Epigenetics in the modern era of crop improvements.

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits.

Binding mechanism and antagonism of the vesicular acetylcholine transporter VAChT.

The vesicular acetylcholine transporter (VAChT) has a pivotal role in packaging and transporting acetylcholine for exocytotic release, serving as a vital component of cholinergic neurotransmission. Dysregulation of its function can result in neurological disorders. It also serves as a target for developing radiotracers to quantify cholinergic neuron deficits in neurodegenerative conditions.

Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis.

In plants, microRNAs (miRNAs) participate in complex gene regulatory networks together with the transcription factors (TFs) in response to biotic and abiotic stresses. To date, analyses of miRNAs-induced transcriptome remodeling are at the whole plant or tissue levels. Here, Arabidopsis's ABA-induced single-cell RNA-seq (scRNA-seq) is performed at different stages of time points-early, middle, and late.

MicroRNA analysis reveals two modules that antagonistically regulate xylem tracheary element development in Arabidopsis.

Tracheary elements (TEs) are vital in the transport of various substances and contribute to plant growth. The differentiation of TEs is complex and regulated by a variety of microRNAs (miRNAs). However, the dynamic changes in miRNAs during each stage of TE differentiation remain unclear, and the miRNA regulatory network is not yet complete.

Heterogeneity in Mechanical Properties of Plant Cell Walls.

The acquisition and utilization of cell walls have fundamentally shaped the plant lifestyle. While the walls provide mechanical strength and enable plants to grow and occupy a three-dimensional space, successful sessile life also requires the walls to undergo dynamic modifications to accommodate size and shape changes accurately. Plant cell walls exhibit substantial mechanical heterogeneity due to the diverse polysaccharide composition and different development stages.

Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development.

Background: The evolution and development of flowers are biologically essential and of broad interest. Maize and sorghum have similar morphologies and phylogeny while harboring different inflorescence architecture. The difference in flower architecture between these two species is likely due to spatiotemporal gene expression regulation, and they are a good model for researching the evolution of flower development.

Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.

Background: Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete.

Chromosome-scale assembly and annotation of the wild wheat relative Aegilops comosa.

Wild relatives of wheat are valuable sources for enhancing the genetic diversity of common wheat. Aegilops comosa, an annual diploid species with an MM genome constitution, possesses numerous agronomically valuable traits that can be exploited for wheat improvement. In this study, we report a chromosome-level genome assembly of Ae.

Cas12e orthologs evolve variable structural elements to facilitate dsDNA cleavage.

Exceptionally diverse type V CRISPR-Cas systems provide numerous RNA-guided nucleases as powerful tools for DNA manipulation. Two known Cas12e nucleases, DpbCas12e and PlmCas12e, are both effective in genome editing. However, many differences exist in their in vitro dsDNA cleavage activities, reflecting the diversity in Cas12e's enzymatic properties.

Genetic diversity and population structure of sweet corn in China as revealed by mSNP.

Unlabelled: Corn is a widely grown cereal crop that serves as a model plant for genetic and evolutionary studies. However, the heterosis pattern of sweet corn remains unclear. Here, we analysed the genetic diversity and population structure of 514 sweet corn inbred lines and 181 field corn inbred lines.

Chromatin Topological Domains Associate With the Rapid Formation of Tandem Duplicates in Plants.

In eukaryotes, chromatin is compacted within nuclei under the principle of compartmentalization. On top of that, condensin II establishes eukaryotic chromosome territories, while cohesin organizes the vertebrate genome by extruding chromatin loops and forming topologically associating domains (TADs). Thus far, the formation and roles of these chromatin structures in plants remain poorly understood.

Amplified growth and heavy metal toxicity of Chlorococcum sp. from exposure to low-dose lanthanum(III).

Rare earth elements (REEs) are extensively utilized in industry, agriculture, advanced materials and other fields, leading to their dispersion in water bodies as emerging contaminants. Meanwhile, the coexistence of REEs and heavy metals (HMs) has become a novel form of water contamination (REE-HM co-contamination), though scientists have limited understanding of its hazards. Here, Chlorococcum sp.

Discrimination of leaf diseases in Maize/Soybean intercropping system based on hyperspectral imaging.

In order to achieve precise discrimination of leaf diseases in the Maize/Soybean intercropping system, i.e. leaf spot disease, rust disease, mixed leaf diseases, this study utilized hyperspectral imaging and deep learning algorithms for the classification of diseased leaves of maize and soybean.

Genome-wide identification and expression analysis of the kinesin gene superfamily suggests roles in response to abiotic stress and fertility of wheat (Triticum aestivum L.).

Background: Kinesin is a motor for microtubule-based motility. It plays a vital role in plant growth and development. The kinesin superfamily members are known mainly from Arabidopsis.

NPR1 promotes blue light-induced plant photomorphogenesis by ubiquitinating and degrading PIF4.

Light is a major determinant of plant growth and survival. NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1) acts as a receptor for salicylic acid (SA) and serves as the key regulator of SA-mediated immune responses. However, the mechanisms by which plants integrate light and SA signals in response to environmental changes, as well as the role of NPR1 in regulating plant photomorphogenesis, remain poorly understood.

Unlocking epigenetic breeding potential in tomato and potato.

Tomato () and potato (), two integral crops within the nightshade family, are crucial sources of nutrients and serve as staple foods worldwide. Molecular genetic studies have significantly advanced our understanding of their domestication, evolution, and the establishment of key agronomic traits. Recent studies have revealed that epigenetic modifications act as "molecular switches", crucially regulating phenotypic variations essential for traits such as fruit ripening in tomatoes and tuberization in potatoes.

The Arabidopsis RING-Type E3 Ligase TEAR4 Controls Seed Germination by Targeting RGA for Degradation.

Light and DELLA proteins are central factors controlling seed germination which is critical for seed plant survival and agricultural production. However, the mechanisms underlying DELLA degradation under different light conditions during seed germination remain to be clarified. Here, it is reported that TIE1-ASSOCIATED RING-TYPE E3 LIGASE4 (TEAR4) and other TEARs redundantly promote DELLA degradation to positively regulate seed germination in Arabidopsis.

Semantic segmentation for weed detection in corn.

Background: Reliable, fast, and accurate weed detection in farmland is crucial for precision weed management but remains challenging due to the diverse weed species present across different fields. While deep learning models for direct weed detection have been developed in previous studies, creating a training dataset that encompasses all possible weed species, ecotypes, and growth stages is practically unfeasible. This study proposes a novel approach to detect weeds by integrating semantic segmentation with image processing.

EMF1 functions as a 3D chromatin modulator in Arabidopsis.

It is well known that genome organizers, like mammalian CCCTC-binding factor (CTCF) or Drosophila architectural proteins CP190 and BEAF-32, contribute to the three-dimensional (3D) organization of the genome and ensure normal gene transcription. However, bona fide genome organizers have not been identified in plants. Here, we show that EMBRYONIC FLOWER1 (EMF1) functions as a genome modulator in Arabidopsis.

CAT Bridge: an efficient toolkit for gene-metabolite association mining from multiomics data.

Background: With advancements in sequencing and mass spectrometry technologies, multiomics data can now be easily acquired for understanding complex biological systems. Nevertheless, substantial challenges remain in determining the association between gene-metabolite pairs due to the nonlinear and multifactorial interactions within cellular networks. The complexity arises from the interplay of multiple genes and metabolites, often involving feedback loops and time-dependent regulatory mechanisms that are not easily captured by traditional analysis methods.

Spatial transcriptome analysis reveals de novo regeneration of poplar roots.

Propagation through cuttings is a well-established and effective technique for plant multiplication. This study explores the regeneration of poplar roots using spatial transcriptomics to map a detailed developmental trajectory. Mapping of the time-series transcriptome data revealed notable alterations in gene expression during root development, particularly in the activation of cytokinin-responsive genes.

N-glycosylation facilitates the activation of a plant cell-surface receptor.

Plant receptor kinases (RKs) are critical for transmembrane signalling involved in various biological processes including plant immunity. MALE DISCOVERER1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) is a unique RK that recognizes a family of immunomodulatory peptides called SERINE-RICH ENDOGENOUS PEPTIDEs (SCOOPs) and activates pattern-triggered immunity responses. However, the precise mechanisms underlying SCOOP recognition and activation of MIK2 remain poorly understood.