Marc Libault

University of Missouri | Mizzou

Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This vir1 phenotype results in smaller stature, weaker stems, and a smaller root system with smaller nodules. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon seque...

Single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon t...

The cell cycle controls division and proliferation of all eukaryotic cells and is tightly regulated at multiple checkpoints by complexes of core cell cycle proteins. Due to the difficulty in accessing female gametes and zygotes of flowering plants, little is known about the molecular mechanisms underlying embryogenesis initiation despite the crucia...

Editorial on the Research Topic New insights into mechanisms of epigenetic modifiers in plant growth and development, volume II As we have learned, chromatin modifications, including histone modifications and DNA methylation, play a key role in plant development (Ng and Bird, 1999). However, accumulated evidence shows that, besides chromatin bioche...

The soybean root system is complex. In addition to being composed of various cell types, the soybean root system is also composed of the nodule, an organ in which mutualistic symbiosis with the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens occurs. Notably, the soybean root nodule is characterized by a central infection zone where the atmo...

Single-cell transcriptomics technologies allow researchers to investigate how individual cells, in complex multicellular organisms, differentially use their common genomic DNA. In plant biology, these technologies were recently applied to reveal the transcriptomes of various plant cells isolated from different organs and different species and in re...

Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria as well as the initiation of nodule primordia from root c...

Plant single-cell RNA-seq technology quantifies the abundance of plant transcripts at a single-cell resolution. Deciphering the transcriptomes of each plant cell, their regulation during plant cell development, and their response to environmental stresses will support the functional study of genes, the establishment of precise transcriptional progr...

Membrane proteins work in large complexes to perceive and transduce external signals and to trigger a cellular response leading to the adaptation of the cells to their environment. Biochemical assays have been extensively used to reveal the interaction between membrane proteins. However, such analyses do not reveal the unique and complex compositio...

Due to the difficulty in accessing to gametes and zygotes in flowering plants, which are controlled in single cells deeply embedded in multiple tissues, little is known about how the initiation of plant embryogenesis may reflect or contrast from such systems in other eukaryotes. In this study we has developed an approach of isolation and transfecti...

The cell cycle controls division and proliferation of all eukaryotic cells and is tightly regulated at multiple checkpoints by complexes of core cell cycle proteins. Due to the difficulty in accessing female gametes and zygotes of flowering plants, little is known about the molecular mechanisms underlying initiation embryogenesis despite the crucia...

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these...

The pig skin architecture and physiology are similar to those of humans. Thus, the pig model is very valuable for studying skin biology and testing therapeutics. The single-cell RNA sequencing (scRNA-seq) technology allows quantitatively analyzing cell types, compositions, states, signaling, and receptor-ligand interactome at single-cell resolution...

Gene expression depends on the binding of transcription factors with DNA regulatory sequences. The level of accessibility for these sequences varies between cells and cell types. Until recently, using the Tn5 assay for transposase-accessible chromatin for sequencing (ATAC-seq) technology allowed assessing the profiles of chromatin from an entire or...

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identi...

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identi...

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identi...

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identi...

Plants are composed of cells that physically interact and constantly adapt to their environment. To reveal the contribution of each plant cells to the biology of the entire organism, their molecular, morphological, and physiological attributes must be quantified and analyzed in the context of the morphology of the plant organs. The emergence of sin...

The Pigskin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at h...

Similar to other complex organisms, plants consist of diverse and specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs. As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant g...

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identi...

The characterization of the transcriptional similarities and differences existing between plant cells and cell types is important to better understand the biology of each cell composing the plant, to reveal new molecular mechanisms controlling gene activity, and to ultimately implement meaningful strategies to enhance plant cell biology. To gain a...

Similar to other complex organisms, plants consist of diverse and highly specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs and their associated regulatory mechanisms. Recently, single cell transcriptomic approaches have...

Myocarditis is a common occurrence in children and adolescents that can lead to dilated cardiomyopathy. Since it is difficult to identify the triggers of this complex disease, mechanistic understanding of DCM pathogenesis may create avenues to develop new treatment strategies. We have been engaged in delineating the autoimmune pathways underlying t...

Myocarditis is a common occurrence in children and adolescents that can lead to dilated cardiomyopathy. Since it is difficult to identify the triggers of this complex disease, mechanistic understanding of DCM pathogenesis may create avenues to develop new treatment strategies. We have been engaged in delineating the autoimmune pathways underlying t...

Membrane microdomains/nanodomains are sub-compartments of the plasma membrane enriched in sphingolipids and characterized by their unique protein composition. They play important roles in regulating plant development and plant-microbe interactions including mutualistic symbiotic interactions. Several protein families are associated with the microdo...

In eukaryotic cells, chromatin, a highly dynamic nucleoprotein complex, plays a critical role in controlling gene expression notably by regulating the interaction between transcription factors and regulatory elements. The structure of the chromatin is determined by epigenetic mechanisms, including DNA methylation, histone modifications, and chromat...

Phytohormones regulate the mutualistic symbiotic interaction between legumes and rhizobia, nitrogen-fixing soil bacteria, notably by controlling the formation of the infection thread in the root hair (RH). At the cellular level, the formation of the infection thread is promoted by the translocation of plasma membrane microdomains at the tip of the...

The availability of essential nutrients such as nitrogen (N) is often a limitation to plant development. In order to overcome this constraint, several plant species develop a mutualistic symbiotic relationship with actinorhizal bacteria (e.g. Frankia) and proteobacteria (e.g. Rhizobia) which are able to fix and assimilate the atmospheric nitrogen f...

Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through...

Several plant growth systems are available to enhance the observation of the root system (e.g., hydroponic and aeroponic plant growth systems, use of transparent soils, etc.). This article describes the use of the ultrasound aeroponic system (USAS) to treat and to enhance access to the root systems of various model plant and crop species (e.g., Ara...

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialogue between...

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite the significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialog betwe...

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 re...

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, is able to bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance,...

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological adv...

Plasma membrane microdomains are plasma membrane sub-compartments enriched in sphingolipids and sterols, and composed by a specific set of proteins. They are involved in recognizing signal molecules, transducing these signals, and controlling endocytosis and exocytosis processes. In a recent study, applying biochemical and microscopic methods, we c...

Key message: A comparative transcriptomic and genomic analysis between Arabidopsis thaliana and Glycine max root hair genes reveals the evolution of the expression of plant genes after speciation and whole genome duplication. Our understanding of the conservation and divergence of the expression patterns of genes between plant species is limited b...

Phosphorus is a major plant macronutrient involved in many and different biological processes, such as energy transfer (ATP), photosynthesis, respiration, biosynthesis of nucleic acids and proteins, membrane biosynthesis (e.g., phospholipids), and signaling pathways. Legumes, including soybean, are highly dependent on the availability of scarcely a...

Plants constantly interact with pathogenic and symbiotic microorganisms. Recent studies have revealed several regulatory mechanisms controlling these interactions. Among them, the plant defense system is activated not only in response to pathogenic, but also in response to symbiotic microbes. Interestingly, shortly after symbiotic microbial recogni...

The soybean gene GmFWL1 (FW2.2-like1) belongs to a plant-specific family that includes the tomato FW2-2 and the maize CNR1 genes, two regulators of plant development. In soybean, GmFWL1 is specifically expressed in root hair cells in response to rhizobia and in nodules. Silencing of GmFWL1 expression significantly reduced nodule numbers supporting...

Nitrogen is one of the most essential plant nutrients and one of the major factors limiting crop productivity. Having the goal to perform a more sustainable agriculture, there is a need to maximize biological nitrogen fixation, a feature of legumes. To enhance our understanding of the molecular mechanisms controlling the interaction between legumes...

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the ti...

The root hair cell is the primary site of infection of legumes by rhizobia. Its morphological, physiological, and molecular responses to this symbiotic mutualistic bacterium have been intensively investigated during the past decade especially through the screen of mutants in model legumes such as Medicago truncatula and Lotus japonicus. The identif...

Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (WGD, whole genome duplication) event, approximately 56.5 million years ago (MYA), followed by a Glycine-specific polyploidy, ~10 MYA. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs),...

Main conclusion: Chemical analyses and glycome profiling demonstrate differences in the structures of the xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I isolated from soybean ( Glycine max ) roots and root hair cell walls. The root hair is a plant cell that extends only at its tip. All other root cells have the ability to grow...

Three soybean [Glycine max (L) Merr.] small RNA libraries were generated and sequenced using the Illumina platform to examine the role of miRNAs during soybean nodulation. The small RNA libraries were derived from root hairs inoculated with Bradyrhizobium japonicum (In_RH) or mock-inoculated with water (Un_RH), as well as from the comparable inocul...

Plants unlike other living forms are sessile thereby facing severe biotic and abiotic stresses. Plants have evolved different efficient defence responses which thrive upon a number of intrinsic factors, such as genotypic and phenotypic constitutions and developmental circumstances, and extrinsic factors like severity and duration of the stresses. S...

Plant microRNAs (miRNAs) play important regulatory roles in a number of developmental processes. The present work investigated the roles of miRNAs during nodule development in the crop legume soybean (Glycine max). Fifteen soybean small RNA libraries were sequenced from different stages of nodule development, including young nodules, mature nodules...

Plants unlike other living forms are sessile thereby facing severe biotic and abiotic stresses. Plants have evolved different efficient defence responses which thrive upon a number of intrinsic factors, such as genotypic and phenotypic constitutions and developmental circumstances, and extrinsic factors like severity and duration of the stresses. S...

in addition to preventing infection from pathogenic bacteria like any other plant, legumes also developed a mutualistic symbiotic relationship with one gender of soil bacteria: rhizobium. This interaction leads to the development of a new root organ, the nodule, where the differentiated bacteria fix for the plant the atmospheric dinitrogen (atmN2)....

Expression pattern of medicago genes orthologous to the soybean GmNMNagene (Supplemental Figure 1) and soybean and medicago genes orthologous to the common bean PvNF-YC1 (Supplemental Figure 1). GmNMNa and PvNF-YC1 are two legume genes controlling the nodulation process.

Functional genomics encompasses RNA transcription, protein expression and metabolomics as well as forward and reverse genetics. In recent years several resources like transcriptomes, proteomes, metabolomes, regulatory elements and mutant libraries using TILLING methods have been developed for legumes. These provide powerful molecular resources to i...

Plant root is an organ composed of multiple cell types with different functions. This multicellular complexity limits our understanding of root biology because -omics studies performed at the level of the entire root reflect the average responses of all cells composing the organ. To overcome this difficulty and allow a more comprehensive understand...

Micro-RNAs (miRNAs) play a pivotal role in the control of gene expression and regulate plant developmental processes. MicroRNA172 is a conserved miRNA in plants reported to control the expression of genes involved in developmental phase transition, floral organ identity and flowering time. However, the specific role of miR172 in legume nodulation i...

Gene expression analysis requires the use of reference genes constitutively expressed independently of tissues or environmental conditions. Housekeeping genes (e.g., actin, tubulin, ribosomal, polyubiquitin, and elongation factor 1-α) are commonly used as reference genes with the assumption that they are uniformly expressed. In many cases, however,...

Root hairs are a terminally differentiated single cell type, mainly involved in water and nutrient uptake from the soil. The soybean root hair cell represents an excellent model for the study of single cell systems biology. In this study, we identified 5702 proteins, with at least two peptides, from soybean root hairs using an accurate mass and tim...

The soybean (Glycine max L. Merr.) genome contains 18 members of the 14-3-3 protein family, but little is known about their association with specific phenotypes. Here, we report that the Glyma0529080 (SGF14c) and Glyma08g12220 (SGF14l) genes, encoding 14-3-3 proteins, appear to play essential roles in soybean nodulation. QRT-PCR and western immunob...

Polyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result in extensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally and evolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 million years ago) that have resulted in 75% of...

Root hairs are single hair-forming cells on roots that function to increase root surface area, enhancing water and nutrient uptake. In leguminous plants, root hairs also play a critical role as the site of infection by symbiotic nitrogen fixing rhizobia, leading to the formation of a novel organ, the nodule. The initial steps in the rhizobia-root h...

Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, na...

Nitrogen fixation in legume root nodules is very important for their agricultural performance and is beneficial to the environment. Apyrases are divalent cation-dependent, tri- and di-nucleotide phosphatases that are ubiquitously found in eukaryotes and prokaryotes. We are studying the soybean ecto-apyrase GS52, which is expressed rapidly upon rhiz...

The soybean (Glycine max) genome contains 18 members of the 14-3-3 protein family, but little is known about their association with specific phenotypes. Here, we report that the Glyma0529080 Soybean G-box Factor 14-3-3c (SGF14c) and Glyma08g12220 (SGF14l) genes, encoding 14-3-3 proteins, appear to play essential roles in soybean nodulation. Quantit...

Microbe-associated molecular pattern-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. However, most of our knowledge of MTI comes from studies of model systems with relatively little work done with crop plants. In this work, we report on variation in both the microbe-associated molecula...

The symbiotic interaction between legumes and soil bacteria (e.g., soybean [Glycine max L.] and Bradyrhizobium japonicum]) leads to the development of a new root organ, the nodule, where bacteria differentiate into bacteroids that fix atmospheric nitrogen for assimilation by the plant host. In exchange, the host plant provides a steady carbon suppl...

Nitrogen is an essential nutrient for plant growth. In the Rhizobium-legume symbiosis, root nodules are the sites of bacterial nitrogen fixation, in which atmospheric nitrogen is converted into a form that plants can utilize. While recent studies suggested an important role for the soybean (Glycine max) ecto-apyrase GS52 in rhizobial root hair infe...

Plant functional genomic studies have largely measured the response of whole plants, organs and tissues, resulting in the dilution of the signal from individual cells. Methods are needed where the full repertoire of functional genomic tools can be applied to a single plant cell. Root hair cells are an attractive model to study the biology of a sing...

The tomato FW2.2 quantitative trait locus, which regulates tomato fruit size, was genetically and physically mapped around 15 years ago. Subsequently, the FW2.2 gene was cloned and shown to contain a PLAC8 domain, originally identified in mammalian placental proteins. Data suggest that FW2.2 likely controls tomato cell size, perhaps by direct inter...

Nodulation of soybean (Glycine max) root hairs by the nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum is a complex process coordinated by the mutual exchange of diffusible signal molecules. A metabolomic study was performed to identify small molecules produced in roots and root hairs during the rhizobial infection process. Metabolites...

Soybean (Glycine max L.) is a major crop providing an important source of protein and oil, which can also be converted into biodiesel. A major milestone in soybean research was the recent sequencing of its genome. The sequence predicts 69,145 putative soybean genes, with 46,430 predicted with high confidence. In order to examine the expression of t...

Plant organs and tissues are composed of many differentiated cell types. Most functional genomic studies sample whole tissues, which dilutes the signals that may arise from individual cells within the population. The result is an averaging of the cellular response. In order to overcome these issues of "signal dilution", methods are needed to allow...

A soybean homolog of the tomato FW2.2 gene, here named GmFWL1 (Glycine max FW2.2-like 1), was found to respond strongly to inoculation with the nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum. In tomato, the FW2.2 gene is hypothesized to control 30% of the variance in fruit weight by negatively regulating cell division. In the present...

Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge...

Small non-coding RNAs (21 to 24 nucleotides) regulate a number of developmental processes in plants and animals by silencing genes using multiple mechanisms. Among these, the most conserved classes are microRNAs (miRNAs) and small interfering RNAs (siRNAs), both of which are produced by RNase III-like enzymes called Dicers. Many plant miRNAs play c...

A supplemental document. The supplemental document includes three parts. Part A: all the modules with correlation coefficient greater than 0.600. Part B: the list of numbers used to represent different experimental conditions in gene regulatory network figures shown in Part C. Part C: the detailed information of the modules with correlation coeffic...

Figure S4 The HMM family classification web page. Users can paste or type in a query amino acid sequence. Click on the "Predict" button will execute family classification by HMM.

Figure S2 The PSI-BLAST search web page. Users can paste or type in a query amino acid sequence and specify PSI-BLAST parameters on the web page. Click on the "Run" button will execute PSI-BLAST.

Figure S3 The result web page of PSI-BLAST search. PSI-BLAST result page shows the hit TF sequence ID, and the PSI-BLAST score and E-value. The hits are listed in a decreasing order of the PSI-BLAST score. Click on the sequence ID can open the web page showing detailed TF information, as shown in Figure 3.

Predicted miRNA list identified in soybean. The list of all 129 predicted miRNA and the miRNA family assigned to those matching already known miRNA.

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromoso...

Nodulation is the result of a mutualistic interaction between legumes and symbiotic soil bacteria (e.g. soybean [Glycine max] and Bradyrhizobium japonicum) initiated by the infection of plant root hair cells by the symbiont. Fewer than 20 plant genes involved in the nodulation process have been functionally characterized. Considering the complexity...

All eukaryotic organisms have a diversity of transcription factor (TF) gene families, encoding key-proteins regulating gene expression. TF families are strongly conserved across eukaryotic organisms, especially plants. The specific function of each of these TF genes is of interest due to their role in controlling plant developmental processes and r...

Nodulation is the result of a symbiosis between legumes and rhizobial bacteria in soil. This symbiosis is mutually beneficial, with the bacteria providing a source of nitrogen to the host while the plant supplies carbon to the symbiont. Nodule development is a complex process that is tightly regulated in the host plant cell through networks of gene...