Single-cell transcriptomic analyses reveal cellular and molecular patterns of rubber tree response to early powdery mildew infection

Unveiling the spatiotemporal strategies of plants in response to biotic and abiotic stresses:A comprehensive review

Plant functions are governed by complex regulatory mechanisms that operate across diverse cell types in various tissues. However, the challenge of dissecting plant tissues has hindered the widespread application of single-cell technologies in plant research. Recent advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have propelled the field forward. scRNA-seq enables the examination of gene expression at the single-cell level, while ST preserves the spatial context of cellular organization. While previous reviews have discussed the breakthroughs of scRNA-seq and ST in plants, none have comprehensively addressed the use of these technologies to study plant responses to environmental stress at the cellular level. This review provides an in-depth analysis of the development, advantages, and limitations of single-cell and spatial transcriptomics, highlighting their critical role in unraveling plant strategies for coping with biotic and abiotic stresses. We also explore the challenges and future prospects of integrating scRNA-seq and ST in plant research. Understanding cell-specific responses and the complex interactions between cellular entities within the plant under stress is essential for advancing our knowledge of plant biology.

Uncovering differences in cadmium accumulation capacity of different Ipomoea aquatica cultivars at the level of root cell types

Water spinach (Ipomoea aquatica) can accumulate cadmium (Cd) even in mildly contaminated soils, but the roles of its root tip cell types in Cd fixation and transport remain unclear. Single-cell RNA sequencing revealed nine cell types in root tips in both the QLQ cultivar (low Cd accumulation) and the T308 cultivar (high Cd accumulation). High expression of LAC2 and PER72 in the QLQ epidermis was associated with enhanced lignin deposition, which may facilitate fixation of Cd and reduce its translocation to the shoot. In T308, PER72 and hormone-related genes (PIN1, ARF8, IAA17, and EIN3) were upregulated, which was hypothesized to promote xylem and trichoblast development, potentially facilitating Cd uptake and transport. Fluorescence assays suggested that the higher pectin demethylation and lignin content in QLQ may limit Cd movement, whereas the more developed tissues in T308 may contribute to increased Cd accumulation in the shoots. These findings clarify the mechanisms by which Cd accumulates in water spinach and offer insights into mitigating Cd uptake in crops.

Identification of maize genes that condition early systemic infection of sugarcane mosaic virus through single-cell transcriptomics

During the early systemic infection of plant pathogens, individual cells can harbor pathogens at various stages of infection, ranging from absent to abundant. Consequently, gene expression levels within these cells in response to the pathogens exhibit significant variability. These variations are pivotal in determining pathogenicity or susceptibility, yet they remain largely unexplored and poorly understood. Sugarcane mosaic virus (SCMV) is a representative member of the monocot-infecting potyviruses with a polyadenylated RNA genome, which can be captured by single-cell RNA sequencing (scRNA-seq). Here, we performed scRNA-seq on SCMV-infected maize leaves during early systemic infection (prior to symptom manifestation) to investigate the co-variation patterns between viral accumulation and intracellular gene expression alterations. We identified five cell types and found that mesophyll-4 (MS4) cells exhibited the highest levels of viral accumulation in most cells. Early systemic infection of SCMV resulted in a greater upregulation of differentially expressed genes, which were mainly enriched in biological processes related to translation, peptide biosynthesis, and metabolism. Co-variation analysis of the altered maize gene expression and viral accumulation levels in MS1, 2, and 4 revealed several patterns, and the co-expression relationships between them were mainly positive. Furthermore, functional studies identified several potential anti- or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection. These results not only provide new insights into plant gene regulation during viral infection but also offer a foundation for future investigations of host-virus interactions across molecular, cellular, and physiological scales.

Single-Cell Transcriptome Reveals the Cellular Response to PEG-Induced Stress in Wheat Leaves

Drought is a major factor limiting the production and yield of wheat bread (Triticum aestivum). Therefore, investigating the wheat drought-related response mechanism is an urgent priority. Here, the single-cell transcriptome of drought-nonsusceptible and susceptible wheat seedlings subjected to PEG-induced stress was systematically analyzed to study the drought-related response at the cellular level. We identified five major cell types using known marker genes and constructed a wheat leaf cell atlas. On this foundation, several potential specific marker genes for each cell type were identified, which provide a reference for further cell type annotation. Moreover, we identified cellular heterogeneity in the drought-related response mechanisms and regulatory networks among cell types. Specifically, the drought response of mesophyll cells was correlated with the photosynthetic pathway. Pseudotime trajectory analysis revealed the transition of epidermal cells from their normal function to a defense response under stress. Moreover, we also characterized the genes associated with the drought response. Notably, we identified two transcription factors (TraesCS1D02G223600 and TraesCS1D02G072900) as master regulators in most cell types. Our study provides detailed insights into the response heterogeneity of cells under PEG-induced stress. The gene resources obtained in our study could be applied to breed better crop plants with improved drought tolerance.

Single-Cell and Spatial Transcriptomics Reveals a Stereoscopic Response of Rice Leaf Cells to Magnaporthe oryzae Infection

Infection by the fungal pathogen Magnaporthe oryzae elicits dynamic responses in rice. Utilizing an integrated approach of single-cell and spatial transcriptomics, a 3D response is uncovered within rice leaf cells to M. oryzae infection. A comprehensive rice leaf atlas is constructed from 236 708 single-cell transcriptomes, revealing heightened expression of immune receptors, namely Pattern Recognition Receptors (PRRs) and Nucleotide-binding site and leucine-rich repeat (NLRs) proteins, within vascular tissues. Diterpene phytoalexins biosynthesis genes are dramatically upregulated in procambium cells, leading to an accumulation of these phytoalexins within vascular bundles. Consistent with these findings, microscopic observations confirmed that M. oryzae is prone to target leaf veins for invasion, yet is unable to colonize further within vascular tissues. Following fungal infection, basal defenses are extensively activated in rice cells, as inferred from trajectory analyses. The spatial transcriptomics reveals that rice leaf tissues toward leaf tips display stronger immunity. Characterization of the polarity gene OsHKT9 suggests that potassium transport plays a critical role in resisting M. oryzae infection by expression along the longitudinal axis, where the immunity is stronger toward leaf tip. This work uncovers that there is a cell-specific and multi-dimensional (local and longitudinal) immune response to a fungal pathogen infection.

Unraveling the Intricacies of Powdery Mildew: Insights into Colonization, Plant Defense Mechanisms, and Future Strategies

Powdery mildew, a debilitating phytopathogen caused by biotrophic fungi within the order Erysiphales, endangers crop yields and global food security. Although traditional approaches have largely emphasized resistant cultivar development and chemical control, novel strategies are necessary to counter the advent of challenges, such as pathogen adaptation and climate change. This review fully discusses three principal areas of pathogen effector functions, e.g., the reactive oxygen species (ROS)-suppressive activity of CSEP087, and host susceptibility factors, like vesicle trafficking regulated by Mildew Locus O (MLO). It also briefly mentions the transcriptional regulation of resistance genes mediated by factors, like WRKY75 and NAC transcription factors, and post-transcriptional regulation via alternative splicing (As). In addition, this discussion discusses the intricate interactions among powdery mildew, host plants, and symbiotic microbiomes thereof, highlighting the mechanism through which powdery mildew infections disrupt the foliar microbiota balance. Lastly, we present a new biocontrol approach that entails synergistic microbial consortia, such as combinations of Bacillus and Trichoderma, to induce plant immunity while minimizing fungicide dependency. Through the study of combining knowledge of molecular pathogenesis with ecological resilience, this research offers useful insights towards climate-smart crop development and sustainable disease-management strategies in the context of microbiome engineering.

A single-cell transcriptomic atlas reveals the cell differentiation trajectory and the response to virus invasion in swelling clove of garlic

The garlic bulb comprises several cloves, the swelling growth of which is significantly hindered by the accumulation of viruses. Herein, we describe a single-cell transcriptomic atlas of swelling cloves with virus accumulation, which comprised 19 681 high-quality cells representing 11 distinct cell clusters. Cells of two clusters, clusters 7 (C7) and 11 (C11), were inferred to be from the meristem. Cell trajectory analysis suggested the differentiation of clove cells to start from the meristem cells, along two pseudo-time paths. Investigation into the cell-specific activity of invasive viruses demonstrated that garlic virus genes showed relatively low-expression activity in cells of the clove meristem. There were 2060 garlic genes co-expressed with virus genes, many of which showed an association with the defense response. Five glutathione synthase/reductase genes co-expressed with virus genes displayed up-regulated expression, and the glutathione and related metabolites level showed an alteration in virus-invasive garlic clove, implying the role of glutathione in viral immunity of garlic. Our study offers valuable insights into the clove organogenesis and interaction between garlic and virus at single-cell resolution.

Opportunities and challenges in the application of single-cell transcriptomics in plant tissue research

Single-cell transcriptomics overcomes the limitations of conventional transcriptome methods by isolating and sequencing RNA from individual cells, thus capturing unique expression values for each cell. This technology allows unprecedented precision in observing the stochasticity and heterogeneity of gene expression within cells. However, single-cell RNA sequencing (scRNA-seq) experiments often fail to capture all cells and genes comprehensively, and single-modality data is insufficient to explain cell states and systemic changes. To address this, the integration of multi-source scRNA-seq and single-cell multi-modality data has emerged, enabling the construction of comprehensive cell atlases. These integration methods also facilitate the exploration of causal relationships and gene regulatory mechanisms across different modalities. This review summarizes the fundamental principles, applications, and value of these integration methods in revealing biological changes, and analyzes the advantages, disadvantages, and future directions of current approaches.

Single-cell transcriptomic profiling of maize cell heterogeneity and systemic immune responses against Puccinia polysora Underw

Southern corn rust (SCR), caused by Puccinia polysora Underw (P. polysora), is a catastrophic disease affecting maize, leading to significant global yield losses. The disease manifests primarily as pustules on the upper surface of corn leaves, obscuring our understanding of its cellular heterogeneity, the maize's response to its infection and the underlying gene expression regulatory mechanisms. In this study, we dissected the heterogeneity of maize's response to P. polysora infection using single-cell RNA sequencing. We delineated cell-type-specific gene expression alterations in six leaf cell types, creating the inaugural single-cell atlas of a maize leaf under fungal assault. Crucially, by reconstructing cellular trajectories in susceptible line N110 and resistant line R99 during infection, we identified diverse regulatory programs that fortify R99's resistance across different leaf cell types. This research uncovers an immune-like state in R99 leaves, characterized by the expression of various fungi-induced genes in the absence of fungal infection, particularly in guard and epidermal cells. Our findings also highlight the role of the fungi-induced glycoside hydrolase family 18 chitinase 7 protein (ZmChit7) in conferring resistance to P. polysora. Collectively, our results shed light on the mechanisms of maize resistance to fungal pathogens through comparative single-cell transcriptomics, offering a valuable resource for pinpointing novel genes that bolster resistance to P. polysora.

Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement

Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on the application of these technologies in crop improvement. The heterogeneity of different cell populations within a tissue plays a crucial role in the coordinated response of an organism to its environment. Single-cell transcriptomics enables the dissection of this heterogeneity, offering insights into the cell-specific transcriptomic responses of plants to various environmental stimuli. Spatial transcriptomics technologies complement single-cell approaches by preserving the spatial context of gene expression profiles, allowing for the in situ localization of transcripts. Together, single-cell and spatial transcriptomics facilitate the discovery of novel genes and gene regulatory networks that can be targeted for genetic manipulation and breeding strategies aimed at enhancing crop yield, quality, and resilience. This review highlights significant findings from recent studies, discusses the expanding roles of these technologies, and explores future opportunities for their application in crop improvement.

PM-YOLO: A Powdery Mildew Automatic Grading Detection Model for Rubber Tree

Powdery mildew has become a significant disease affecting the yield and quality of rubber trees in recent years. It typically manifests on the leaf surface at an early stage, rapidly infecting and spreading throughout the leaves. Therefore, early detection and intervention are essential to reduce the resulting losses due to this disease. However, the conventional methods of disease detection are both time-consuming and labor-intensive. In this study, we proposed a novel deep-learning-based approach for detecting powdery mildew in rubber trees, even in complex backgrounds. First, to address the lack of existing datasets on rubber tree powdery mildew, we constructed a dataset comprising 6200 images and 38,000 annotations. Second, based on the YOLO framework, we integrated a multi-scale fusion module that combines a Feature Focus and Diffusion Mechanism (FFDM) into the neck of the detection architecture. We designed an overall focus diffusion architecture and introduced a Dimension-Aware Selective Integration (DASI) module to enhance the detection of small powdery mildew targets, naming the model PM-YOLO. Furthermore, we proposed an automatic grading detection algorithm to evaluate the severity of powdery mildew on rubber tree leaves. The experimental results demonstrated that the proposed method achieved 86.9% mean average precision (mAP) and 85.6% recall, which outperformed the standard YOLOv10 by 7.6% mAP and 8.2% recall. This approach offered accurate and real-time detection of powdery mildew rubber trees, providing an effective solution for early diagnosis through automated grading.

Large-volume fully automated cell reconstruction generates a cell atlas of plant tissues

The geometric shape and arrangement of individual cells play a role in shaping organ functions. However, analyzing multicellular features and exploring their connectomes in centimeter-scale plant organs remain challenging. Here, we established a set of frameworks named Large-Volume Fully Automated Cell Reconstruction (LVACR), enabling the exploration of three-dimensional (3D) cytological features and cellular connectivity in plant tissues. Through benchmark testing, our framework demonstrated superior efficiency in cell segmentation and aggregation, successfully addressing the inherent challenges posed by light sheet fluorescence microscopy (LSFM) imaging. Using LVACR, we successfully established a cell atlas of different plant tissues. Cellular morphology analysis revealed differences of cell clusters and shapes in between different poplar (P. simonii Carr. and P. canadensis Moench.) seeds, whereas topological analysis revealed that they maintained conserved cellular connectivity. Furthermore, LVACR spatiotemporally demonstrated an initial burst of cell proliferation, accompanied by morphological transformations at an early stage in developing the shoot apical meristem. During subsequent development, cell differentiation produced anisotropic features, thereby resulting in various cell shapes. Overall, our findings provided valuable insights into the precise spatial arrangement and cellular behavior of multicellular organisms, thus enhancing our understanding of the complex processes underlying plant growth and differentiation.

Advances in Cotton Genomics, Genetics and Breeding

The cotton is an industrial crop of global significance, providing its fibers for the predominant textile material and its seed accumulating abundant oil and protein for other utilizations [...].

Breaking barriers: improving time and space resolution of arbuscular mycorrhizal symbiosis with single-cell sequencing approaches

The cell and molecular bases of arbuscular mycorrhizal (AM) symbiosis, a crucial plant-fungal interaction for nutrient acquisition, have been extensively investigated by coupling traditional RNA sequencing techniques of roots sampled in bulk, with methods to capture subsets of cells such as laser microdissection. These approaches have revealed central regulators of this complex relationship, yet the requisite level of detail to effectively untangle the intricacies of temporal and spatial development remains elusive.The recent adoption of single-cell RNA sequencing (scRNA-seq) techniques in plant research is revolutionizing our ability to dissect the intricate transcriptional profiles of plant-microbe interactions, offering unparalleled insights into the diversity and dynamics of individual cells during symbiosis. The isolation of plant cells is particularly challenging due to the presence of cell walls, leading plant researchers to widely adopt nuclei isolation methods. Despite the increased resolution that single-cell analyses offer, it also comes at the cost of spatial perspective, hence, it is necessary the integration of these approaches with spatial transcriptomics to obtain a comprehensive overview.To date, few single-cell studies on plant-microbe interactions have been published, most of which provide high-resolution cell atlases that will become crucial for fully deciphering symbiotic interactions and addressing future questions. In AM symbiosis research, key processes such as the mutual recognition of partners during arbuscule development within cortical cells, or arbuscule senescence and degeneration, remain poorly understood, and these advancements are expected to shed light on these processes and contribute to a deeper understanding of this plant-fungal interaction.

Opportunities and Challenges in Advancing Plant Research with Single-cell Omics

Plants possess diverse cell types and intricate regulatory mechanisms to adapt to the ever-changing environment of nature. Various strategies have been employed to study cell types and their developmental progressions, including single-cell sequencing methods which provide high-dimensional catalogs to address biological concerns. In recent years, single-cell sequencing technologies in transcriptomics, epigenomics, proteomics, metabolomics, and spatial transcriptomics have been increasingly used in plant science to reveal intricate biological relationships at the single-cell level. However, the application of single-cell technologies to plants is more limited due to the challenges posed by cell structure. This review outlines the advancements in single-cell omics technologies, their implications in plant systems, future research applications, and the challenges of single-cell omics in plant systems.

Single-cell transcriptome landscape elucidates the cellular and developmental responses to tomato chlorosis virus infection in tomato leaf

Plant viral diseases compromise the growth and yield of the crop globally, and they tend to be more serious under extreme temperatures and drought climate changes. Currently, regulatory dynamics during plant development and in response to virus infection at the plant cell level remain largely unknown. In this study, single-cell RNA sequencing on 23 226 individual cells from healthy and tomato chlorosis virus-infected leaves was established. The specific expression and epigenetic landscape of each cell type during the viral infection stage were depicted. Notably, the mesophyll cells showed a rapid function transition in virus-infected leaves, which is consistent with the pathological changes such as thinner leaves and decreased chloroplast lamella in virus-infected samples. Interestingly, the F-box protein SKIP2 was identified to play a pivotal role in chlorophyll maintenance during virus infection in tomato plants. Knockout of the SlSKIP2 showed a greener leaf state before and after virus infection. Moreover, we further demonstrated that SlSKIP2 was located in the cytomembrane and nucleus and directly regulated by ERF4. In conclusion, with detailed insights into the plant responses to viral infections at the cellular level, our study provides a genetic framework and gene reference in plant-virus interaction and breeding in the future research.

Advances in Single-Cell Transcriptome Sequencing and Spatial Transcriptome Sequencing in Plants

"Omics" typically involves exploration of the structure and function of the entire composition of a biological system at a specific level using high-throughput analytical methods to probe and analyze large amounts of data, including genomics, transcriptomics, proteomics, and metabolomics, among other types. Genomics characterizes and quantifies all genes of an organism collectively, studying their interrelationships and their impacts on the organism. However, conventional transcriptomic sequencing techniques target population cells, and their results only reflect the average expression levels of genes in population cells, as they are unable to reveal the gene expression heterogeneity and spatial heterogeneity among individual cells, thus masking the expression specificity between different cells. Single-cell transcriptomic sequencing and spatial transcriptomic sequencing techniques analyze the transcriptome of individual cells in plant or animal tissues, enabling the understanding of each cell's metabolites and expressed genes. Consequently, statistical analysis of the corresponding tissues can be performed, with the purpose of achieving cell classification, evolutionary growth, and physiological and pathological analyses. This article provides an overview of the research progress in plant single-cell and spatial transcriptomics, as well as their applications and challenges in plants. Furthermore, prospects for the development of single-cell and spatial transcriptomics are proposed.

Single-cell transcriptomic analysis of pea shoot development and cell-type-specific responses to boron deficiency

Understanding how nutrient stress impacts plant growth is fundamentally important to the development of approaches to improve crop production under nutrient limitation. Here we applied single-cell RNA sequencing to shoot apices of Pisum sativum grown under boron (B) deficiency. We identified up to 15 cell clusters based on the clustering of gene expression profiles and verified cell identity with cell-type-specific marker gene expression. Different cell types responded differently to B deficiency. Specifically, the expression of photosynthetic genes in mesophyll cells (MCs) was down-regulated by B deficiency, consistent with impaired photosynthetic rate. Furthermore, the down-regulation of stomatal development genes in guard cells, including homologs of MUTE and TOO MANY MOUTHS, correlated with a decrease in stomatal density under B deficiency. We also constructed the developmental trajectory of the shoot apical meristem (SAM) cells and a transcription factor interaction network. The developmental progression of SAM to MC was characterized by up-regulation of genes encoding histones and chromatin assembly and remodeling proteins including homologs of FASCIATA1 (FAS1) and SWITCH DEFECTIVE/SUCROSE NON-FERMENTABLE (SWI/SNF) complex. However, B deficiency suppressed their expression, which helps to explain impaired SAM development under B deficiency. These results represent a major advance over bulk-tissue RNA-seq analysis in which cell-type-specific responses are lost and hence important physiological responses to B deficiency are missed. The reported findings reveal strategies by which plants adapt to B deficiency thus offering breeders a set of specific targets for genetic improvement. The reported approach and resources have potential applications well beyond P. sativum species and could be applied to various legumes to improve their adaptability to multiple nutrient or abiotic stresses.

Application and prospects of single-cell and spatial omics technologies in woody plants

Over the past decade, high-throughput sequencing and high-resolution single-cell transcriptome sequencing technologies have undergone rapid development, leading to significant breakthroughs. Traditional molecular biology methods are limited in their ability to unravel cellular-level heterogeneity within woody plant tissues. Consequently, techniques such as single-cell transcriptomics, single-cell epigenetics, and spatial transcriptomics are rapidly gaining popularity in the study of woody plants. In this review, we provide a comprehensive overview of the development of these technologies, with a focus on their applications and the challenges they present in single-cell transcriptome research in woody plants. In particular, we delve into the similarities and differences among the results of current studies and analyze the reasons behind these differences. Furthermore, we put forth potential solutions to overcome the challenges encountered in single-cell transcriptome applications in woody plants. Finally, we discuss the application directions of these techniques to address key challenges in woody plant research in the future.

Single-cell transcriptome analyses reveal cellular and molecular responses to low nitrogen in burley tobacco leaves

Tobacco (Nicotiana tabacum) is cultivated and consumed worldwide. It requires great amounts of nitrogen (N) to achieve the best yield and quality. With a view to sustainable and environmentally friendly agriculture, developing new genotypes with high productivity under low N conditions is an important approach. It is unclear how genes in tobacco are expressed at the cellular level and the precise mechanisms by which cells respond to environmental stress, especially in the case of low N. Here, we characterized the transcriptomes in tobacco leaves grown in normal and low-N conditions by performing scRNA-seq. We identified 10 cell types with 17 transcriptionally distinct cell clusters with the assistance of marker genes and constructed the first single-cell atlas of tobacco leaves. Distinct gene expression patterns of cell clusters were observed under low-N conditions, and the mesophyll cells were the most important responsive cell type and displayed heterogene responses among its three subtypes. Pseudo-time trajectory analysis revealed low-N stress decelerates the differentiation towards mesophyll cells. In combination with scRNA-seq, WGCNA, and bulk RNA-seq results, we found that genes involved in porphyrin metabolism, nitrogen metabolism, carbon fixation, photosynthesis, and photosynthesis-antenna pathway play an essential role in response to low N. Moreover, we identified COL16, GATA24, MYB73, and GLK1 as key TFs in the regulation of N-responsive genes. Collectively, our findings are the first observation of the cellular and molecular responses of tobacco leaves under low N stress and lay the cornerstone for future tobacco scRNA-seq investigations.

Application of single-cell multi-omics approaches in horticulture research

Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.