植物科学

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a widely used programmable nuclease system for gene modification in many organisms, including Physcomitrium patens. P. patens is a model species of moss plants, a basal land plant group, which has been extensively studied from the viewpoint of evolution and diversity of green plant lineages. So far, gene modifications by CRISPR/Cas9 in P. patens have been carried out exclusively by the polyethylene glycol (PEG)-mediated DNA transfer method, in which a transgene (or transgenes) is introduced into protoplast cells prepared from protonemal tissues. However, this PEG-mediated method requires a relatively large amount of transgene DNA (typically 30 µg for a single transformation), consists of many steps, and is time-consuming. Additionally, this PEG-mediated method has only been established in a few species of moss. In the current protocol, we succeeded in CRISPR/Cas9-induced targeted mutagenesis of P. patens genes by making good use of the biolistic method, which i) requires amounts of transgene DNA as low as 5 μg for each vector, ii) consists of fewer steps and is time-saving, and iii) is known to be applicable to a wide variety of species of plants.

Oomycetes are a predominantly plant-pathogenic group of organisms often considered and managed as fungi; however, due to their evolutionary divergence from true fungi, many conventional fungicides are ineffective against them. Their unique physiological characteristics make them challenging to work with, highlighting the need for a standardized and reproducible procedure for anti-oomycete assays. Previous studies describe methods to obtain sporulation forms in the laboratory, but there remains a disconnect between spore production and the subsequent screening process for potential biological pesticides based on microbial organic extracts. This protocol bridges that gap by providing a complete and reliable workflow from spore production to screening. In this study, we present an efficient in vitro protocol to identify microbial extracts with activity against Phytophthora capsici and Pythium ultimum. The protocol includes a method for obtaining zoospores of P. capsici and oospores of P. ultimum, followed by a simple and rapid screening assay to detect microbial extracts that inhibit the growth of these pathogens. The extracts are dispensed onto plates in two concentrations and allowed to dry. This facilitates pauses in the protocol and allows for storage of the plates until the biological material is ready for the assay. The protocol’s effectiveness has been validated with these two oomycetes, resulting in the identification of active extracts in both cases. Moreover, it can be adapted to other pathogens.

This protocol outlines a reliable method for the micropropagation of Nicotiana benthamiana using axillary shoot branching. Axillary shoot induction involves stimulating the outgrowth of dormant buds located at the leaf axils, allowing for the development of genetically stable shoots without callus formation or the use of exogenous plant growth regulators. Nodal explants are cultured on MS medium supplemented with kinetin and indole-3-butyric acid (IBA) to induce shoot formation. Isolated shoots are then transferred to hormone-free MS medium for rooting. This method is simple, reproducible, and supports rapid plant multiplication for downstream applications such as agroinfiltration or transient protein expression.

Fusarium crown rot (FCR), mainly caused by Fusarium pseudograminearum, is a devastating soil-borne disease of wheat that results in severe yield and quality reduction. FCR is characterized by stem base necrosis and whitehead development. In recent years, FCR has escalated in both incidence and severity, emerging as a critical threat to global wheat production, particularly within key cultivation zones such as China's Huang-Huai-Hai Plain. The development of resistant cultivars is an effective and environmentally sustainable strategy for FCR disease control. However, the lack of standardized and reproducible inoculation protocols has hindered the accurate assessment and screening of disease-resistant wheat germplasms. To address this limitation, we established a robust FCR inoculation system utilizing F. pseudograminearum propagated on a millet grain substrate, facilitating rapid and reliable evaluation of both host resistance and fungal pathogenicity. Laboratory validation demonstrated high infection efficiency and strong reproducibility of this method.

Adult muscle stem cells (MuSCs) are the key cellular source for regenerating skeletal muscle in vertebrates. MuSCs are typically identified in skeletal muscle by the expression of the paired box protein 7 (PAX7) protein. Here, we developed a combined RNA fluorescent in situ hybridization (FISH) using RNAscope technology and an immunofluorescence (IF) protocol for the simultaneous detection of Pax7 mRNA and PAX7 protein in individual MuSCs in vivo. Interestingly, we show that while most PAX7⁺ (protein) MuSCs express Pax7 mRNA, there is a subset of Pax7⁺ (mRNA) cells that do not express PAX7 protein. Altogether, we developed a combined FISH/IF protocol that allows for the co-detection of mRNA and protein in MuSCs in vivo, a strategy that can be applied to any target gene. The functional significance of the Pax7-expressing subset of cells lacking PAX7 protein prior to injury remains unknown.

Phospholipids are major structural and regulatory elements of biological membranes and are involved in many different cellular and physiological processes. In this protocol, we provide an easy, cost-effective, and efficient method to obtain an overview of the phospholipid composition using high-performance thin layer chromatography (HPTLC). While the currently known phospholipid separation methods based on HPTLC display co-migration of certain lipid classes, the method we describe here allows the separation of all phospholipid classes, including anionic phospholipids in plant samples. This protocol combines elements of the classical Vitiello and Touchstone solvent systems to optimize phospholipid separation in a scaled pattern. Here, we provide a full characterization of this method, including statistical analyses of the retention factor of each phospholipid to show the robustness of the method and its efficiency in separating all phospholipid classes of a biological sample.

Rhamnogalacturonan-II (RG-II) is one of the least studied domains of pectin, primarily due to its low abundance, the lack of reliable antibodies, and the complexity of its structure. The present study builds upon existing protocols and procedures used to analyse RG-II in tissues where it is more abundant, combining and adapting them for the isolation of RG-II from Arabidopsis seed mucilage—a structure previously thought to lack RG-II. By applying these adapted methods, we first confirmed the presence of RG-II in seed mucilage and subsequently succeeded in isolating it from a tissue where it is typically present in low abundance, thereby enabling future studies on this previously overlooked component.

Despite its significant relevance to drought adaptation, optimization of nutrient acquisition, and carbon sequestration in soil, genetic factors determining root depth remain poorly explored, mostly due to the limitations of the methods currently available to estimate it. Although several such methods have been developed for crops, their applicability to large-scale studies and those involving smaller, more fragile root systems is severely limited. To address this, we have developed ClearDepth, a simple, non-destructive, low-cost method. In ClearDepth, the root system develops naturally inside the soil in clear pots. As it expands, secondary roots reach the transparent walls of the pot ("wall roots"), becoming visible. The shallowness of each wall root is then measured (wall root shallowness, WRS), and the depth of the root system is expressed as the average of all single WRS measurements. We demonstrated the suitability of ClearDepth for root depth studies using Arabidopsis thaliana and Oryza sativa (rice), two species with contrasting root system architecture (RSA) and root size. The robustness and sensitivity of the WRS trait allow us not only to reproducibly discriminate between shallow and deep root systems but also to detect smaller yet significant differences in depth determined by the influence of environmental factors, such as light. Here, we present a comprehensive protocol for utilizing this method.

In response to environmental changes, chloroplasts, the cellular organelles responsible for photosynthesis, undergo intracellular repositioning, a phenomenon known as chloroplast movement. Observing chloroplast movement within leaf tissues remains technically challenging in leaves consisting of multiple cell layers, where light scattering and absorption hinder deep tissue visualization. This limitation has been particularly problematic when analyzing chloroplast movement in the mesophyll cells of C₄ plants, which possess two distinct types of concentrically arranged photosynthetic cells. In response to stress stimuli, mesophyll chloroplasts aggregate toward the inner bundle sheath cells. However, conventional methods have not been able to observe these chloroplast dynamics over time in living cells, making it difficult to assess the influence of adjacent bundle sheath cells on this movement. Here, we present a protocol for live leaf section imaging that enables long-term and detailed observation of chloroplast movement in internal leaf tissues without chemical fixation. In this method, a leaf blade section prepared either using a vibratome or by hand was placed in a groove made of a silicone rubber sheet attached to a glass slide for microscopic observation. This technique allows for the quantitative tracking of chloroplast movement relative to the surrounding cells. In addition, by adjusting the sectioning angle and thickness of the unfixed leaf sections, it is possible to selectively inactivate specific cell types based on their size and shape differences. This protocol enables the investigation of the intercellular interactions involved in chloroplast dynamics in leaf tissues.

The root meristem navigates the highly variable soil environment where water availability limits water absorption, slowing or halting growth. Traditional studies use uniform high osmotic potentials, poorly representing natural conditions where roots gradually encounter increasing osmotic potentials. Uniform high osmotic potentials reduce root growth by inhibiting cell division and shortening mature cell length. This protocol describes a simple and effective in vitro system using a gradient mixer that generates a vertical gradient in an agar gel based on the principle of communicating vessels, exploiting gravity to generate a continuous mannitol concentration gradient (from 0 to 400 mM mannitol) reaching osmotic potentials of -1,2 MPa. It enables long-term Arabidopsis root growth analysis under progressive water deficit, improving phenotyping and molecular studies in soil-like conditions.