A suberized exodermis is required for tomato drought tolerance

Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place

Transcriptional Regulation of Xylem Development and Secondary Cell Wall Composition

ABSTRACTThe plant vascular system is comprised of specialized tissues known as xylem and phloem. The interconnected network of xylem vessel elements, with their elongated structures and reinforced secondary cell walls, form a hydraulic system that enables efficient and uninterrupted water transport throughout the organism, contributing to plant growth and fitness. In the first chapter, genetic and genomic methodologies are employed to illustrate the conservation and repurposing of transcriptional regulation within the xylem network in Solanum lycopersicum. Key transcriptional regulators of xylem cell differentiation are identified in the tomato root, uncovering a partial conservation of the xylem developmental master regulators (VND6 and VND7) between Arabidopsis and tomato. Furthermore, through functional validation of putative orthologs of known xylem patterning and differentiation genes, examples of conservation (HD-ZIPIII TFs) as well as a novel regulator (SlKNAT1) are revealed in the tomato xylem regulatory network. The focus of the second chapter is directed towards the function of VND6 and VND7 in the Arabidopsis inflorescence stem. An integrated approach combining glycome profiling, an in vitro immunoanalytical platform, and in situ immunolocalization was employed to identify, for the first time, the differential abundance of specific cell wall biopolymers at cellular resolution in vnd6 and vnd7 mutants. Further gene expression profiling reveals perturbed expression of multiple cell-wall associated genes in the mutant backgrounds that could partially contribute to the observed cell wall phenotypes in the mutants. The third chapter delves deeper into functional conservation within the VND transcription factor family in the tomato root. It is demonstrated that various tomato VND TFs have iii expression in the vascular tissue in the root and are sufficient to induce ectopic xylem differentiation. The results here emphasize both the evolutionary conservation and distinct variations within the VND TF family concerning xylem development between two evolutionarily distant plant species. Lastly, utilizing an inducible VND7 system, an investigation is conducted on the hysteretic or memory feature associated with a bistable switch system linked to xylem cell fate determination. The findings obtained from this study indicate the necessity of an alternative inducible system, one that possesses both the "on" and "off" features. Such a system is crucial for the effective exploration of VND7-dependent hysteresis in the xylem cell differentiation. The research presented here has broad implications for understanding the molecular mechanisms underlying the plant vascular system, which is crucial for efficient water transport and plant growth. This understanding can have applications in areas such as agriculture and forestry, where efficient water use and plant growth are essential. Additionally, the insights gained from this research can inform the development of new strategies for improving plant growth and crop yields in the face of climate change and other environmental challenges. Overall, this research has significant potential for advancing our knowledge of plant biology and contributing to the development of sustainable agriculture practices. This study expands our knowledge of the molecular mechanisms governing xylem cell differentiation. It highlights both similarities and differences in the gene regulatory network of xylem across different plant species. Additionally, this research sheds light on thefunctions of VND6 and VND7 in regulating secondary cell wall composition, challengingthe earlier notions regarding functional redundancy within the VND gene family

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Summary: Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli. : The application of single-cell transcriptome profiling to plants has been limited. Shulse et al. performed Drop-seq on Arabidopsis roots, generating a transcriptional resource for >12,000 cells across major populations. This revealed marker genes for distinct cell types, cell frequency changes resulting from sucrose addition, and genes dynamically regulated during development. Keywords: single-cell RNA-seq, plant, root, Arabidopsis, transcriptomics, endodermis, development, sucros

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types.

Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli

A suberized exodermis is required for tomato drought tolerance.

Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place

Viral Diversity in Autochthonous Croatian Grapevine Cultivars

A survey was conducted on nine autochthonous grapevine cultivars grown along the Croatian coastal region. In total, 48 vines (44 from germplasm collection, 4 from vineyards) originating from 23 sites were tested for 26 viruses using molecular methods. Results revealed high infection rates with Grapevine leafroll-associated virus 3 (GLRaV-3); Grapevine virus A (GVA, both 91.7%); Grapevine fleck virus (GFkV, 87.5%); and Grapevine rupestris stem pitting-associated virus (GRSPaV, 83.3%). Other detected viruses were: Grapevine fanleaf virus (GFLV); Grapevine leafroll-associated viruses 1, 2, and strains of 4 (GLRaV-1, GLRaV-2, GLRaV-4); Grapevine viruses B, D, F (GVB, GVD, GVF); Grapevine red globe virus (GRGV); Grapevine vein feathering virus (GVFV); Grapevine Syrah virus 1 (GSyV-1); and Grapevine Pinot gris virus (GPGV). No virus-free vine was found. Mixed infections were determined in all vines, the number of viruses in a single vine ranged from three to nine. GLRaV-3 variant typing confirmed presence of group I, II, and III. Four vines with leaf deformation and mottling were positive for GPGV. Seven viruses (GLRaV-4-like group, GVD, GVE, GVF, GRGV, GSyV-1, and GVFV) were detected for the first time in Croatia. This survey confirmed the deteriorated sanitary status of autochthonous Croatian grapevine cultivars

Innovation, conservation, and repurposing of gene function in root cell type development

Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals