A single nucleotide deletion in CsSCP4 disrupts brassinosteroid biosynthesis and confers a super compact phenotype in cucumber.

Identification of candidate genes associated with albino phenotype in 'Huangjinya' tea plant through genome resequencing.

Cytokinin is a plant hormone that regulates several yield-related traits in plants. Previously, it was demonstrated that in tetraploid oilseed rape (Brassica napus L.), mutation of all four cytokinin-degrading BnCKX3 and both BnCKX5 genes resulted in increased cytokinin concentration, larger and more active inflorescence meristems, and a higher number of ovules per gynoecium. This resulted in the formation of more flowers and pods on the main stem, thereby increasing seed yield from the main stem of the plants. Here, we investigated the relative contributions of distinct combinations of BnCKX3 and BnCKX5 genes of the A and C genomes to these yield components. Our analysis revealed an unexpectedly strong role for BnCKX5 in regulating these traits and identified distinct supportive BnCKX3 gene mutant combinations. These findings facilitate the selection of relevant alleles for breeding. Furthermore, seeds from BnCKX gene mutant plants showed oil content and concentrations of unsaturated fatty acids similar to those of the wild type. Taken together, this study provides further insight into the role of cytokinin and BnCKX genes in regulating yield components in oilseed rape and provides novel information on functionally relevant alleles.

ANAC032 directly bind to the promoter regions of XTH31 and XTH33 and repress their expression, and loss-of-function xth31 mutant plants exhibited increased sensitivity to Ni stress, with phenotypes similar to those of NAC32-overexpressing plants.

Two kinesin-12 class proteins are involved in post-cytokinetic membrane trafficking required for auxin responses in Arabidopsis.

IntroductionIron is an essential microelement for animals, humans, and plants. Notably, approximately one-third of the world’s soils are alkaline, leading to iron deficiency. Therefore, understanding the mechanism of iron absorption and transport in plants is crucial for improving iron bioavailability in crops. MethodsIn this research, reverse genetics was used to identify the transcription factor MYB30 as a positive regulator of the plant response to iron deficiency.Results and DiscussionPhenotype analysis demonstrated that MYB30 mutant plants were sensitive to iron deficiency, exhibiting reduced root length, lower chlorophyll content, and elevated lipid peroxidation, whereas MYB30 overexpression lines showed enhanced tolerance. Metabolomic analysis of myb30 plant roots by mass spectrometry indicated decreased antioxidant activity and detoxification capacity under iron-deficient conditions. Interestingly, 22 metabolic pathways were altered in the myb30 plant under iron deficiency. This metabolic reprogramming likely compromises plant growth. Furthermore, MYB30 reduced reactive oxygen species accumulation under iron deficiency stress by activating related genes and enhancing antioxidant enzyme activity. In summary, metabolite analysis provides detailed molecular insights into plant iron deficiency stress and supports molecular genetic breeding efforts to improve mineral nutrition in crops.

Photosynthesis genes in plant chloroplasts are transcribed by the plastid-encoded RNA polymerase called PEP. Consequently, PEP-deficient mutants cannot generate a photosynthetic apparatus and develop non-viable albino seedlings. Inducible complementation of such mutants thus could provide interesting insights in PEP action and chloroplast biogenesis. Here we show the effects of photo-inducible complementation in the albino Arabidopsis mutant pap7-1 using a red/blue optoswitch with monochromatic LEDs. Expression of a blue-light-induced PAP7 construct that is silent under red light reconstitutes PEP at any time point of pap7-1 development resulting in proper chloroplast biogenesis that rescues the non-viable mutant. Induction of chloroplast biogenesis, however, can only occur in very young leaf tissues indicating the existence of a cell-autonomous, biogenic coupling between cell and organelle development. We further uncover that initial PEP formation and function is independent of photosynthesis. The optoswitch termed blue-light valved biogenesis opens experimental avenues to study non-viable plant mutants.

Cold acclimation is a crucial physiological process that enables plants to adapt to low temperatures. A key aspect of this acclimation is lipid remodeling, which preserves membrane fluidity and integrity under cold stress. Proteins of the chloroplast envelope membranes are increasingly recognized for their role in acclimation to changing environmental conditions. While lipid synthesis occurs at the inner envelope membrane, little is known about specific proteins involved in lipid remodeling during cold acclimation. In this study, we investigated the role of Chloroplast Lipid Remodeling Protein 23 (CLRP23) as a component of the inner chloroplast envelope membrane. Subcellular fractionation combined with protease protection assays provided evidence for its orientation toward the intermembrane space. To explore its function, we analyzed the physiological performance and lipid composition in CLRP23-deficient mutant plants. Under cold stress, we observed significant impairments in photosynthesis and increases in the galactolipid response, suggesting CLRP23 is involved in lipid remodeling. Lipid overlay assays, supported by in silico docking analyses, demonstrated that CLRP23 can directly interact with chloroplast lipids, including galactolipids. Complementary transcriptomic and proteomic analyses revealed broader effects on cold-responsive pathways, supporting the view that CLRP23 contributes to the integration of membrane and metabolic responses during acclimation. These findings expand our understanding of protein-mediated processes during cold acclimation.

Eucalyptus leaf blight is a globally distributed disease caused by Calonectria fungi, with C. pseudoreteaudii being the dominant pathogen in Fujian, China. The crude toxin produced by C. pseudoreteaudii is a key virulent factor. To investigate the resistance mechanism triggered by crude toxin infection, transcriptome sequencing, physiological observations, and qRT-PCR analyses were conducted. Transcriptome analysis of Arabidopsis thaliana treated with C. pseudoreteaudii crude toxin revealed that a flavin-containing monooxygenase 1 gene (AtFMO1) exhibited the highest differential expression with DMSO control. Compared with Arabidopsis ecotype Col-4 (the wild type, WT), AtFMO1 knockout mutant (Δfmo1) plants displayed dose-dependent leaf margin yellowing accompanied by reduced callose deposition and hydrogen peroxide (H2O2) accumulation under crude toxin treatment. qRT-PCR analysis of key genes from two immune pathways showed that the salicylic acid-dependent (SA-dependent) pathway was likely Arabidopsis's primary response pathway for crude toxin. In E. grandis, a total of 38 EgFMOs were identified, with eight EgFMO1s, based on the protein sequence similarity, conserved domain, and motif pattern. qRT-PCR analysis of EgFMO1s revealed two major expression patterns in response to crude toxin treatment: an initial downregulation followed by upregulation, and continuous upregulation. Collectively, these results suggest FMO1 plays a positive role in resistance to C. pseudoreteaudii crude toxin in both A. thaliana and E. grandis.

Abscisic acid (ABA), a phytohormone that affects key biological processes, is best known for causing stomata closure to protect plants against environmental stresses. The prevailing mechanism for ABA perception is through the PYL/PYR/RCAR family of proteins but reports of other ABA-interacting proteins such as the guard cell outward rectifying K+ channel (GORK), have encouraged the search for more ABA-sensitive proteins. Here, we identified a similar ABA-interacting site as GORK, in an Arabidopsis thaliana ANTHRANILATE SYNTHASE (ASA2). We found that asa2 mutant plants have obvious aberration in ABA-dependent stomata closing. Leaf transcriptomics revealed significantly fewer ABA-induced DEGs in asa2-1 as compared to Col-0. ABA- and other hormone-related terms were also under-represented, indicating an overall reduced genomic sensitivity to ABA. Computational analysis hinted plausible ABA interaction at the predicted site and both indirect and direct in vitro interaction studies showed that ASA2 could interact with ABA in a specific and ligand dependent manner. Importantly, single amino acid substitutions at the ABA site resulted in various degrees of reduced ABA affinities. Further examination of how ABA interaction affects the enzymatic activity of ASA2 and the flow of information in the chloroplast could reveal molecular targets for agrochemical design that will improve plant resilience.

DNA methylation is a conserved epigenetic modification crucial for silencing genes and transposable elements (TEs). However, the mechanisms that cause silencing remain unclear, partly because methyl reader protein mutants in both plants and animals show minimal transcriptional changes. To explore the possibility of redundancy among these silencing mechanisms, we generated combinatorial mutants of H1.1, H1.2, ADCP1, MOM1, MBD2, MBD5, and MBD6 lacking key methyl readers and related silencing pathways. We observed massive derepression of genes and TEs at DNA-methylated loci, showing that these pathways account for 73% of silencing compared to DNA methylation-free mutants. We also observed that immune response genes were upregulated, causing an imbalance between growth and defense. Loss of downstream silencing pathways further disrupted 3D genome organization, leading to increased euchromatin-heterochromatin interactions. These findings highlight the cooperative action of multiple downstream mechanisms in DNA methylation-mediated silencing and genome organization.

The selective degradation of aberrant mRNAs plays a vital role in ensuring cellular survival under stress conditions. Here, we investigated the role of OsFKBP20-1b, a splicing factor, in dehydration stress response in rice (Oryza sativa). We show that OsFKBP20-1b associates with the core nonsense-mediated mRNA decay (NMD) components, UP-FRAMESHIFT1 (OsUPF1) and OsUPF2, enhances their stability, thereby supporting the efficient degradation of aberrant transcripts during dehydration stress. These associations were demonstrated using bimolecular fluorescence complementation (BiFC), co-immunoprecipitation (Co-IP), and in vitro binding assays. Integrative analyses combining ribosome profiling and transcriptome sequencing further revealed that OsFKBP20-1b influences both alternative splicing (AS) patterns and translational dynamics of stress-responsive transcripts. Notably, loss of OsFKBP20-1b compromises OsUPF1- and OsUPF2-mediated decay of aberrant mRNAs under dehydration conditions. Consistent with these molecular defects, osfkbp20-1b mutant plants exhibited heightened sensitivity to dehydration stress. Together, our findings identify OsFKBP20-1b as a key regulator linking pre-mRNA splicing with cytoplasmic RNA surveillance during dehydration stress, thereby providing mechanistic insight into post-transcriptional control of stress adaptation in rice. These results advance our understanding of RNA quality control pathways in plants and suggest potential molecular targets for improving drought-resilience in crops.

At the core of cell wall integrity (CWI) mechanisms that enable plant cells to coordinate their growth with their cell wall status, lies the transmembrane Malectin-like receptor kinase FERONIA (FER) and its family members. FER itself controls a myriad of plant developmental processes including sexual reproduction, cell growth and morphogenesis, often intersecting with phytohormones-dependent pathways such as abscisic acid (ABA) signaling or plant immunity. Interestingly, FER together with its downstream receptor-like cytoplasmic kinase MARIS (MRI) have been shown to similarly control root hair and rhizoid integrity in the vascular angiosperm Arabidopsis thaliana and the early diverging bryophyte Marchantia polymorpha, respectively. It remains uncertain however whether FER and MRI cooperate beyond tip growth in Marchantia, and which of their functions in Arabidopsis originate from mechanisms established early in land plant evolution. Here, we conducted comparative transcriptomic and proteomic analyses on the M. polymorpha mutant plants, Mpfer-1 and Mpmri-1, alongside their corresponding wild-type accessions. We observed large and significant overlaps between differentially expressed genes and abundant proteins between both mutants. Our multi-omics approach revealed that MpFER and MpMRI largely cooperate to repress transcriptional networks, particularly those associated with plant defense and ABA responses. Nonetheless, our phenotypic analyses showed that MpFER and MpMRI exert distinct functions in response to abiotic stresses such as ABA and salt treatment. Specifically, Mpfer-1, but not Mpmri-1, plants exhibited hypersensitivity to ABA-dependent growth inhibition, indicating that FER's role in negatively regulating ABA-mediated growth responses is conserved between bryophytes and vascular plants.

Inositol phosphates and pyrophosphates are small, water-soluble molecules involved in a range of physiological processes across eukaryotic organisms, including plants. Over the past two decades, significant advancements in inositol (pyro)phosphate detection and chemical synthesis, coupled with the characterization of plant mutants and the structural analysis of receptors and associated proteins, have greatly enhanced our understanding of their production, degradation, and perception in plants. This growing knowledge base demonstrates that inositol (pyro)phosphates are crucial for regulating key processes, such as phosphorus homeostasis, hormone signaling, and plant-microbe interactions. We provide a global perspective on these processes, highlighting recent discoveries, new possibilities, and unresolved questions.

Ethylene plays an indispensable role in regulating plant growth and stress responses. However, the mechanisms underlying the regulation of Na+/H+ homoeostasis by ethylene and subsequent mediation of maize growth under salt stress remain unclear. ZmACO2, which encodes ethylene biosynthesis enzyme 1-aminocyclopropane-1-carboxylate oxidase2, is induced by salt stress. Thus, ZmACO2-overexpressing (ACO2-OE) and mutant (aco2-cr) plants were used to investigate how ethylene regulates Na+/H+ homoeostasis in maize under salt stress. The aco2-cr mutants exhibited significantly lower Na⁺ accumulation and Na⁺/K⁺ ratios than the wild-type and ACO2-OE plants. This phenotype was attributed to their higher expression of ZmSOS1 and ZmHKT1, which increased root net Na⁺ efflux by 20.65% and decreased Na⁺ transport from roots to shoots by 42.49% (p < 0.001), respectively. Compared to the other plants, aco2-cr mutants showed higher ZmMHA2 expression and plasma membrane H+-ATPase activities, which promoted net root H+ efflux to provide a greater H+ proton gradient for salt-overly-sensitive 1 (SOS1). Inhibition efficiencies of Na+ efflux and H+ influx by sodium orthovanadate were lower in aco2-cr mutants than in ACO2-OE and wild-type plants under salt stress; however, ACO2-OE plants showed a salt-sensitive phenotype. Overall, these findings showed that salt-induced ethylene inhibited plasma membrane H+-ATPase and SOS1 from disrupting Na+/H+ homoeostasis, thereby decreasing Na+ efflux in maize roots and also provided a strategy to improve salt tolerance by optimising ethylene levels in maize.

Glucose mitigates spatial heterogeneous cold damage in wheat via enhanced carbohydrate allocation to spike.

The critical role of autophagy in mitigating acid stress-induced hypersusceptibility response in Arabidopsis thaliana.

In higher plants, both normal meiosis and timely degradation of tapetal cells are crucial for gametophyte development, and abnormal reactive oxygen species (ROS) levels are detrimental to this process. However, the molecular mechanisms underlying their coordination remain unclear. Here, we isolated and characterized a sterile rice mutant, designated as abnormal meiocytes and tapetum 1 (Osamt1). Compared with the wild-type (WT), Osamt1 mutant plants exhibited meiotic chromosomal fragmentation, arrest of pollen mother cell development at meiotic prophase I, abnormal tapetal development, and excessive accumulation of ROS. Map-based cloning revealed that the OsAMT1 gene encodes a protein containing a DUF1771 domain with a Small MutS-related (SMR) domain, whose function is related to DNA repair. Sequence analysis revealed that a single-nucleotide mutation occurred at the splice site between the 5th exon and its adjacent intron of Osamt1, leading to a longer transcript than that in the WT. This aberrant splicing resulted in a frameshift and consequently introduced a premature stop codon. Subcellular localization showed that OsAMT1 is localized to the endoplasmic reticulum (ER). Tissue expression analysis demonstrated that OsAMT1 is strongly expressed in tapetal cells during the early stage of anther development. Biochemical analyses further established that OsAMT1 can physically interact with OsMT2b, a key mediator of ROS scavenging. Further RT-qPCR assays indicated that OsAMT1 affects the reproductive process by influencing the expression of genes related to meiosis and tapetal development. Collectively, our study identifies OsAMT1 as a key regulator of meiosis and tapetum development, expanding the network of reproductive development in rice.

SlBBX20 is a regulator of plant development in response to shade in tomato.

Mutations in TaPRR59 impact transcript levels of some key flowering genes and show earlier heading time and reduced plant height. Favorable haplotype TaPRR59-A1-Hapla was positively selected in wheat breeding programs. The circadian clock system is a crucial endogenous rhythmic regulatory mechanism with a significant role in plant growth and development. The pseudo-response regulator (PRR) family is a pivotal component of circadian networks. In the present study, we cloned the wheat PRR family member TaPRR59 and investigated its function using gene editing, transcriptome sequencing, haplotype analysis, and association analysis. The expression profile of TaPRR59 over a 24-h period exhibited a diurnal rhythmic expression pattern. Luciferase transient transcriptional assay demonstrated that TaPRR59 acts as a transcriptional repressor in the nucleus. The taprr59-ABD-KO gene-edited lines produced using the CRISPR/Cas9 genome-editing system had earlier heading time and reduced plant height. Overexpression of TaPRR59-D1 in rice significantly delayed the heading date, reduced plant height and thousand-grain weight, and increased the number of grains per panicle. Transcriptome analysis revealed the transcript levels of several key flowering genes and chlorophyll a-b binding protein-related genes were up- or down-regulated in the taprr59 mutant plants. Association analysis showed that natural variations at TaPRR59-A1, TaPRR59-B1, and TaPRR59-D1 were significantly associated with yield traits such as plant height, thousand-grain weight, and heading date. Geographical analysis showed distinctive distribution characteristics of TaPRR59 haplotypes in different agroecological production zones. Additionally, the significant difference in frequency of the favorable haplotype TaPRR59-A1-Hapla between landraces and modern cultivars indicates that it has been subject to directional selection during wheat breeding. This research provided novel insights into the influence of the circadian clock system on agronomic traits and provided useful molecular markers and genetic resources for wheat breeding.