Search Results (723)

The floral morphology of Rosa chinensis significantly influences its ornamental value. However, the molecular mechanisms underlying specific floral types remain poorly understood. Viridiflora, a stable genetic variant of R. chinensis, exhibits homeotic transformation of floral organs into sepal-like structures, providing a valuable model for studying floral organ identity and development. In this study, Viridiflora was compared with Old Blush to elucidate floral development through morphological observation, transcriptomic profiling, and functional genetics. Four distinct developmental stages were defined, encompassing the formation of sepal, petal, stamen, and pistil primordia. Transcriptome analysis identified candidate genes associated with the Viridiflora phenotype, among which RcAGAMOUS2 (RcAG2) and RcFRUITFULL (RcFUL) were selected for in-depth functional characterization. The proteins encoded by these two genes are hydrophilic, lack signal peptides and transmembrane domains, and contain multiple phosphorylation sites. They feature typical MADS-box family domains and show close phylogenetic affinity to Rosa rugosa. Subcellular localization showed their nuclear presence. Heterologous overexpression of RcAG2 and RcFUL in Arabidopsis resulted in notable phenotypic alterations: RcAG2 caused petal reduction and stamen exposure, while RcFUL led to greenish, leaf-like petals with pigmentation gradients, increased sepal number, and failed seed set. Conclusion: These results suggest that RcAG2 and RcFUL play key roles in floral organ development through genetic regulation, providing a theoretical foundation for further research on floral development in R. chinensis. Full article

Background/Objectives: Detection of carbapenemases (KPC, OXA-48, VIM, IMP, NDM) from blood cultures (BCs) by standard methods takes 48–72 h and includes BC seeding, susceptibility testing and carbapenemase detection. Automated qPCR panels provide results in 1 h but are very costly. We aim to evaluate a low-cost and rapid immunochromatographic (IC) test directly from positive BCs using the reference method as a comparator. Methods: Ninety-one positive BCs from real-world patients and sixty-four simulated BCs were included. BC broth was treated with SDS and washed before analysis with the K.N.I.V.O. carbapenemase detection IC test. Discordant results were confirmed through the NG Carba-5 IC test and GeneXpert Carba-R qPCR test. Results: The test detected 100% of the 87 carbapenemase-producing BCs tested (sensitivity: 100% [CI95%: 95.8–100%]). However, 13 BCs generated false positive bands for NDM and/or OXA-48 (specificity: 80.8% [CI95%: 69.5–89.4%). The positive and negative predictive values were 87.0% (CI95%: 80.4–91.6%) and 100% (CI95%: 93.5–100%). Analysis of BCs providing false positive results through both confirmatory tests showed that BCs were negative for these carbapenemases. Conclusions: This is the first evaluation of the K.N.I.V.O. IC test directly from positive BCs, with a pragmatic confirmation algorithm using a second IC test or qPCR in case of NDM or OXA-48, that addresses K.N.I.V.O.’s specificity gap. The main limitation of this work is that confirmatory testing was performed only in false positives. The implementation of the K.N.I.V.O. IC test would contribute to early carbapenemase detection in BCs and is an alternative for low-resource hospitals where qPCR panels are not available. Full article

Seed germination of celery (Apium graveolens L.) is notoriously slow and asynchronous, which severely constrains uniform seedling establishment and crop yield. Seed priming is an effective technique to improve germination, and acidic electrolyzed water, characterized by low pH and high oxidation–reduction potential, has emerged as a novel priming agent. However, the effect of acid electrolyzed water priming (EWP) on celery seed germination and the underlying mechanisms still need to be explored. The present study aimed to investigate the physiological and molecular mechanisms by which EWP promotes celery seed germination, with a focus on the roles of the phenylpropane metabolism and the antioxidant enzyme system. Celery seeds were treated with EWP, hydro-priming (HYD), and untreated (CK). It was found that the EWP treatment significantly enhanced germination characteristics compared to both CK and HYD. Transcriptome analysis revealed that EWP triggered more extensive transcriptional reprogramming than HYD, and EWP specifically enriched “Phenylpropanoid biosynthesis” and “Flavonoid biosynthesis” pathways, downregulating upstream genes (PAL, 4CL) while upregulating downstream genes (CCR, CHI, F3H) in the phenylpropane pathway. Physiologically, EWP significantly increased CHI activity and the contents of total phenols and flavonoids at all sampling time points, and enhanced the activities of SOD, POD, CAT, and APX. Consequently, the DPPH and FRAP free radical scavenging capacities were significantly strengthened in EWP-treated seeds. In conclusion, it is believed that EWP activation promotes celery seed germination by coordinating the phenylpropane pathway and antioxidant enzyme system, ensuring effective radical scavenging activities and cell protection. These findings provide a theoretical basis for the application of EWP and highlight the potential as a novel priming technology for celery and other horticultural crops. Full article

Protein phosphatase 2Cs (PP2Cs) constitute a widespread family of signaling regulators in plants and play central roles in abscisic acid (ABA)-mediated stress signaling; however, the PP2C gene family has not yet been systematically identified and characterized in pea (Pisum sativum), a salt-sensitive legume crop. In this study, we identified 89 PsPP2C genes based on domain features and sequence homology. These genes are unevenly distributed across seven chromosomes and classified into ten subfamilies, providing a comparative framework for evaluating structural and regulatory diversification within the PsPP2C family. The encoded proteins vary substantially in length, physicochemical properties, and predicted subcellular localization, while most members contain the conserved PP2Cc catalytic domain. Intra- and interspecies homology analyses identified 19 duplicated gene pairs in pea and numerous orthologous relationships with several model plants; all reliable gene pairs exhibited Ka/Ks < 1, indicating pervasive purifying selection. PsPP2C genes also showed broad variation in exon number and intron phase, and their promoter regions contained diverse light-, hormone-, and stress-related cis-elements with heterogeneous positional patterns. Expression profiling across 11 tissues revealed pronounced tissue-specific differences, with generally higher transcript abundance in roots and seeds than in other tissues. Under salt treatment, approximately 20% of PsPP2C genes displayed concentration- or time-dependent transcriptional changes. Among them, PsPP2C67 and PsPP2C82—both belonging to the clade A PP2C subfamily—exhibited the most pronounced induction under high salinity and at early stress stages. Functional annotation indicated that these two genes are involved in ABA-related processes, including regulation of abscisic acid-activated signaling pathway, plant hormone signal transduction, and MAPK signaling pathway-plant. Collectively, this study provides a systematic characterization of the PsPP2C gene family, including its structural features, evolutionary patterns, and transcriptional responses to salt stress, thereby establishing a foundation for future functional investigations. Full article

Contemporary seed gene bank management emphasizes the importance of understanding seed storage behaviour to maximize the preservation of genetic material. In this context, the patterns of naturally occurring ageing-related changes in physiological and biochemical markers were evaluated by comparing the performance of freshly regenerated seed samples (control) to samples kept under cold storage (CS) for 37 years (original, CS1 samples) and five years (CS2 samples). A significant decline in seed viability and physiological quality—initial seedling development—was directly associated with the duration of cold storage, leading to a marked reduction in seedling vigour index (SVI) performance. Key biochemical markers influencing early seedling growth and vigour included total protein, the glutelins protein fraction, fructose, sucrose, both insoluble-bound and soluble-free phenolics—including phenolic acids, and β-carotene. The CS2 samples, which experienced severe water deficit during the post-zygotic phase, exhibited increased sucrose, insoluble-bound p-coumaric acid (p-CouA), insoluble-bound ferulic acid (FA), and α-tocopherol contents. Conversely, glutelins and glucose contents decreased, while genotype-specific variations were observed in albumins, globulins, fructose, maltose, insoluble-bound caffeic acid, and soluble-free p-CouA, as well as in β+γ- and δ-tocopherol contents. Given the consistent pattern of natural ageing-related changes, β-carotene, lutein+zeaxanthin, insoluble-bound FA, and particularly soluble-free FA emerge as relevant biomarkers for improved monitoring of ageing processes under ex situ conservation. Full article

Scots pine (Pinus sylvestris L.) is a key species in boreal forests, valued both economically and ecologically, in part due to its associations with foliar fungi. These fungi influence plant health, nutrient cycling, and resistance induction. To investigate these interactions, we collected 1367 needle and shoot samples across 12 plus tree genotypes grown in 4 progeny trials in Estonia. Amplifying the ITS1-5.8S-ITS2 gene region, we obtained over 1.3 million high-quality sequences and identified 1261 fungal OTUs at the 98% species hypothesis level. Among the identified OTUs, 24.6% were classified as saprotrophic and 18.2% as pathogenic fungi. Fungal diversity varied significantly between tree tissue types, progeny trial locations, and plus tree origins. Fungal community composition varied across tissue types, with older needles tending to harbor more complex communities. Plus trees 593 and 267-1 progenies stood out for their high phyllosphere fungal richness, and genotype-specific correlations indicated associations between fungal diversity and tree height or needle retention, suggesting potential genotype-dependent effects on tree performance. Heritability of fungal diversity between ramets in seed orchard and progeny trees was found for saprotrophic fungi but was negligible for total fungi and pathogens, indicating strong influence of microclimate conditions. These findings underscore the potential value of integrating fungal community traits into Scots pine breeding programs. Considering microbial associations alongside traditional growth traits may help identify genotypes better suited for future forestry needs under changing environmental conditions. Additionally, Setomelanomma holmii is reported here as a new fungal pathogen on Scots pine shoots in Estonia. Full article

C2H2-type zinc-finger transcription factors (ZFPs) play essential roles in plant stress signaling and development; however, their putative functions in safflower have not been systematically characterized. Leveraging the reference genome of the safflower cultivar ‘Jihong-1’ (Carthamus tinctorius L.), we investigated the C2H2 family and identified 62 CtC2H2 genes. Comparative phylogeny with Arabidopsis revealed six subfamilies characterized by shared features such as exon–intron organization and conserved QALGGH motif. Promoter analysis identified multiple light- and hormone-responsive cis-elements (e.g., G-box, Box 4, GT1-motif, ABRE, CGTCA/TGACG), suggesting potential multi-layered regulation. RNA-seq and qRT-PCR analysis identified tissue-specific candidate genes, with CtC2H2-22 emerging as the most petal-specific (6-fold upregulation), alongside CtC2H2-02, CtC2H2-23, and CtC2H2-24 in seeds (~3-fold), and CtC2H2-21 in roots (3-fold). Under abiotic stresses, CtC2H2 genes also demonstrated rapid and dynamic responses. Under cold stress, CtC2H2 genes showed a rapid temporal pattern of expression, with early increase for genes like CtC2H2-45 (>4-fold at 3–6 h) and a delayed increase for CtC2H2-23 at 9 h. A majority of CtC2H2 genes (8/12) were upregulated by ABA treatment, with CtC2H2-47 suggesting 3.5-fold induction. ABA treatment also led to a significant increase (2.5-fold) in total leaf flavonoid content at 24h, which is associated with the significant upregulation of flavonoid pathway genes CtANS (5-fold) and CtCHS (3.3-fold). Simultaneously, UV-B radiation induced two distinct expression patterns: a significant suppression of four genes (CtC2H2-23 decreased to 30% of control) and a complex fluctuating pattern, with CtC2H2-02 upregulated at 48 h (2.8-fold). MeJA elicitation revealed four complex expression profiles, from transient induction (CtC2H2-02, 2.5-fold at 3 h) to multi-phasic oscillations, demonstrating the functional diversity of CtC2H2-ZFPs in jasmonate signaling. Together, these results suggest stress and hormone-responsive expression modules of C2H2 ZFPs for future functional studies aimed at improving stress adaptation and modulating specialized metabolism in safflower. Full article

Transcription factors (TFs) orchestrate plant growth and development, yet the functional landscape of many TF gene families remains incomplete. Here, we systematically characterize OsWRKY7, an unannotated WRKY TF in rice. Phylogenomic analyses revealed that the WRKY7 subfamily originated in basal angiosperms and evolved under strong purifying selection. We demonstrate OsWRKY7 functions as a WRKY transcriptional activator, with its activity uniquely encoded within the N-terminal domain—a distinctive mechanism among WRKY proteins. The promoter is enriched with cis-elements responsive to hormone and stress signaling, and the gene shows predominant expression in seeds. Strikingly, haplotype analysis revealed exceptionally low genetic diversity at the OsWRKY7 locus, suggesting evolutionary constraint or a recent selective sweep. Our findings establish OsWRKY7 as a conserved regulator with unique molecular features, specifically the WRKY domain, providing a strategic target for both fundamental research and crop improvement. Full article

Seed physical dormancy, also known as hard-seededness, is a characteristic commonly found in higher plants, which functions to prevent water and oxygen from passing through the impermeable seed coat. Background: Notably, seed dormancy has emerged as a critical factor in the domestication of leguminous plants. Alfalfa (Medicago sativa L.) is a globally cultivated high-quality legume forage crop, while the seeds from different varieties maintain varying degrees of hard-seededness. However, the molecular mechanisms underlying physical dormancy in alfalfa seeds remain poorly understood. In particular, the regulatory mechanisms at the transcriptomic level remain unclear, which has hindered the breeding process of varieties with low hard-seededness. Methods: In this study, we performed global transcriptome analysis to discover the genes specifically expressed in the alfalfa seed coat and provide insights into alfalfa seeds’ physical dormancy domestication traits. RNA sequencing was performed on various alfalfa tissues, including roots, stems, leaves, flowers, and seed coats. Results: This analysis led to the identification of 4740 seed coat-specific expressed genes, including key genes such as KNOX4 (a class II KNOTTED-like homeobox gene), qHs1 (encoding endo-1,4-β-glucanase), GmHs1-1 (encoding a calcineurin-like metallophosphoesterase), and KCS12 (β-ketoacyl-CoA synthase). In addition, several seed coat-specific transcription factor families were identified, including ERF, B3, and NAC, among others. Furthermore, a comparison of gene expression profiles between seeds with and without physical dormancy revealed 60 upregulated and 197 downregulated genes associated with physical dormancy. Crucially, functional enrichment analysis demonstrated that these genes are predominantly associated with lipid metabolism pathways, particularly those involved in the formation of “monolayer-surrounding lipid storage bodies.” Conclusions: This key finding suggests that the establishment of physical dormancy is closely linked to the biosynthesis and deposition of specialized lipid-based layers in the seed coat, which likely constitute the primary barrier to water penetration. Our study thus provides fundamental insights and a valuable genetic resource for future functional studies aimed at deciphering and manipulating physical dormancy in alfalfa. Full article

This review presents soybean responses to drought, heat, and salinity within a signal–transcript–chromatin framework. In this framework, calcium/reactive oxygen species and abscisic acid cues converge on abscisic acid-responsive element binding factor (ABF/AREB), dehydration-responsive element binding protein (DREB), NAC, and heat shock factor (HSF) families. These processes are modulated by locus-specific chromatin and non-coding RNA layers. Base-resolved methylomes reveal a high level of CG methylation in the gene body, strong CHG methylation in heterochromatin, and dynamic CHH ‘islands’ at the borders of transposable elements. CHH methylation increases over that of transposable elements during seed development, and GmDMEa editing is associated with seed size. Chromatin studies in soybean and model species implicate the reconfiguration of salt-responsive histone H3 lysine 27 trimethylation (H3K27me3) in G. max and heat-linked H2A.Z dynamics at thermoresponsive promoters characterized in Arabidopsis and other plants, suggesting that a conserved chromatin layer likely operates in soybean. miR169–NF-YA, miR398–Cu/Zn Superoxide Dismutases(CSD)/copper chaperone of CSD(CCS), miR393–transporter inhibitor response1/auxin signaling F-box (TIR1/AFB), and miR396–growth regulating factors (GRF) operate across leaves, roots, and nodules. Overexpression of lncRNA77580 enhances drought tolerance, but with context-dependent trade-offs under salinity. Single-nucleus and spatial atlases anchor these circuits in cell types and microenvironments relevant to stress and symbiosis. We present translational routes, sentinel epimarkers (bisulfite amplicons, CUT&Tag), haplotype-by-epigenotype prediction, and precise cis-regulatory editing to accelerate marker development, genomic prediction and the breeding of resilient soybean varieties with stable yields. Full article

Submergence stress is a major constraint in direct-seeded rice production. This study investigated the effect and biochemical mechanism of sprouting, a traditional agronomic practice, on improving submergence tolerance in rice. Our findings demonstrate that sprouting is an effective seed treatment that significantly enhances the plant’s ability to withstand flooding. Specifically, 48 h sprouting increased shoot height and root length by 163% and 423%, respectively, in the YLYJ48 variety under 6-day submergence. Sprouting upregulated the activity of glutathione reductase (GR) and the expression of its related genes, thereby significantly promoting the biosynthesis of glutathione (GSH). GSH content in seeds increased from 64.86 µg g⁻¹ FW (0 h) to 83.00 µg g⁻¹ FW (48 h) in HZ, and from 82.14 to 92.52 µg g⁻¹ FW in YLYJ48. This process provides critical antioxidant protection for seedlings to implement a rapid “escape strategy,” ultimately enhancing their submergence tolerance. Functional verification showed that seed soaking with exogenous GSH (0.1%) effectively improved submergence tolerance by increasing antioxidant reserves. Exogenous GSH treatment elevated shoot height by approximately 50% in both HZ and YLYJ48 varieties under submergence. Field trials further demonstrated that exogenous GSH application significantly enhanced seedling establishment rates by 30–35% and improved seedling growth traits under submergence tolerance stress across multiple rice varieties. This study reveals part of the mechanism by which sprouting enhances submergence tolerance by influencing glutathione metabolism, offering practical strategies for flood-resilient direct-seeded rice cultivation. Full article

Modern head cabbage (Brassica oleracea var. capitata L.) breeding is based on the application of molecular markers through marker-assisted selection (MAS). In hybrid breeding, critical markers are deployed to assess cytoplasmic male sterility (CAPS and SSR for orf138), genic male sterility (KASP markers for Ms-cd1, InDel for ms3, and BoCYP704B1), fertility restoration (InDel marker for Rfo), combining ability and genetic diversity (using SSR and KASP marker sets), and to ensure F₁ hybrid seed genetic purity (RAPD and SSR markers sets). Disease resistance, a well-developed category due to frequent monogenic control, includes markers for major pathogens, including those for Fusarium wilt (for Foc-Bo1 gene), black rot (race 1–7 specific SSR and InDel markers), clubroot (Kamogawa, Anno, and Yuki isolates), and downy mildew (BoDMR2 InDel marker). Markers have also been identified for key agronomic and morphological traits, such as those governing petal color (InDel markers for BoCCD4), leaf waxiness (BoGL1, BoGL-3, Cgl1, Cgl2, BoWax1, and BoCER2), and leaf color (ygl-1, BoMYB2, BoMYBL2-1). The review also included markers for resistance to abbioticaly induced negative physiological processes, such as head splitting (QTL SPL-2-1, Bol016058), bolting (resistance loci-associated SSR marker), prolonged flowering time (BoFLC1,2 genes), and high- and low-temperature tolerance (BoTPPI-2, BoCSDP5, BoCCA1). Despite these advancements, the review highlights that the marker repertoire for cabbage remains limited compared with other Brassicaceae species, particularly for complex polygenic traits. This synthesis is a valuable resource for breeders and researchers, facilitating the development of superior head cabbage cultivars and hybrids. Full article

Mitogen-Activated Protein Kinases (MAPKs) play crucial roles in plant stress signaling, but the mechanisms of MAPK genes in Portulaca oleracea remain functionally uncharacterized. In this study, transcriptomic screening of P. oleracea under salt stress identified PoMPK3 as a candidate gene, showing significant root-specific upregulation. Phylogenetic analysis classified it as a Group A MAPK protein, and subcellular localization confirmed its membrane association. Heterologous expression of PoMPK3 in Arabidopsis thaliana significantly enhanced salt tolerance, as evidenced by improved seed germination rates, longer primary roots, increased biomass, and reduced stress symptoms. Mechanistically, PoMPK3 expression activated ABA signaling, leading to increased ABA levels and upregulation of AtNCED3, AtPYR1, and AtABF3. Furthermore, it strengthened the antioxidant defense, as evidenced by elevated antioxidant enzyme activity, leading to a reduction in oxidative stress. The transgenic lines also demonstrated enhanced osmotic adjustment through osmolytes accumulation and ionic homeostasis, evidenced by tissue-specific Na⁺/K⁺ ratios (low in shoots, high in roots) resulting from the concerted upregulation of AtSOS1, AtNHX1, and AtHKT1. In addition, gene co-expression network analysis and molecular docking predicted phosphorylation of WRKY transcription factors, suggesting a novel mechanism for transcriptome reprogramming. Collectively, our findings not only advance the understanding of salt tolerance mechanisms in purslane but also identify PoMPK3 as a key genetic determinant, thereby laying the foundation for its use in breeding programs aimed at enhancing salt stress resilience in crops. Full article

AINTEGUMENTA-LIKE6 (AIL6) is a transcription factor specifically expressed in embryos. It is a key to improving peony regeneration through tissue culture. Based on transcriptomic data from our previous research and the published genome data of Paeonia ostii, we identified the PoAIL6 gene associated with somatic embryogenesis (SE) in Paeonia ostii ‘Fengdan’. Structural and phylogenetic analyses were conducted on the PoAIL6-encoded protein, and its expression pattern across tissues and embryo developmental stages were explored using real-time quantitative PCR. Our results revealed that PoAIL6 contained two AP2 conserved domains and the characteristic motif of AIL6 genes. Phylogenetic analysis revealed that the PoAIL6 gene has similarity to grape (Vitis vinifera) and cocoa (Theobroma cacao). PoAIL6 exhibited the highest expression during early embryonic development, with expression levels gradually decreasing throughout SE progression. It was most highly expressed in peony seeds and showed relatively high expression in callus tissue. This study underscores the pivotal role of PoAIL6 in the early SE and lays a playground for elucidating its molecular mechanisms, supporting the development of efficient and stable regeneration and transformation systems in peony. Full article

Polycomb Group (PcG) proteins, particularly E(z) (Enhancer of Zeste) genes, play essential roles in transcriptional repression and developmental regulation. To investigate their evolutionary history, we conducted a comprehensive comparative genomic analysis of E(z) homologs across green plants. Phylogenetic analysis revealed that E(z) genes are highly conserved, predominantly occurring as single copies in green algae and early land plants. In seed plants, however, E(z) homologs diverged into two major clades, CLF and SWN, likely originating from an ancient duplication predating seed plant diversification. Conserved domain and motif analyses showed that while all E(z) proteins contain the hallmark SET domain, certain lineages also harbor CXC and SANT domains. Moreover, lineage-specific motif divergence was observed, suggesting functional diversification. In angiosperms, further duplications shaped the SWN lineage: in Brassicaceae, SWN genes split into SWN and MEA subclades, whereas in Fabaceae, SWN genes diverged into SWN1 and SWN2. Structural comparisons revealed that both Brassicaceae MEA and Fabaceae SWN2 proteins independently lost approximately 200 amino acids in the central region, indicating convergent structural modifications. Molecular evolutionary analysis showed that Fabaceae SWN1 genes are under purifying selection, consistent with retention of ancestral functions, whereas SWN2 genes experienced strong positive selection, implying functional innovation. Expression profiling of soybean E(z) genes further supported this scenario: SWN1 is broadly expressed across tissues, while SWN2 expression is restricted to the heart-shaped embryo. This pattern mirrors Arabidopsis MEA, suggesting that Fabaceae SWN2 may have evolved imprinted gene functions critical for seed development. Together, our results highlight the evolutionary conservation of E(z) genes in plants and reveal how gene duplication and lineage-specific divergence have driven functional specialization, particularly in Fabaceae SWN2. Full article