Pentatricopeptide repeat (PPR) proteins constitute a large superfamily of nuclear-encoded proteins characterized by tandem helical repeats. They function as critical coordinators of nucleus-organelle communication by modulating RNA metabolism within chloroplasts and mitochondria. This review summarizes recent advances in understanding the functional mechanisms of PPR proteins in major cereal and oilseed crops, with a focus on their roles in regulating seedling growth, stress responses, seed development, and cytoplasmic male sterility (CMS) restoration. We highlight how chloroplast-localized PPR proteins mediate RNA metabolism to ensure proper chloroplast biogenesis and seedling photosynthesis, while mitochondrial-targeted PPR proteins are crucial for RNA processing events that support respiration, embryo and endosperm development, and fertility restoration in CMS systems. We also describe how certain PPR proteins mediate biotic and abiotic stress responses through their functions in cold, drought, salt, and disease resistance, with specific members localized in chloroplasts or mitochondria. Finally, we outline unresolved questions regarding PPR protein complex assembly and environmental modulation, and highlight the emerging potential of engineered designer PPR (dPPR) proteins as programmable tools for precise RNA targeting and manipulation in organelles.

Transcriptome deep sequencing (RNA-seq) data analysis is often affected by reference bias introduced by the use of a single linear reference (SLR) genome. Graph-based pangenomes can mitigate this bias by integrating the SLR genome with complex genetic variations within a species; however, their application remains limited owing to a lack of dedicated analytical tools. Here, we present PanGraphRNA, an integrated bioinformatics platform for RNA-seq data analysis using a graph pangenome as reference. Built on the Galaxy web-based framework, PanGraphRNA provides functional modules for constructing, evaluating, and applying graph pangenomes across different population scales, thus enabling accessibility, traceability, and reproducibility throughout the analysis. Applied to both real and simulated RNA-seq data sets from Arabidopsis (Arabidopsis thaliana), PanGraphRNA outperformed the SLR approach, achieving higher read alignment accuracy and more precise gene expression quantification. PanGraphRNA enabled the identification of drought stress-induced genes and flowering time-related quantitative trait loci that were previously missed with the conventional SLR approach. Furthermore, we successfully applied PanGraphRNA to process RNA-seq data sets from rice (Oryza sativa) and maize (Zea mays). By providing standardized, containerized workflows, PanGraphRNA will facilitate transcriptomic research in key plant species, including Arabidopsis, rice, and maize.

Soil salinization is a major abiotic stress factor that reduces soybean production. Studies have shown that application of Chlorella promotes plant growth; however, its potential to mitigate salt stress, and the active components involved and the underlying mechanisms, remains unclear. In this study, the application of Chlorella vulgaris significantly mitigated salt stress in soybean seedlings. To identify the active components, we fractionated C. vulgaris and found that the extracellular secretions were primarily responsible for the mitigation. Furthermore, we isolated and characterized exosomes from these secretions. Phenotypic and physiological assessments confirmed that C. vulgaris exosomes alleviated salt stress in soybean seedlings to an extent similar to the intact organism. We identified the key metabolites (linolenic acid and inosine) as the active components within these exosomes. Notably, when applied in combination, they showed a strong synergistic effect, collectively promoting seedling growth, restoring ion homeostasis, and improving redox homeostasis under salt stress. To investigate the molecular mechanisms of salt stress alleviation, the transcriptomes of soybean seedlings subjected to different treatments were analyzed. Salt stress induced widespread changes in gene expression; however, application of linoleic acid (LA), inosine, and especially their combination, led to substantial transcriptomic reprogramming. Enrichment analysis indicated that these modifications were coordinated across energy metabolism, redox homeostasis, carbohydrate metabolism, and ion transport. Importantly, the LA + inosine combination induced a synergistic rather than simply additive transcriptional response, which explains its superior effect on salt tolerance at the molecular level. In this study, we successfully isolated and identified, for the first time, exosomes as the functional components through which C. vulgaris alleviates salt stress in soybean seedlings. Further analysis identified LA and inosine within the exosomes as the key active metabolites. These findings provide a novel theoretical basis for improving crop salt tolerance and are important for developing novel algal nanovesicle-based biostimulants.

Enhancing crop resilience to guarantee stable, high yields under adverse conditions has long been a central goal of rice breeding, but it remains challenging because of inherent trade-offs. Here, we show that the transcriptional activity of the aldehyde-dehydrogenase OsALDH2B1 simultaneously increases grain length and alkaline tolerance. Upon alkali stress, the plasma-membrane leucine-rich-repeat receptor-like kinase SERL1 phosphorylates OsALDH2B1 at Thr-481, thereby blocking its 26S-proteasome-mediated degradation. Stabilized OsALDH2B1 directly represses GS3, a negative regulator of both grain size and alkaline tolerance, and activates all three catalase genes, leading to reduced hydrogen-peroxide (H₂O₂) accumulation. OsALDH2B1 over-expression enlarged grains and raised grain yield under field alkalinity, whereas osaldh2b1 mutants were hypersensitive. CRISPR knockouts of SERL1 or the catalase genes phenocopied these defects, confirming that the SERL1–OsALDH2B1 module constitutes an integrated signaling axis that links membrane perception to nuclear reprogramming through GS3 repression and catalase activation. This dual-purpose circuit provides an immediate, breeder-friendly target for high-yield, alkaline-resilient rice.

Plant cells can undergo cellular reprogramming, enabling pluripotent callus formation from excised leaves. Despite this pluripotency, organs regenerated from leaf callus have predominantly been confined to conventional shoots and roots, leaving the potential to regenerate other specialized organs unknown. In this study, we identified that stolons can be regenerated from potato leaf callus. Furthermore, we demonstrate that Agrobacterium tumefaciens stimulation efficiently induces stolon regeneration and subsequent tuber development from potato leaf callus. The induction of stolon regeneration is abolished when biological activity is removed from the bacterial cultures, indicating that viable bacterial cells are required for this process. Comparative assays using various strains reveal that the C58 chromosomal background is essential for this enhancement. Integrating transcriptome analysis with transgenic functional validation, we find that phosphatidylethanolamine-binding protein (PEBP) family genes are closely involved in this response. Furthermore, we observe that viruses do not readily spread to regenerated stolons through the callus, which lacks a continuous vascular system to serve as a pathway for virus movement. Our findings demonstrate that bacterial stimulation triggers stolon regeneration from pluripotent leaf callus, offering a potential approach for the production of virus-free storage organs in potato.

Many dicotyledonous plants exhibit considerable developmental plasticity and are capable of regenerating new organs upon wounding. Leveraging this wound‐induced cellular pluripotency, a simple, efficient, and genotype‐independent “cut‐dip‐ budding” transformation system has been developed in recent years. Although genetic transformation in dicotyledonous crops like tomato is still largely based on tissue culture methods, and research into their molecular regulatory mechanisms and regeneration factors is extensive, the mechanisms underlying cut‐induced shoot regeneration (cut‐budding) remain poorly understood. This study investigated the molecular basis of cut‐budding in tomato, focusing on the role of GROWTH‐REGULATING FACTOR1 (GRF1) and its association with gibberellin (GA) signaling. By combining single‐cell RNA sequencing, time‐course transcriptome analysis, and genetic validation, we elucidated the key stages of shoot regeneration and identified SlGRF1 as a critical regulator. SlGRF1 was revealed to be essential for shoot initiation, with its expression significantly upregulated during cut‐budding. Functional characterization using CRISPR/Cas9 knockout mutants (grf1‐cr) demonstrated that SlGRF1 is required for pluripotency acquisition and shoot formation. Additionally, GA signaling negatively regulated shoot initiation by repressing SlGRF1 expression. An exogenous GA treatment inhibited shoot regeneration, while a paclobutrazol (GA biosynthesis inhibitor) treatment had the opposite effect. Moreover, grf1‐cr mutants were similar to GA1‐treated samples in terms of transcriptional changes and phenotypes, further indicating that GA signaling represses SlGRF1 expression. A ChIP‐seq analysis showed that SlGRF1 controls cut‐budding by activating the expression of shoot apical meristem regulator‐encoding genes, including NAM1, EPF4, and ER2. NAM1 overexpression rescued the defective regeneration of grf1‐cr1 mutants, highlighting the role of NAM1 as a downstream effector of SlGRF1. The study findings further clarify the molecular mechanisms governing cut‐budding in tomato.

The subgenus Soja, including annual wild (Glycine soja) and cultivated soybean (Glycine max), is the primary germplasm source of soybeans. We analyzed the genome constitution of 750 wild and cultivated accessions from the Chinese Soybean Germplasm Population (CSGP), covering ~20.42% genic and ~79.58% intergenic regions. Most previous genomic studies focused on gene compositions and functions, with intergenic regions being non‐emphasized yet. Our results showed: (i) We defined 48,465 gene blocks (2–23 alleles/gene block) in the genic region. For intergenic region partitioning, the linkage‐disequilibrium (LD) confidence interval (CI) method performed the best, identifying 137,104 SNP LD blocks (SNPLDBs, 2–24 haplotypes/SNPLDB). (ii) Wild and cultivated accessions shared 98.5%/80.9% genes/alleles and 88.0%/80.8% SNPLDBs/haplotypes, indicating high wild genomic contribution to the cultivated genome; genic and intergenic regions exhibit distinct allele/haplotype dynamics during domestication. (iii) We proposed the three‐case restricted two‐stage multi‐locus multi‐allele genome‐wide association study (three‐case RTM‐GWAS), identifying 82 day‐to‐flowering (DTF) main‐effect genes and 47 intergenic‐SNPLDB‐impacted genes (by 34 SNPLDBs) (total 129 genes, 746 alleles). These explained 98.87% of phenotypic variance (PV), with main‐effect and SNPLDB‐impacted genes accounting for 68.61% and 30.26% PV, respectively; gene‐allele(s) impacted by SNPLDB‐haplotype (one/both sides) were also identified. (iv) Domestication process excluded more large‐effect positive alleles that shorten DTF in cultivated accessions, enhancing DTF's transgressive recombination potential in earliness. This study provides insights into genic/intergenic genome regions, offering a novel understanding of soybean functional genomics.

Wheat (Triticum aestivum L.) yield and quality are critically influenced by starch and seed storage protein (SSP) content. In this study, we demonstrate that the transcriptional adapter ADA2 physically interacts with histone acetyltransferase GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) and regulates starch synthesis and SSP content in wheat grains. In ada2 mutants, reduced H3K9ac enrichment was observed in the promoter regions of key starch synthesis genes and the SSP regulator NAC019 during endosperm development. This reduction leads to lower expression levels, resulting in decreased starch content, smaller grains, reduced yield, and poor gluten quality. We also found that ADA2 contains an intrinsically disordered region 2 (IDR2) that undergoes liquid–liquid phase separation (LLPS) and forms nuclear condensates. In vitro assays, the LLPS of ADA2 is affected by GCN5 through direct interaction with IDR2, and the ratio of their concentrations determines the behavior of phase‐separated condensates and HAT activity. High levels of GCN5 can dissolve ADA2 aggregates, while excessive ADA2 recruits and sequesters GCN5 into co‐aggregated droplets, with lower HAT activity. This potential dynamic regulatory mechanism may facilitate the efficient promotion of transcription by the ADA2–GCN5 complex in wheat. Finally, we identified an elite haplotype of ADA2‐B Hap2, which is significantly associated with grain size and weight, highlighting its potential as a candidate gene for genetic improvement of wheat yield.

Rhododendron, a globally important group of alpine flowering plants, provides an exceptional system for investigating ecological adaptation and stress resistance owing to its high-altitude specialization. Using 18 Rhododendron species, a graph-based pangenome was constructed that captures 72,089 nonredundant structural variants. The findings support the integration of subgenus Azaleastrum into subgenus Tsutsusi, with their comparatively smaller genome sizes likely resulting from the contraction of multiple gene families during lineage differentiation. Gene families specific to high-altitude Rhododendron species were significantly enriched in pathways associated with stress resistance. High-altitude-specific long terminal repeat retrotransposons operate through similar regulatory mechanisms, predominantly influencing stress-responsive genes and promoting adaptive evolution. Through an integrated analysis of population genetics (389 re-sequenced samples with a mean coverage of 50.2×), transcriptomics, and real-time quantitative polymerase chain reaction, conserved genes and gene families linked to alpine adaptation in Rhododendron were identified. These include genes implicated in cold-stress responses and ultraviolet (UV) tolerance, such as CML18, CPK1, DREB1E, LPAT2, GPC1, and UVR8. Structural variant profiles within several of these genes offer insights into divergent adaptive mechanisms between high- and low-altitude Rhododendron species. The rapid induction of cold-sensing genes and CBF/DREB1-centered cold-stress signaling pathways indicates an evolutionary adaptation of alpine Rhododendron species to low-temperature habitats. Furthermore, transgenic analyses indicate that cold-resistance genes, such as GPC1 derived from high-altitude Rhododendron, markedly improve cold tolerance in Arabidopsis thaliana and tobacco. Collectively, this study advances insights into high-altitude adaptation in ornamental plants and underscores the value of super-pangenome resources for evolutionary and functional genomics research.

Seed storability is crucial for maintaining vigor at the sowing stage and ensuring agricultural sustainability. Although molecular chaperones are well characterized in protein homeostasis, their roles in regulating ABA receptor stability and starch integrity during seed aging remain unclear. Here, we demonstrate that OsCPN10a enhances storability by maintaining ABA homeostasis, suppressing ROS accumulation, and preserving starch granule structure. Genetic and biochemical analyses reveal that OsCPN10a functions upstream of the OsCPN20–OsHSP60‐3B cascade, directly interacts with both partners to promote complex assembly, and negatively regulates ABA signaling. The resulting trimeric complex interacts with OsPYL10, facilitating receptor dissociation and high‐affinity association with the PP2C phosphatase OsABIL1 to attenuate signaling. This study reveals a non‐canonical function of molecular chaperones in directly modulating hormone receptor signaling, establishing a mechanistic link between protein homeostasis and ABA sensitivity in seeds.

Rapid softening of fig (Ficus carica L.) fruit during ripening leads to extremely short shelf life; the regulatory mechanisms underlying this process remain largely unknown. Fig softening during ripening is largely attributed to pectin degradation, and we identified FcPG12 as the crucial polygalacturonase gene involved in the process. We then identified a NAM (ATAF1/2-CUC2) transcription factor, termed FcNOR and sharing 53.09% amino acid identity with Solanum lycopersicum NOR, which binds directly to the promoter of FcPG12 to activate its transcription. The activity of FcNOR increased robustly following FcMAPK4 phosphorylation of Ser-78 and Ser-343, which are essential for FcNOR DNA binding and transcriptional activity, respectively. Ethylene also enhanced FcMAPK4 kinase activity and promoted FcNOR phosphorylation, leading to the latter's elevated activity. APETALA2/Ethylene Response Factor 5 (FcERF5) functioned as a transcriptional activator of FcPG12 expression, which was synergistically enhanced by interaction between FcNOR and FcERF5. Moreover, FcNOR binds to the promoter of FcERF5, increasing the latter's transcription and forming a FcNOR–FcERF5 positive-feedback loop. Collectively, integration of ethylene signaling with MAPK-mediated phosphorylation by the FcMAPK4–FcNOR–FcERF5 regulatory module, leading to transcriptional regulation of FcPG12 expression to drive pectin degradation, reveals new insights into the mechanism of fruit softening.

A novel allelic variant of the heat shock protein 101, designated neo-tetraploid rice fertility gene 1 (NTRF1), has been identified and is implicated in regulating fertility in neo-tetraploid rice (NTR); however, its regulatory mechanism remains unclear. In this study, we identified the ntrf1 mutant and demonstrated that its significantly reduced seed-setting rate was due to pollen developmental defects. Mechanistically, NTRF1 deficiency disrupts reactive oxygen species (ROS) homeostasis in anthers, thereby delaying the progression of programmed cell death (PCD) in tapetal cells. RNA-seq analysis of mutant anthers revealed dysregulated expression of abscisic acid (ABA) signaling components (OsPP2C49, OsbZIP23) and ROS-related genes (OsRBOH1, OsRBOH8), along with a significant downregulation of key tapetal developmental regulators (OsGAmyb, CYP703A3). Integrated multi-omics analysis showed that the reduced pollen viability in the ntrf1 mutant is associated with the pyruvate metabolic pathway. Protein interaction assays confirmed that NTRF1 directly binds SAPK2, a core kinase in ABA signaling transduction. This interaction explained how exogenous ABA application partially restored the reduced seed-setting rate in ntrf1 mutants. Collectively, our findings elucidated an NTRF1-centered regulatory network that coordinates ABA signaling with ROS homeostasis to ensure timely tapetal PCD and subsequent pollen maturation. This study provides valuable molecular targets for advancing the genetic improvement of polyploid rice.