) acquisition in gramineous plant species. S-metabolite derived ligands, notably phytochelatins (PCs), metallothioneins (MTs), and nicotianamine (NA), perform essential functions in cytosolic chelation, buffering free ion concentrations to prevent toxicity, facilitating intracellular trafficking, and delivering trace metals to enzymes and organelles. Sulfur also is indispensable for the biosynthesis of critical cofactors including the Fe-S clusters and molybdenum (Mo) cofactor (Moco). On the other hand, Fe deficiency and metal(loid) stresses modulate the uptake and homeostasis of S. This intricate interplay positions S metabolism as a key regulator of micronutrient efficiency and metal(loid) detoxification. Optimizing S assimilation pathways has the potential to biofortify micronutrients and prevent excessive accumulation of toxic metal(loid)s in food crops.

Arbuscular mycorrhizal fungi establish mutualistic associations with the roots of most vascular plants, enhancing plant immunity and activating mycorrhiza-induced resistance (MIR). MIR is a crucial mechanism for plant protection against a wide variety of attackers that is mediated by the priming of jasmonate-dependent defense responses, but the contribution of self-damage perception to MIR remains unexplored. We hypothesised that differential recognition of endogenous damage signals contributes to MIR in tomato plants. To test this hypothesis, we compared responses in mycorrhizal and non-mycorrhizal tomato plants after applying the cell-wall derived damage signal oligogalacturonides (OGs). We explored early plant defense responses to OGs at the proteomic, metabolic, and transcriptomic level, and the later effects on plant resistance to the necrotrophic pathogen Botrytis cinerea. We demonstrate that mycorrhizal plants are more sensitive to the damage signals, responding stronger to lower doses as compared to non-mycorrhizal plants. Specifically, mycorrhizal plants show primed accumulation of defense proteins, receptor kinases, flavonoids, and primed activation of the jasmonic acid and ethylene signaling pathways in response to OGs. Expression levels of the tomato wall-associated kinase 1 (slWAK1) gene are elevated in mycorrhizal plants, and MIR against B. cinerea is abolished in a wak1 mutant. Together, these results provide the first indication that self-damage recognition contributes to inducing MIR against B. cinerea.

Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) constitutes a major means to increase transcriptome complexity in higher eukaryotes and critically contributes to the re-programming of gene expression in response to internal and environmental signals. Technological advances have enabled us to determine transcriptome-wide AS patterns at unprecedented accuracy, depth, and throughput. Furthermore, powerful tools for examining the regulatory mechanisms underlying AS decisions have been successfully established for plants, including methods for profiling the in vivo interaction landscape of splicing regulatory proteins with their target pre-mRNAs. Combining these novel approaches with functional studies of individual AS events identified many critical components of the plant splicing code, consisting of cis-regulatory elements on the pre-mRNA and trans-acting factors, such as splicing regulatory proteins. Their concerted action affects splice site selection by the spliceosome, thereby generating highly dynamic and complex AS outputs. Here, we will review our current knowledge of AS regulation by RNA sequence and structural motifs in cis and networks of trans-acting splicing regulators. We will also discuss how, despite overall low complexity of the target motifs for binding of splicing regulators and their often-redundant functions, high levels of precision and specificity in AS can be achieved.

Effectors are small molecules secreted by microbial pathogens that disrupt host basal functioning and responses during infection by targeting various plant susceptibility factors. This study reports a candidate selection approach for identifying novel, potential plant nuclear localized effectors from Fusarium graminearum secretory proteins. From a dataset of core secretory proteins conserved across several Fusarium strains, candidates were selected based on predicted nuclear localization, structural characteristics, and expression profiles during infection. Transient expression in Nicotiana benthamiana confirmed accumulation in the plant nucleus, that were further confirmed in wheat protoplasts. One of these proteins was selected for yeast two-hybrid (Y2H) screening to identify wheat protein targets, using a Fusarium-infected wheat spike cDNA library specifically generated for this study. The screening identified a high confident interaction with a nuclear-localized wheat beta-amylase 2. The structural modeling of the protein complex between beta-amylase 2 and the putative effector was used to predict interacting amino acid residues and informed a deletion analysis to disrupt the interaction. This research identifies a Fusarium graminearum secretory core protein that interacts with a conserved wheat beta-amylase 2, showcasing a method to select pathogenicity factors conserved across multiple pathogens and host plants, with implications for developing broad-spectrum resistance strategies.