Natural variation in ZmNRT2.5 modulates husk leaf width and promotes seed protein content in maize.

The husk leaf of maize (Zea mays) encases the ear as a modified leaf and plays pivotal roles in protecting the ear from pathogen infection, translocating nutrition for grains and warranting grain yield. However, the natural genetic basis for variation in husk leaf width remains largely unexplored. Here, we performed a genome-wide association study for maize husk leaf width and identified a 3-bp InDel (insertion/deletion) in the coding region of the nitrate transporter gene ZmNRT2.

The blue-light receptor CRY1 serves as a switch to balance photosynthesis and plant defense.

Plant stomata open in response to blue light, allowing gas exchange and water transpiration. However, open stomata are potential entry points for pathogens. Whether plants can sense pathogens and mount defense responses upon stomatal opening and how blue-light cues are integrated to balance growth-defense trade-offs are poorly characterized.

Temperature-driven changes in membrane fluidity differentially impact FILAMENTATION TEMPERATURE-SENSITIVE H2-mediated photosystem II repair.

The Arabidopsis (Arabidopsis thaliana) yellow variegated2 (var2) mutant, lacking functional FILAMENTATION TEMPERATURE-SENSITIVE H2 (FtsH2), an ATP-dependent zinc metalloprotease, is a powerful tool for studying the photosystem II (PSII) repair process in plants. FtsH2, forming hetero-hexamers with FtsH1, FtsH5, and FtsH8, plays an indispensable role in PSII proteostasis. Although abiotic stresses like cold and heat increase chloroplast reactive oxygen species (ROS) and PSII damage, var2 mutants behave like wild-type plants under heat stress but collapse under cold stress.

RDBSB: a database for catalytic bioparts with experimental evidence.

Catalytic bioparts are fundamental to the design, construction and optimization of biological systems for specific metabolic pathways. However, the functional characterization information of these bioparts is frequently dispersed across multiple databases and literature sources, posing significant challenges to the effective design and optimization of specific chassis or cell factories. We developed the Registry and Database of Bioparts for Synthetic Biology (RDBSB), a comprehensive resource encompassing 83 193 curated catalytic bioparts with experimental evidences.

Induction and Suspension Culture of Callus Tissue for the Production of Secondary Metabolic Active Substances.

Using as research material, callus induction and culture were carried out, and high-yielding cell lines were screened to establish a suspension culture system that promotes callus growth and the accumulation of the "total saponins" (total content of triterpenoid glycosides or ginsenosides). Using the root as an explant, the medium for callus induction and proliferation was optimized by adjusting culture conditions (initial inoculation amount, carbon source, shaking speed, hormone concentration, culture time) and a high-yielding cell line with efficient proliferation and high total saponins content was screened out. The conditions of suspension culture were refined to find out the most suitable conditions for the suspension culture of callus, and finally, the suspension culture system was established.

JCVI: A versatile toolkit for comparative genomics analysis.

The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons.

Reciprocal conversion between annual and polycarpic perennial flowering behavior in the Brassicaceae.

The development of perennial crops holds great promise for sustainable agriculture and food security. However, the evolution of the transition between perenniality and annuality is poorly understood. Here, using two Brassicaceae species, Crucihimalaya himalaica and Erysimum nevadense, as polycarpic perennial models, we reveal that the transition from polycarpic perennial to biennial and annual flowering behavior is a continuum determined by the dosage of three closely related MADS-box genes.

Flowering time: From physiology, through genetics to mechanism.

Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators.

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

Single-cell and single-nucleus RNA-sequencing 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 treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing.

Histone dynamics responding to internal and external cues underlying plant development.

Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues.

Perenniality: From model plants to applications in agriculture.

To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors.

The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid-dependent stress responses in Arabidopsis.

N 6-methyladenosine (m6A) is a common epitranscriptional mRNA modification in eukaryotes. Thirteen putative m6A readers, mostly annotated as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins, have been identified in Arabidopsis (Arabidopsis thaliana), but few have been characterized. Here, we show that the Arabidopsis m6A reader ECT1 modulates salicylic acid (SA)-mediated plant stress responses.

Endocytosis-mediated entry of a caterpillar effector into plants is countered by Jasmonate.

Insects and pathogens release effectors into plant cells to weaken the host defense or immune response. While the imports of some bacterial and fungal effectors into plants have been previously characterized, the mechanisms of how caterpillar effectors enter plant cells remain a mystery. Using live cell imaging and real-time protein tracking, we show that HARP1, an effector from the oral secretions of cotton bollworm (Helicoverpa armigera), enters plant cells via protein-mediated endocytosis.

The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution.

Bryophytes represent a sister to the rest of land plants. Despite their evolutionary importance and relatively simple body plan, a comprehensive understanding of the cell types and transcriptional states that underpin the temporal development of bryophytes has not been achieved. Using time-resolved single-cell RNA sequencing, we define the cellular taxonomy of Marchantia polymorpha across asexual reproduction phases.

Analysis of meristems and plant regeneration at single-cell resolution.

Rapid development of high-throughput single-cell RNA sequencing (scRNA-seq) technologies offers exciting opportunities to reveal new and rare cell types, previously hidden cell states, and continuous developmental trajectories. In this review, we first illustrate the ways in which scRNA-seq enables researchers to distinguish between distinct plant cell populations, delineate cell cycle continuums, and infer continuous differentiation trajectories of diverse cell types in shoots, roots, and floral and vascular meristems with unprecedented resolution. We then highlight the emerging power of scRNA-seq to dissect cell heterogeneity in regenerating tissues and uncover the cellular basis of cell reprogramming and stem cell commitment during plant regeneration.

A protocol for measuring the response of Arabidopsis roots to gravity and treatment for simulated microgravity.

We present a protocol to quantify the response of both normal and mutant Arabidopsis seedlings to gravity and simulated microgravity under earth-normal gravity conditions. We describe the steps to simulate microgravity using a three-dimensional (3D) clinostat, which changes the rate and direction at random and consistently rotates the axis horizontally and vertically to counteract the standard gravity at the Earth's surface. We then detail the gravity stimulation experiment, followed by the assessment of root responses using ImageJ-based analysis.

Biotinylated Tn5 transposase-mediated CUT&Tag efficiently profiles transcription factor-DNA interactions in plants.

In contrast to CUT&Tag approaches for profiling bulk histone modifications, current CUT&Tag methods for analysing specific transcription factor (TF)-DNA interactions remain technically challenging due to TFs having relatively low abundance. Moreover, an efficient CUT&Tag strategy for plant TFs is not yet available. Here, we first applied biotinylated Tn5 transposase-mediated CUT&Tag (B-CUT&Tag) to produce high-quality libraries for interrogating TF-DNA interactions.

Cooperative role of AtRsmD and AtRimM proteins in modification and maturation of 16S rRNA in plastids.

Chloroplast pre-ribosomal RNA (rRNA) undergoes maturation, which is critical for ribosome assembly. While the central and auxiliary factors in rRNA maturation have been elucidated in bacteria, their mode of action remains largely unexplored in chloroplasts. We now reveal chloroplast-specific factors involved in 16S rRNA maturation, Arabidopsis thaliana orthologs of bacterial RsmD methyltransferase (AtRsmD) and ribosome maturation factor RimM (AtRimM).

Anisotropic cell growth at the leaf base promotes age-related changes in leaf shape in Arabidopsis thaliana.

Plants undergo extended morphogenesis. The shoot apical meristem (SAM) allows for reiterative development and the formation of new structures throughout the life of the plant. Intriguingly, the SAM produces morphologically different leaves in an age-dependent manner, a phenomenon known as heteroblasty.

Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds.

Weed species are detrimental to crop yield. An understanding of how weeds originate and adapt to field environments is needed for successful crop management and reduction of herbicide use. Although early flowering is one of the weed trait syndromes that enable ruderal weeds to overcome frequent disturbances, the underlying genetic basis is poorly understood.

GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.

Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.