Functional divergence of gene homologs enables species to evolve unique physiological processes, such as nitrogen fixation of nodules in legumes. Nodulation is initiated via rhizobia-induced reactivation of root cortical cells into stem cells, yet the molecular mechanism underlying this process has remained elusive. There are eight florigen homologs in the soybean genome, including GmFT2a and GmFT5a, which are produced in leaves and possibly translocated to roots to promote nodulation. Here, we report the identification of a distinct florigen homolog, GmFT5b, and its partner GmFDL23, both of which are locally upregulated in the root cortex upon rhizobia infection. This GmFT5b-GmFDL23 module directly suppresses GmCLV3-1 expression in the root cortex, thereby alleviating its repression of the stem cell regulator GmWUS1, which further drives cortical cell reprogramming into nodule stem cells. Our findings delineate a florigen-mediated pathway that spatiotemporally controls stem cells in cortex to drive nodule formation.

Calcium-dependent protein kinases (CDPKs) function as key sensors of Ca2+ signals in plants; however, their roles in soybean-rhizobial symbiosis and biological nitrogen fixation remain poorly understood. This study demonstrates that GmCDPK14, a member of the soybean CDPK gene family, is specifically induced following rhizobial infection and is predominantly expressed in primary root tissues and nodules. Functional analyses revealed that GmCDPK14 plays a positive regulatory role in symbiotic nodulation. Loss-of-function mutants showed substantial decreases in nodule number, root dry weight, shoot dry weight, nitrogenase activity, and infection thread formation, whereas overexpression of GmCDPK14 produced the opposite effects. Transcriptomic analysis showed that GmRINRK1, a key symbiotic gene, was significantly downregulated in GmCDPK14-deficient lines. Moreover, overexpression of GmRINRK1 in the Gmcdpk14 mutant background partially rescued the nodulation defects. These results suggest that GmCDPK14 enhances soybean-rhizobium symbiotic nodulation by positively regulating GmRINRK1 expression, offering new insights into the role of CDPKs in controlling legume-rhizobium interactions.

Rhizobial type Ⅲ effectors (T3Es) contribute to the establishment of symbiotic interactions with legume host plants in conjunction with Nod factors. However, the functions of most rhizobial T3Es, as well as the regulatory and molecular mechanisms underlying their symbiotic effects—particularly in soybean—remain poorly documented. Here, we characterize the function of the T3E nodulation outer protein C (NopC) from the broad-host-range rhizobium Sinorhizobium fredii HH103 in promoting symbiosis in soybean. The NopC genotype influences root nodulation across diverse host germplasms; this effect is further modulated by GmRAC1, which encodes a ROP/RAC family GTPase in soybean. GmRAC1 physically interacts with NopC and subsequently induces expression of the essential symbiotic genes GmNIN2a/2b and GmENOD40. Knockdown of GmNIN2a/2b results in failure of NopC to promote symbiosis, and Gmrac1 mutants develop fewer nodules than the wild type. NopC facilitates multiple stages of infection, whereas the requirement for GmRAC1 is pronounced during infection-thread progression and nodule primordium initiation. Natural variation in the GmRAC1 promoter largely determines the symbiotic contribution of NopC during symbiosis establishment. Elite GmRAC1 haplotypes associated with strong expression were artificially selected during soybean breeding. Transgenic overexpression and elite GmRAC1 haplotypes increase plant height, 100-seed weight, and overall yield. GmRAC1 functions as a key regulator of NopC-mediated symbiosis promotion and offers translational potential for enhancing symbiotic nitrogen fixation in soybean molecular breeding.

Organ abscission represents a critical adaptive strategy for plant survival, yet the post-translational mechanisms ensuring its irreversible remain poorly understood. Here, we unveil a signaling module, MITOGEN-ACTIVATED PROTEIN KINASE 3 (RhMPK3)-LATERAL ORGAN BOUNDARIES DOMAIN 41 (RhLOB41)-WRKY DNA-BINDING PROTEIN 9 (RhWRKY9), that gates ethylene-induced petal abscission in rose (Rosa hybrida) by orchestrating reactive oxygen species (ROS) homeostasis. We demonstrate that the transcription factor RhWRKY9 acts as a dual-function regulator, concurrently activating ROS production via activation of RESPIRATORY BURST OXIDASE HOMOLOGUE D (RhRBOHD) and suppressing scavenging via repression of CATALASE 2 (RhCAT2), thereby generating a ROS burst that locks abscission progression. Ethylene primes this process by destabilizing RhLOB41, a transcriptional repressor of RhWRKY9, through RhMPK3-mediated phosphorylation at Ser30. Phosphorylation creates a phosphodegron that targets RhLOB41 for autophagy-dependent degradation. Our findings redefine ROS as decisive executors of abscission and establish bidirectional ROS control as a paradigm for irreversible developmental transitions.

Seasonal growth modulation is a key adaptive trait in perennials that supports overwinter survival. During winter, many perennials adopt a rosette growth habit by suppressing both vegetative extension and flowering, but the mechanism that coordinates these two distinct developmental programs remains unclear. Here, we show that prolonged chilling primarily acts at the shoot apex to confer extension growth and flowering competence in chrysanthemum (Chrysanthemum morifolium). Long-term chilling is accompanied by marked changes in gene expression in the rib zone of the shoot apex. Notably, the expression of CmDREBa is associated with the transition from extension growth to rosette growth. Chilling induces CmDREBa expression, which suppresses both extension growth and flowering; when temperatures rise, CmDREBa expression declines, allowing both processes to resume. CmDREBa directly induces the expression of MADS AFFECTING FLOWERING (MAF) genes, which in turn promote rosette growth. Together, these findings identify CmDREBa as a key regulator of chilling-responsive seasonal growth.

Polyploidization can generate morphological and physiological variation in plants, but the molecular basis underlying leaf trait changes after genome doubling in grapevine remains insufficiently understood. This study aimed to characterize phenotypic, physiological, transcriptomic, and metabolomic differences between diploid and induced autotetraploid plants of ‘Thompson Seedless’ and to identify biological processes potentially associated with the observed leaf trait variation. In this study, autotetraploid plants were induced from axillary buds of ‘Thompson Seedless’ using colchicine treatment, and ploidy levels were confirmed by flow cytometry and chromosome counting. Phenotypic, physiological, transcriptomic, and metabolomic analyses were performed to compare diploid and tetraploid plants. Compared with diploids, tetraploids exhibited enlarged leaves, reduced plant stature, larger but less dense stomata, increased chloroplast number in guard cells, and higher total chlorophyll and carotenoid contents. Fv/Fm remained unchanged, whereas increased Vj and decreased ψEo and φEo suggested differences in electron transport-related characteristics beyond QA. Transcriptomic analysis identified 1564 differentially expressed genes, and metabolomic profiling detected 618 differentially accumulated metabolites. Integrated analyses highlighted coordinated molecular differences associated mainly with cell-wall processes, secondary metabolism, redox-related functions, and carbon-related pathways. These findings identify candidate biological processes for future functional validation and provide a basis for evaluating the potential value of autotetraploid germplasm in grapevine breeding.

Symbiotic nitrogen fixation (SNF) serves as a vital process through which legumes acquire atmospheric nitrogen, directly influencing plant growth, yield, and soil fertility. Nitrogenase activity represents a key determinant of SNF efficiency, yet only a limited number of genes regulating this process have been identified in soybean nodules. In this study, a genome-wide association analysis uncovered a major quantitative trait locus (QTL) on chromosome 5, named NAR5 (Nitrogenase Activity Related Gene 5), which governs variation in nitrogenase activity among natural soybean populations under controlled greenhouse conditions. NAR5 encodes a subtilisin-like serine protease. Functional characterization demonstrated that NAR5 overexpression downregulates the transcription of senescence-associated genes in nodules, thereby sustaining nitrogenase function. Moreover, plants overexpressing NAR5 exhibited enhanced field performance, with increased yield and improved adaptation to low-nitrogen conditions. Population analysis revealed that NAR5 is subject to selection pressure during domestication, and that the elite haplotype NAR5HapI-1 linked to superior nitrogenase activity and greater seed weight has been preferentially incorporated into modern breeding germplasm. In summary, these findings identify NAR5 as a candidate genetic regulator of SNF efficiency in soybean, providing a promising molecular target for breeding high-yield, nitrogen-efficient cultivars.

Perennial plants have evolved complex regulatory networks that allow them to perceive environmental changes and trigger adaptive growth responses. Many perennial herbs exhibit a rosette growth habit during winter, and then undergo extension growth/stem elongation growth and flowering in the following spring. However, the mechanisms underlying this seasonal transition are still not well understood. Here, using the perennial herb chrysanthemum (Chrysanthemum morifolium), we identified CmKN1, a class I KNOTTED (KN1)-like homeobox transcription factor, that mediates extension growth and flowering competence in response to prolonged chilling exposure. The rosette growth of chrysanthemum rhizomes in late autumn coincides with downregulation of CmKN1 expression. Overexpression of CmKN1 promotes premature rhizome extension growth and flowering, whereas the kn1 heterozygous mutant shows suppression of these processes. Furthermore, seasonal growth regulation involves the abscisic acid (ABA) signaling pathway. Shoot apices in the rosette state accumulate higher levels of ABA than those in the extension growth state. Notably, in response to ABA, CmKN1 expression is downregulated by CmABI5. Our results demonstrated that the CmABI5-CmKN1 module mediates extension growth and flowering competence in response to chilling, thereby facilitating the perennial growth habit of chrysanthemum.

The molecular and genetic mechanisms regulating female germline development remain largely unknown in basal and early-divergent angiosperms. This contrasts with recent progress in model eudicots such as Arabidopsis thaliana and monocots, such as rice, barley, and maize. In this study, we investigate the genetic pathway governing female germline development in the early-divergent angiosperm Annona cherimola. Using a region-specific transcriptome study, key orthologs of germline regulators were identified, followed by spatio-temporal expression pattern analysis and a functional assay. Expression patterns were compared to those in Arabidopsis. While some genes like DMC1 show similar expression patterns across species, most genes display notable differences, though they are still transcribed in or around the germline. AcWUS, despite its differential expression compared to Arabidopsis, maintains its essential role in ovule and plant development. Our findings offer insight into the evolutionary conservation of pathways regulating germline development, highlighting both similarities and differences in the expression of key genes. These may stem from the phylogenetic distance and/or different nucellar morphologies between early-divergent magnoliids and derived eudicots.

Cadmium (Cd) is a widespread and highly toxic environmental contaminant that poses serious threats to agricultural productivity and human health. MicroRNAs (miRNAs), as key post-transcriptional regulators, play essential roles in plant growth, development, and adaptation to environmental stress. However, the regulatory functions and mechanisms of miRNAs in soybean Cd tolerance remain insufficiently characterized. In this study, we employed integrated multi-omics approaches to identify miRNA-mRNA regulatory modules associated with differential Cd tolerance between the soybean cultivars DN50 and SN14. Through combined miRNAome, transcriptome, and degradome analyses, we identified the miR9746a-GmCIN1 module as a critical determinant of Cd sensitivity in SN14, where miR9746a mediates the post-transcriptional repression of GmCIN1. Functional validation confirmed that this regulatory interaction contributes to enhanced Cd susceptibility and exogenous application of synthetic miR9746a mitigated Cd toxicity in soybean. Furthermore, miR166i-HB module regulates Cd tolerance in both soybean and rice, demonstrating cross-species functionality of this regulatory molecule. Collectively, our findings establish the miR9746a-GmCIN1 module as a central component of soybean Cd stress responses and provide proof-of-concept evidence that external miRNA delivery can modulate heavy metal tolerance. This work offers new insights into miRNA-mediated regulation under Cd stress and proposes a promising strategy for genetic improvement and innovative crop management approaches aimed at reducing Cd accumulation.

Soybean (Glycine max) is a key crop in China grown as a source of edible oil and plant-derived protein, and its production is closely linked to national food security. Insufficient nitrogen availability remains a key constraint on soybean yield. In legumes, symbiotic nitrogen fixation (SNF) enables the conversion of atmospheric nitrogen into bioavailable forms, thereby reducing reliance on synthetic fertilizers and improving soil quality. Nitrogenase activity is a central determinant of SNF efficiency; however, its regulatory mechanisms in soybean nodules are not yet fully understood. In this study, transcriptomic data from two soybean accessions with contrasting SNF performance (Suinong 14 and ZYD00006) were analyzed, leading to the identification of Glyma.04G013500 as a member of the GmRD22 gene family. This study verified that this gene is potentially associated with nitrogenase activity. Functional characterization revealed that this gene acts as a negative regulator of nodulation by influencing the expression of genes associated with nodule development. Haplotype analysis further uncovered a pattern consistent with domestication, as the elite haplotype (HapI) with enhanced nitrogen fixation capacity, exhibited a progressive increase in frequency from wild soybean populations to landraces and modern cultivars. These findings suggest that GmRD22 has undergone directional selection during soybean domestication and improvement. Overall, these results offer new insights into the genetic control of SNF and establish promising targets for breeding soybean varieties with improved nitrogen fixation efficiency.

High temperatures driven by climate change are increasingly limiting crop growth and quality. Fruit ripening is a genetically programmed process regulated by transcription factors (TFs), while the phytohormone ethylene plays key roles in both ripening and abiotic stress responses. However, the underlying regulatory mechanisms remain poorly understood. We identified Solanum lycopersicum jasmonic acid 2-like (SlJA2L), a tomato NAC TF that is transcriptionally responsive to both heat stress (HS) and fruit ripening, suggesting that it acts as a molecular integrator of HS adaptation and fruit developmental processes. Overexpression of SlJA2L enhanced heat tolerance and promoted fruit ripening, whereas clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9)-mediated knockout led to heat sensitivity and ripening delay. Mechanistically, SlJA2L directly activates SlHsfA3 and SlCAT3 under HS. During ripening, it promotes ethylene biosynthesis via the SlJA2L-SlACO1 module and enhances carotenoid accumulation by activating SlCRTISO. Moreover, ethylene was shown to contribute to thermotolerance, as exogenous 1-aminocyclopropane-1-carboxylic acid improved heat tolerance, while silencing SlACO1 reduced it. Our findings demonstrate that SlJA2L integrates ethylene signaling to regulate both thermotolerance and fruit ripening in tomato. This study provides new insights into the molecular coordination of stress responses and developmental transitions, offering a potential strategy for improving crop resilience and fruit ripening under climate stress.

Auxin plays a critical role in the inhibition of organ abscission. The changing of auxin gradient across the abscission zone (AZ) is the primary determinant of the abscission initiation and activation. To better understand the role of auxin, the distribution and content of auxin at different developmental stages of AZ need to be determined. This protocol provides a convenient and efficient procedure for precise localization of auxin in the petal AZ of rose (Rosa hybrida). It can be combined with plant hormone metabolomics to more accurately reflect changes in auxin during the abscission process. This method serves as a powerful tool for auxin detection and can be applied to broader plant hormone research.

Members of genus Chrysanthemum,comprising approximately 40 species,hold economic significance as edible,medicinal,and ornamental plants.Among these species,Chrysanthemum indicum and the cultivated chrysanthemum C.morifolium have been used for tea and traditional Chinese medicine to treat common cold symptoms,impaired vision,dizziness,and skin irritation.

Brassinosteroids (BRs) are key phytohormones influencing soybean development, yet their role in symbiosis remains unclear. Here, the RNA-Seq was used to identify important gene associated with BRs and symbiotic nitrogen fixation, and the function of candidate gene was verified by transgenic hairy roots. The result shows that the RNA-Seq analysis was conducted in which BR signaling was found to suppress nodule formation and many DEGs enriched in immunity-related pathways. WGCNA analyses led to the identification of GmWRKY33a as being responsive to BR signaling in the context of symbiosis establishment. Transgenic hairy roots analyses indicated that GmWRKY33a served as a negative regulator of the establishment of symbiosis. The qRT-PCR analysis confirmed that BR signaling upregulates GmWRKY33a, leading to nodulation suppression and activation of soybean immune responses. In summary, our research revealed that BR suppresses root nodule formation by modulating the immune signaling pathway in soybean roots. We further identified that GmWRKY33a, a crucial transcription factor in BR signaling, plays a negative role in the symbiotic establishment.

Flavones, a key group of flavonoids, play a significant role in plant adaptation to ecological niches and are valuable medicinal resources. However, the genetic basis underlying their contribution to ecological adaptation remains largely unknown. Here, using metabolite-based genome-wide association study, we report that the natural variation of flavone contents in Chrysanthemum indicum, a wild chrysanthemum and medicinal herb, is mainly determined by a recently duplicated flavone synthase II gene CiFNSII-1.2. Enzymatic assays and molecular dynamics simulations reveal that the key amino acid residues 246th and 261th confer the higher enzymatic activity of CiFNSII-1.2 compared with its ancestral form. These residues act as critical modulators, regulating the flexibility of the external entrance and contributing to the enzyme's improved functionality. Transgenic evaluation demonstrate that CiFNSII-1.2 contributes to flavone accumulation and drought adaptation. Our findings provide insights into the biochemical and evolutionary role of flavones in facilitating adaptation to drought-prone habitats in chrysanthemum.

A novel powdery mildew resistance gene Pm7C from Aegilops caudata was introgressed into common wheat through ph1b-induced homoeologous recombination and mapped to the 7CL bin FL 0.90–0.96 on chromosome 7C. Wheat powdery mildew poses a significant threat to wheat grain yield and quality. Developing resistant wheat varieties through the deployment of resistance genes is the most effective, economically feasible, and environmentally sustainable strategy to combat this disease. Aegilops caudata (2n = 2x = 14, CC), a wild relative of common wheat, has been identified as a valuable genetic resource harboring novel resistance loci. Specifically, chromosome 7C of Ae. caudata carries a novel broad-spectrum resistance gene, tentatively designated as Pm7C. However, the structural variations in chromosome 7C, coupled with the unavailability of a reference genome for Ae. caudata, have hindered the introgression of this resistance gene into common wheat and its mapping. In this study, we report the development of wheat-Ae. caudata 7C recombinants via ph1b-induced homoeologous recombination and the cytological mapping of the resistance gene Pm7C. By integrating the analysis of 69 7C-specific markers with breakpoint mapping of 7C recombinants using in situ hybridization, we characterized 35 wheat-Ae. caudata 7C recombinants, categorizing them into 10 distinct types. This enabled the construction of a physical map of 7C, comprising nine chromosomal bins defined by 69 specific markers. Subsequent evaluation of powdery mildew resistance in these recombinants mapped Pm7C to the long arm of 7C within the interval of FL 0.90–0.96. Additionally, terminal recombinant 7CT1 (T7DL.7DS-7CL) and intercalary recombinant 7CT4 (Ti7DL.7DS-7CL-7DS) were identified as containing small 7CL segments that harbor Pm7C. These resources are expected to facilitate wheat disease-resistant breeding and further efforts in cloning and elucidating the resistance mechanism of Pm7C.

Temporal decline in microRNA miR156 expression is crucial for the transition to, and maintenance of, the adult phase and flowering competence in flowering plants. However, the molecular mechanisms underlying the temporal regulation of miR156 reduction remain largely unknown. Here, we investigated the epigenetic mechanism regulating the temporal silencing of cin-MIR156 in wild chrysanthemum (Chrysanthemum indicum), focusing on the role of the lysine-specific demethylase CiLDL1 and the nuclear factor Y complex. CiLDL1 and CiNF-YB8 interact with the classical histone-like fold domain (HFD) of CiNF-YC1 and CiNF-YA3, which form distinct heterotrimers binding to the 'CCAAT' box in the promoter region of cin-MIR156ab. CiLDL1 and CiNF-YB8 have opposing effects on cin-MIR156ab expression, with influencing histone 3 lysine 4 demethylation (H3K4me2) levels at the cin-MIR156ab locus. During aging, decreased CiNF-YB8 expression leads to a quantitative switch from the CiNF-YA3-CiNF-YC1-CiNF-YB8 heterotrimer to the CiNF-YA3-CiNF-YC1-CiLDL1 heterotrimer, which reduces H3K4me2 levels at the cin-MIR156ab locus, thus temporal silencing its expression. Our results thus reveal that the dynamic regulatory shift between CiLDL1 and CiNF-YB8 ensures proper aging-dependent flowering in chrysanthemum.

Flavonols represent a large subgroup of flavonoids and function as the principal bioactive compounds in tea and medicinal chrysanthemum (Chrysanthemum morifolium) flowers. Low temperature is one of the most significant environmental factors influencing flavonol accumulation. Nevertheless, the regulatory mechanisms governing flavonol biosynthesis in response to low temperature remain predominantly uncharacterized. In this study, we observed decreased flavonol accumulation in chrysanthemum flowers under low-temperature conditions, correlating with reduced expression of the NAC transcription factor VND-INTERACTING2 (VNI2). The suppression of CmVNI2 resulted in diminished flavonol content. DNA affinity purification sequencing and RNA sequencing analyses demonstrated that CmVNI2 directly regulates the expression of CmF3H and CmMYB3, two genes essential for flavonol biosynthesis. In addition, transient overexpression of CmMYB3 in CmVNI2 RNA interference plants restored flavonol accumulation. The study establishes that the CmVNI2–CmMYB3 module plays a crucial role in regulating flavonol biosynthesis in chrysanthemum flowers under low-temperature stress and identifies potential target genes for enhancing the bioactive properties of chrysanthemum as a tea or medicinal herb.

Von Willebrand factor A (vWA) genes play important roles in regulating plant growth and development, as well as biotic stresses. However, limited data are available on the contributions of vWA genes to wheat (Triticum aestivum L.). In this study, 114 TavWA genes were identified in the wheat genome, which were unevenly distributed on 21 chromosomes. According to the phylogenetic analysis, the 114 TavWAs were classified into six groups, two of which (G3 and G6) were unique to wheat. Fifty-five homoeologous gene sets among A, B, and D sub-genomes were detected, which play a crucial role in the expansion of the wheat vWA gene family. Analysis of specific spatiotemporal expression patterns showed that more than 50% of TavWAs (61 out of 114) exhibited tissue-specific expression. These included 71 TavWAs that responded to one or more of the four biotic stress treatments (flg22, chitin, powdery mildew, and stripe rust). Notably, these included TavWA1-7D, a recently reported key growth regulator in wheat, suggesting its additional role in biotic stress responses. RT-qPCR analysis indicated that eight genes (TavWA1-7D, TavWA24-2B, TavWA36-1D, TavWA37-7D, TavWA40, TavWA47, TavWA51, and TavWA53) may play important roles in wheat’s powdery mildew resistance. Collectively, the results of this study provide significant insights for future research on the involvement of vWA genes in the development and stress responses of wheat.