Fruit yield and quality are antagonistically regulated traits in tomato. An excessive focus on increasing yield often leads to a decline in quality. How to achieve the delicate balance between high yield and desirable fruit quality is still a big challenge. In this study, we discovered that disrupting the function of tomato tonoplast sugar transporter 3a (TST3a) can significantly enhance both fruit weight and flavor. In tomato, there are three TSTs, namely SlTST1, SlTST3a and SlTST3b, which possess same sugar transport specificity for fructose and glucose and redundantly control cell expansion during fruit development. The different levels of sugar accumulation in the sltst mutants significantly associated with the fruit size and flavor. The reason for the enlarged fruits of sltst3a mutants, which are a consequence of sugar accumulation, is the increased abundance of SlTST1 at the tonoplast and coupled with the highest sugar transport capacity of SlTST1. Further studies established that SlTST3a prevented the localization of SlTST1 to the tonoplast by inhibiting its interaction with VH1-interacting kinase (SlVIK). Mutation of SlTST3a in the cultivated tomatoes can simultaneously enhance tomato fruit size and sugar content. Our findings present potential avenues for simultaneously improving both fruit quality and yield and provide valuable insights into the mechanisms underlying the storage sugar for fruit development.

The Chinese white pear (Pyrus bretschneideri) is an economically significant fruit crop worldwide. Previous versions of the P. bretschneideri genome assembly contain numerous gaps and unanchored genetic regions. Here, we generated two high-quality, gap-free genome assemblies for 'Dangshansu' (DS; 503.92 Mb) and 'Lianglizaosu' (ZS; 509.01 Mb), each anchored to 17 chromosomes, achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%. Our genome-wide association studies explored the associations between genetic variations and stone cell traits, revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene, designated PbdsZF. Through genetic transformation, we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation, as it transcriptionally activates multiple genes involved in these processes. By binding to the CT-rich motifs CT1 (CTTTTTTCT) and CT2 (CTCTTTTT), PbdsZF significantly influences the transcription of genes essential for lignin production, underscoring its regulatory importance in plant lignin metabolism. Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation, thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.

Plant cell death is mediated by calcium, iron, and reactive oxygen species (ROS) signaling in plant immunity. The reconstruction of a nucleotide-binding leucine-rich repeat receptor (NLR) supramolecular structure, called the resistosome, is intimately involved in the hypersensitive response (HR), a type of cell death involved in effector-triggered immunity (ETI). Iron is a crucial redox catalyst in various cellular reactions. Ferroptosis is a regulated, non-apoptotic form of iron- and ROS-dependent cell death in plants. Pathogen infections trigger iron accumulation and ROS bursts in plant cells, leading to lipid peroxidation via the Fenton reaction and subsequent ferroptosis in plant cells similar to that in mammalian cells. The small-molecule inducer erastin triggers iron-dependent lipid ROS accumulation and glutathione depletion, leading to HR cell death in plant immunity. Calcium (Ca) is another major mediator of plant immunity. Cytoplasmic Ca influx through calcium-permeable channels, the resistosomes, mediates iron- and ROS-dependent ferroptotic cell death under reduced glutathione reductase (GR) expression levels in the ETI response in plants. Acibenzolar-S-methyl (ASM), a plant defense activator, enhances Ca influx, ROS and iron accumulation and lipid peroxidation to trigger ferroptotic cell death in plants. These breakthroughs suggest a potential role of Ca signaling in ferroptosis and its coordination with iron and ROS signaling in plant immunity. In this review, we highlight the essential roles of calcium, iron, and ROS signaling in ferroptosis during plant immunity and discuss advances in the understanding of how Ca-mediated ferroptotic cell death orchestrates effective plant immune responses against invading pathogens.

Plant-meditated RNA interference (RNAi), by which double-stranded RNAs (dsRNAs) targeting insect genes are expressed in plants for insect ingestion, has shown great potential for herbivorous insect pest control. Locusts which are among the most destructive agriculture insect pests appear to be resistant to orally delivered naked dsRNA. Moreover, the feasibility of plant-mediated RNAi in suppressing the expression of target genes in locusts remains poorly understood. Using the migratory locust Locusta migratoria, we report here that C-type muscarinic acetylcholine receptor (mAChR-C), a G protein-coupled receptor (GPCR) belonging to bioamine receptor subfamily, played a pivotal role in chitin metabolism by regulating genes responsible for chitin synthesis and degradation. Knockdown of locust mAChR-C by injection-delivered dsRNA caused defective nymph molting and metamorphosis, accompanied by malformation, arrested development and motility. Notably, locusts feeding on transgenic maize expressing locust mAChR-C dsRNAs exhibited defective phenotypes similar to those subjected to injection of mAChR-C dsRNA. However, ingestion of transgenic maize with locust mAChR-C dsRNA had no significant effect on non-target insects including the fall armyworm Spodoptera frugiperda, the cotton bollworm Helicoverpa armigera, the Asian corn borer Ostrinia furnacalis and the oriental armyworm Mythimna separata. Our results suggest that transgene expression of locust mAChR-C dsRNA is an efficient RNAi approach for locusts, which offers a promising eco-friendly strategy for locust management.

Cold stress in temperate rice production regions is responsible for yield losses of up to 30-40%, and improving cold tolerance is a practical strategy to safeguard rice production. Numerous genes and signaling networks for cold stress have been identified in rice. However, little is known about the roles of microRNAs in the cold stress response. Here, we find that a rice-specific pri-miR1850 and its two mature products, miR1850.1 and miR1850.2, are down-regulated by cold stress. Using gain- and loss-of-function genetic approaches in elite japonica cultivars, we show that pri-miR1850 and miR1850.1 negatively regulate cold tolerance at both the young-seedling and booting stages. miR1850.1 targets and suppresses the immune gene NPR3 by mediating transcript cleavage and transitional repression. Upon cold treatment, NPR3 transcripts and proteins are up-regulated due to the alleviation of miR1850.1-mediated repression and the activation of NPR3 transcription. miR1850.1 functions genetically through NPR3 in the cold-stress response. The miR1850.1-NPR3 module also controls rice disease resistance and grain yields. Our findings reveal a cold-signaling network and provide targets for engineering cold-tolerant japonica varieties to endure fluctuating future climates.

Striga hermonthica, an obligate parasitic plant that causes severe agricultural damage, recognizes its hosts by perceiving haustorium-inducing factors (HIFs). Perception of HIFs induces rapid transformation of S. hermonthica radicles into prehaustoria, the early-stage organs of haustorium structures for host invasion. HIFs consist of various aromatic compounds, including quinones, lignin monomers, and flavonoids. However, the downstream molecular pathways that orchestrate the developmental events are largely unknown. Here, we report that S. hermonthica root tip cells rapidly deposit lignin, a major cell-wall component, as a functional response to HIFs. Concomitant with enhanced lignin levels, genes involved in lignin monomer biosynthesis and lignin polymerization, including several respiratory burst oxidase homologs (RBOHs) and Class III peroxidases, are highly induced by HIFs. Perturbing the lignin monomer biosynthesis largely compromises prehaustorium formation. HIF-induced Class III peroxidases facilitate prehaustorium formation by promoting lignification. Our study demonstrates that cell wall lignification is a converged cellular process downstream of various HIFs that functions to guide root meristematic cells to build the prehaustoria.

Researchers have uncovered hundreds of thousands of natural products, many of which contribute to medicine, materials, and agriculture. However, missing knowledge of the biosynthetic pathways to these products hinders their expanded use. Nucleotide sequencing is key in pathway elucidation efforts, and analyses of natural products' molecular structures, though seldom discussed explicitly, also play an important role by suggesting hypothetical pathways for testing. Structural analyses are also important in drug discovery, where many molecular representation systems - methods of representing molecular structures in a computer-friendly format - have been developed. Unfortunately, pathway elucidation investigations seldom use these representation systems. This gap is likely because those systems are primarily built to document molecular connectivity and topology, rather than the absolute positions of bonds and atoms in a common reference frame, the latter of which enables chemical structures to be connected with potential underlying biosynthetic steps. Here, we expand on recently developed skeleton-based molecular representation systems by implementing common reference frame-oriented system. We tested this system using triterpenoid structures as a case study and explored the system's applications in biosynthesis and structural diversity tasks. The common reference frame system can identify structural regions of high or low variability on the scale of atoms and bonds and enable hierarchical clustering that is closely connected to underlying biosynthesis. Combined with phylogenetic distribution information, the system illuminates distinct sources of structural variability, such as different enzyme families operating in the same pathway. These characteristics outline the potential of common reference frame molecular representation systems to support large-scale pathway elucidation efforts.

The combination of flexible electronics and plant science has generated various plant-wearable sensors, yet challenges persist in their applications in real-world agriculture, particularly in high-throughput settings. Overcoming the trade-off between sensing sensitivity and range, adapting them to a wide range of crop types, and bridging the gap between sensor measurements and biological understandings remain the primary obstacles. Here we introduce PlantRing, an innovative, nano-flexible sensing system designed to address the aforementioned challenges. PlantRing employs bio-sourced carbonized silk georgette as the strain sensing material, offering exceptional detection limit (0.03-0.17% strain depending on sensor model), stretchability (tensile strain up to 100 %), and remarkable durability (season long). PlantRing effectively monitors plant growth and water status, by measuring organ circumference dynamics, performing reliably under harsh conditions and being adaptable to a wide range of plants. Applying PlantRing to study fruit cracking in tomato and watermelon reveals novel hydraulic mechanism, characterized by genotype-specific excess sap flow within the plant to fruiting branches. Its high-throughput application enabled large-scale quantification of stomatal sensitivity to soil drought, a long-standing aspiration in plant biology, facilitating drought tolerant germplasm selection. Combing PlantRing with soybean mutant led to the discovery of a potential novel function of the GmLNK2 circadian clock gene in stomatal regulation. More practically, integrating PlantRing into feedback irrigation achieves simultaneous water conservation and quality improvement, signifying a paradigm shift from experience- or environment-based to plant-based feedback control. Collectively, PlantRing represents a groundbreaking tool ready to revolutionize botanical studies, agriculture, and forestry.

Fruit pigmentation is a major signal that attracts frugivores to enable seed dispersal. In most fleshy fruit, green chlorophyll typically accumulates early in development and is replaced in ripening by a range of pigments. Species such as grape and strawberry replace chlorophyll by red anthocyanins generated through the flavonoid biosynthetic pathway. Eggplant (Solanum melongena) is unique as its fruit accumulates anthocyanins starting from fruit set which are later replaced by the yellow flavonoid pathway intermediate naringenin chalcone. To decipher the genetic regulation of such an extraordinary pigmentation shift, we integrated mRNA and microRNA profiling data obtained from developing eggplant fruit. We discovered that while SQUAMOSA PROMOTER BINDING-LIKE (i.e., SPL6a, SPL10, and SPL15), MYB1 and MYB2 transcription factors (TFs) regulate anthocyanin biosynthesis in early fruit development, the MYB12 TF controls late naringenin chalcone accumulation. We further show that microRNA157 and microRNA858 negatively regulate SPLs and MYB12 expression, respectively. Taken together, our model suggests that opposing and complementary expression of microRNAs and TFs controls the pigmentation switch in eggplant fruit skin. Intriguingly, despite the distinctive pigmentation pattern in eggplant, fruit development in other species utilize homologous regulatory factors to control the temporal and spatial production of different pigment classes.

Carrots possess a diverse of falcarin-type polyacetylenes (PAs), which emerge as not only important phytoalexins against pathogens but also potential anti-cancer agents. Despite abundantly found in carrot root tissues, the biosynthesis and evolutionary origins of falcarindiol, a C17-PA, remain unknown. Fatty acid desaturase 2 (FAD2) enzymes play crucial roles in diversifying PAs by introducing various double and/or triple carbon-carbon bonds on fatty acid chains. Here, we apply association analysis and identify candidate FAD2 genes involved in falcarindiol biosynthesis. Using a rapid tobacco transient expression system, we found that DcFAD2 enzymes are highly functionally redundant and promiscuous. Combinatorial assays further uncovered unexpected synergistic and re-directive effects among FAD2 enzymes, complicating the biosynthetic pathway. CRISPR-Cas9-mediated mutagenesis and overexpression studies identified overlooked DcFAD2 hub genes as essential for falcarindiol production. Evolutionary analysis suggests that the expansion of DcFAD2 genes underpins the richness of falcarindiol in carrots, independently of the biosynthetic gene cluster previously identified in tomato. This work underscores the complexity of falcarin biosynthetic network and identifies hub genes essential for falcarindiol biosynthesis in carrot.

During the early systemic infection of plant pathogens, individual cells can harbor pathogens at various stages of infection, ranging from absent to abundant. Consequently, the alterations in gene expression levels within these cells in response to the pathogens exhibit significant variability. These variations are pivotal in determining pathogenicity or susceptibility, yet they remain largely unexplored and poorly understood. Sugarcane mosaic virus (SCMV) is a representative member of the monocot-infecting potyviruses with a polyadenylated RNA genome, which could be captured by single-cell RNA sequencing (scRNA-seq). Here, we performed scRNA-seq with SCMV-infected maize leaves during the early systemic infection (prior to symptom manifestation) to investigate the co-variation patterns between viral accumulation levels and alterations in intracellular gene expression levels. We identified five cell types and found that mesophyll-4 (MS4) cells had the highest viral accumulation levels in most cells. The early systemic infection of SCMV resulted in up-regulation of most differentially expressed genes (DEGs), which were mainly enriched in biological processes related to translation, peptide biosynthesis and metabolism. Co-variation analysis of the altered maize gene expression levels and viral accumulation levels in MS1, 2 and 4 revealed several patterns, and the co-expression relationships between them were mainly positive. Furthermore, functional studies identified several potential anti- or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection. These results not only provide new insights into plant gene regulation during viral infection, but also offer feasible references for future investigations of host-virus interaction across molecular, cellular, and physiological scales.

Orbitides, also known as Caryophyllaceae-type cyclic peptides, from Traditional Chinese Medicine plant Pseudostellaria heterophylla (Mil.) Pax have great potential for improving memory and treating diabetes. Orbitides are ribosomally encoded and post-translationally modified peptides, but this key biosynthesis enzyme is still unknown in P. heterophylla. We investigated the orbitide distribution in P. heterophylla and mined novel precursor peptide genes and peptide cyclase from multiple omics data. The function of the key tailoring gene was elucidated using transient heterologous expression and virus-induced gene silencing systems. Our findings suggest that PhPCY3 is a unique gene involved in the cyclization of linear precursor peptides in planta. Molecular docking and multiple sequence alignment, followed by site-directed mutagenesis, showed that N500 and S502 were the key amino acid residues. More than 100 precursor peptide gene sequences were identified, and known active orbitides, such as heterophyllin B and pseudostellarin E/F/G, were successfully biosynthesized. Four novel orbitides, namely cyclo-[LDGPPPYF], cyclo-[WGSSTPHT], cyclo-[GLPIGAPWG], and cyclo-[FGDVGPVI], were identified using the heterologous expression platform. In this study, we describe a gene-guided approach for elucidating the biosynthesis pathway and discovering novel orbitides. Our work provides a strategy for mining and biosynthesizing novel orbitides in P. heterophylla and other plants to further investigate their activities.

The rapid growth of population-scale whole genome resequencing, RNA sequencing, bisulfate sequencing, metabolomics and proteomic profiling has led quantitative genetics into a big omics data era. Performing omics data association analysis, such as genome, transcriptome, proteome and methylome wide association analysis, and integrative analysis on multiple omics datasets requires various bioinformatics tools that rely on advanced programming skills and command-line tools, which are challenging for wet-lab biologists. Here, we present EasyOmics a stand-alone R Shiny application with a user-friendly interface for wet-lab biologists to perform population-scale omics data association, integration and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, ranging from data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration and visualization etc. A wide range of publication quality graphs can be prepared in EasyOmics with point-and-click. EasyOmics is a platform-independent software that can be run under all operating systems with a docker container for quick installation. It is freely available to non-commercial users at docker hub https://hub.docker.com/r/yuhan2000/easyomics.

Plants develop branches to expand areas for assimilation and reproduction. Branching angles coordinate with branching types, creating diverse plant shapes that are adapted to various environments. Two types of branching angle-the angle between shoots and the angle in relation to gravity or the gravitropic set-point angle (GSA) along shoots-determine the spacing between shoots and the shape of the aboveground plant parts. However, it remains unclear how these branching angles are modulated throughout shoot development and how they interact with other factors that contribute to plant architecture. In this review, we systematically focus on the molecular mechanisms that regulate branching angles across various species, including gravitropism, anti-gravitropic offset, phototropism, and other regulatory factors, which collectively highlight comprehensive mechanisms centered on auxin. We also discuss the dynamics of branching angles during development and their relationships with branching number, stress resistance, and crop yield. Finally, we provide an evolutionary perspective on the conserved role of auxin in the regulation of branching angles.

This study identifies of a zinc metalloproteinase, ZG, that positively regulates both zinc content and grain size in rice. ZG's proteolytic activity increases with higher zinc ion concentrations. These findings, along with haplotype analysis in global rice cultivars, highlight its strong potential for enhancing both yield and nutritional value in rice breeding.