Plant Communications最新文献

Global climate change poses increasing threats to seed production and thus food security. The seed microbiome plays an essential role in regulating the whole seed life cycle. Specific seed endophytes and spermosphere microorganisms orchestrate the maintenance and termination of dormancy towards the synchronization of germination plasticity to meet agricultural demands. In this review, we summarize recent advances by linking seed-microbiome interactions with seed processes. We review the sources of seed microbiomes and their physiological regulation on dormancy and germination in response to environmental changes with a focus on phytohormone crosstalk. We also discuss the molecular mechanisms by which seed-microbe interactions affect seed destiny. Finally, we explore emerging precision applications of microbiomes in the seed industry by integrating cutting-edge technologies such as microbial seed coatings and artificial intelligence (AI) in seed science and technology. In conclusion, harnessing microbiome-based strategies to manipulate seed life cycle holds immense promise for sustainable food production in a changing global climate.

In Arabidopsis thaliana, METHYL-CpG-BINDING DOMAIN 7 (MBD7) and its associated α-crystallin domain (ACD) proteins form a complex that interprets DNA methylation to prevent the silencing of methylated luciferase (LUC) reporter transgenes. However, the mechanism by which the MBD7 complex effectively targets methylated transgenes remains largely unclear. Here, we identify a novel role for SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), extending its function beyond the canonical RNA-directed DNA methylation (RdDM) pathway. We demonstrate that SHH1 prevents the transcriptional silencing of methylated LUC transgenes and a subset of endogenous genes by acting in concert with MBD7 within the same regulatory pathway. SHH1 co-localizes with MBD7 at nuclear foci and physically interacts with it to enhance its stability. Furthermore, SHH1 binds to methylated loci via its SAWADEE domain, which recognizes the H3K9me2 histone mark. This interaction promotes the reciprocal recruitment of SHH1 and MBD7 to methylated loci, revealing a cooperative mechanism that maintains transcriptional activity at promoter-methylated genes. Collectively, our findings unveil a dynamic, mutually reinforcing SHH1-MBD7 module that enhances the expression of promoter-methylated genes, likely by facilitating effective binding to chromatin marked by repressive epigenetic modifications. This work provides important insights into how DNA methylation fine-tunes gene expression in plants by balancing between transcriptional repression and activation.

Long non-coding RNAs (lncRNAs) regulate numerous biological processes in plants, including development and stress responses. Although previous studies have mainly examined their sequences and transcriptional activity, other essential aspects, such as in vivo RNA secondary structure and post-transcriptional regulation, remain poorly understood in plants. Here, we comprehensively characterized lncRNA features, including length, sequence composition, conservation, and in vivo secondary structure, in two representative species: Arabidopsis thaliana (dicot) and durum wheat (monocot). While lncRNAs show limited conservation across the plant kingdom, their sequences display moderate conservation within evolutionary clades. We further identified conserved RNA structural motifs that form stable folds in vivo. Comparative genome-wide analyses of post-transcriptional regulation revealed that plant lncRNAs vary widely in translation efficiency and RNA stability, with RNA structure emerging as a major determinant of both processes. Moreover, transcriptome-wide analyses uncovered structural motifs associated with translation and stability, predominantly enriched at the 3' ends of plant lncRNAs. Together, these findings provide a comprehensive framework for understanding plant lncRNA features and reveal a central role of RNA structure in shaping their post-transcriptional regulation.

Bulked segregant analysis (BSA) is a widely used method for identifying genomic loci associated with traits of interest in crops. However, conventional BSA is limited by its reliance on phenotype-driven bulk sampling, which restricts its scalability and confines its applicability to single-trait analysis. This study introduces a novel method, reverse BSA-QTLseq, which uses genotype-driven bulk reconstruction through bioinformatics, enabling the simultaneous mapping of multiple traits from the same genotypic dataset. Reverse BSA-QTLseq uses a two-step strategy-low-resolution genotyping of the entire population followed by high-resolution sequencing of selected bulks-enabling cost-effective identification of genetically divergent lines to enhance the discovery of quantitative trait loci (QTLs). Using a bread wheat recombinant inbred line (RIL) population as a case study, we mapped loci associated with heading date and plant height , confirming approximately 95% of known QTLs, including both dwarfing genes (e.g., Rht-B1 and Rht-5) and flowering-time regulators (e.g., Vrn-A1), and identified novel QTLs and candidate loci with strong phenotypic effects. The phased genotyping strategy maximized genetic distance in the initial sampling, facilitating the in silico reconstruction of trait-specific contrasting bulks. Integration of transcriptional profiles from the parental lines of the RIL population, from which the bulks were derived, aided in identifying candidate genes and regulatory networks underlying the variation of traits such as photoperiod response, nutrient transport, and stress adaptation. The versatility and potential for data reuse offered by the proposed method represent a significant advancement in QTL mapping, with broad implications for marker-assisted breeding and selection programs. Future integration of transcriptomic and epigenomic data is expected to further enhance the power of reverse BSA-QTLseq, accelerating genetic improvement in crops.

Seed development is a pivotal stage of the soybean life cycle, directly determining yield and nutritional quality related to oil and protein contents. However, the spatiotemporal mechanisms underlying cell differentiation and nutrient accumulation during seed growth remain to be resolved, especially in wild soybean (Glycine soja), which harbors rich genetic diversity for quality traits. Here, spatial transcriptomics and metabolomics were combined to dissect the dynamics of cell differentiation and nutrient accumulation in G. soja seeds at the mid-maturity stage. Differential expression analysis revealed distinct patterns of accumulation in adaxial versus abaxial parenchyma cells of the embryo: abaxial cells are enriched in protein metabolism pathways, whereas adaxial cells are focused on lipid metabolism pathways, consistent with previous reports on spatial nutrient accumulation in G. soja seeds. Pseudotemporal trajectory analyses supported a sequential pattern of transcriptional regulation underlying these differences. Analysis of cell-cell communication provided insight into the interactions that may mediate cell-type-specific differences among seed cells. Key genetic regulators and differentially abundant metabolites were identified through the integration of spatial transcriptomics and metabolomics, and GsMAPK23-4 was identified as a core candidate gene linked to nutrient metabolism in the cotyledon. Functional validation confirmed that GsMAPK23-4 modulates seed quality: knockout mutants had significantly higher levels of amino acids and proteins. These findings reveal cellular characteristics and differentiation processes in G. soja seeds at the mid-maturity stage, providing a molecular basis for understanding this phase and generating targets to improve soybean yield and quality.

Cistanche deserticola (C. deserticola) is a holoparasitic plant of the Orobanchaceae family that parasitizes the roots of Haloxylon ammodendron (H.ammodendron). The absence of a high-quality genome has impeded our understanding of its parasitic mechanisms. Here, we present a chromosome-level genome assembly of C. deserticola (6.26 Gb) based on PacBio high fidelity (HiFi) and high-throughput chromosome conformation capture (Hi-C) sequencing, with a contig N50 of 81.25 Mb, 92.2% Benchmarking Universal Single-Copy Ortholog (BUSCO) completeness, and 54 640 protein-coding genes. Evolutionary analysis shows that C. deserticola diverged from related Orobanchaceae species approximately 38.23 million years ago. Among its key parasitic adaptations is the extensive loss of photosynthetic genes, which is compensated by the retention of transporters and carbon metabolic pathways for the utilization of host-derived nutrition. Bidirectional genetic exchanges include 34 H. ammodendron-derived horizontally transferred genes and 98 mobile mRNAs, as well as 14 C. deserticola-derived horizontally transferred genes and 77 mobile mRNAs targeting host defenses. Spatial transcriptomic data reveal haustorium-specific gene expression related to nutrient extraction and chemical defense, particularly the biosynthesis of phenylethanoid glycosides via dispersed-duplication-driven gene expansion. This genomic resource illuminates the evolutionary trajectory of C. deserticola and provides a foundation for conservation strategies and the biotechnological development of C. deserticola.

Phospholipases are major regulators of lipid-dependent signaling and play crucial roles in plant immunity. Rice (Oryza sativa) phospholipase C4 (OsPLC4) is a major functional enzyme in the rice phospholipase family that regulates intracellular Ca²⁺ levels. Here we show that OsPLC4 translocates primarily to the plasma membrane in a Ca²⁺-dependent manner, with its C2 domain functioning as a membrane trafficker. Transient expression of OsPLC4 and its truncated variants triggers cell death and immune responses in plants. During effector-triggered immunity (ETI) in rice, OsPLC4 expression and Ca²⁺ influx are specifically and strongly induced in response to avirulent Magnaporthe oryzae. Upon infection, the rice Osplc4 knockout mutant (ΔOsplc4) exhibits substantially reduced Ca²⁺, reactive oxygen species (ROS), and Fe³⁺ accumulation, as well as diminished lipid peroxidation and hypersensitive response (HR) cell death. Complementation of ΔOsplc4 can fully restore Ca²⁺-mediated ferroptotic cell death. OsPLC4 expression also activates HR cell death and the expression of defense-related genes such as OsRbohB, OsMEK2, OsMPK1, and OsPAL1 during avirulent M. oryzae infection. The Ca²⁺ chelator ethylene glycol-bis(2-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) substantially inhibits Ca²⁺, ROS, and Fe³⁺ accumulation and HR-related cell death in rice, whereas the Ca²⁺ influx enhancers trifluoperazine hydrochloride (TFP) and acibenzolar-S-methyl (ASM) strongly induce Ca²⁺-mediated ferroptotic cell death. Additionally, OsPLC4 overexpression triggers cell death and immune responses in Arabidopsis. Collectively, our findings demonstrate that OsPLC4 acts as a downstream target of resistosome activation and sustains the co-elevation of Ca²⁺ and ROS levels during rice ETI, thereby promoting Ca²⁺-mediated, lipid ROS-dependent ferroptotic cell death. These results establish OsPLC4 as a key regulator of Ca²⁺-dependent plant immunity.