Search Results (1,998)

Gene family expansion and contraction are key processes underlying functional innovation and genome evolution in plants, yet their roles in the horticultural plant white clover (Trifolium repens) remain poorly understood. In this study, we systematically investigated the association between lineage-specific whole-genome duplication (WGD) and short interspersed nuclear elements (SINEs) with gene family dynamics and stress-responsive transcription. Our results indicate that white clover underwent a lineage-specific WGD, which is associated with increased gene family expansion. SINE copy number was strongly correlated with the proportion of significantly expanded genes (r = 0.637, p = 0.0259, n = 12), but not with the proportion of significantly contracted genes. This result suggests a potential association between SINE insertions and gene family expansion. GO enrichment analyses indicated that expanded gene families are predominantly involved in metabolic processes, environmental stress responses, defense mechanisms, and floral organ development, whereas contracted gene families were mainly enriched in core housekeeping functions, such as ubiquitin-dependent protein catabolism and mitochondrial organization. Transcriptome analyses further showed that genes within expanded families were broadly upregulated under drought, cadmium, and cold stress, while generally upregulated in floral tissues compared with other organs. Collectively, these findings reveal the relationships among WGD, SINE elements, and gene family dynamics in environmental adaptation and flower development, providing a molecular framework for understanding adaptive regulation associated with gene family expansion. Full article

Rhododendron lapponicum (L.) Wahlenb., prized for its vibrant and diverse floral displays, holds significant ornamental and ecological value. However, advances in its molecular breeding have been constrained by the absence of reliable tools for accurate gene expression analysis. A fundamental requirement for such studies is the identification of stable reference genes for qRT-PCR. To date, no systematically validated reference genes exist for normalizing gene expression across R. lapponicum cultivars with diverse flower colors, representing a major technical obstacle to elucidating the molecular mechanisms of color formation. This study aimed to fill this gap by systematically identifying and validating optimal reference genes for petal tissues in six distinct R. lapponicum cultivars. We assessed the expression stability of 11 candidate genes using four independent algorithms and integrated the results via RefFinder. Our comprehensive analysis across multiple algorithms consistently identified RlaEF1-α and RlaACT as the most stably expressed reference genes. Their reliability was robustly validated by normalizing the expression of RlaMYB113, a key anthocyanin regulator; the normalized expression levels showed an extremely significant difference between rose-red and white cultivars (p < 0.001) and produced a coherent, phenotype-correlated profile, in contrast to the distorted patterns obtained with unstable references. This study establishes RlaEF1-α and RlaACT as a precise dual-gene internal control for qRT-PCR. By providing a validated normalization framework, our work enables accurate quantification of color-related genes and directly supports molecular breeding efforts aimed at the targeted development and selection of novel R. lapponicum cultivars with desirable and stable flower colors. Full article

The first female flower node (FFFN) is a crucial trait affecting earliness and yield in bitter gourd (Momordica charantia L.). To identify the genetic locus and candidate gene controlling FFFN, we performed phenotypic and genetic analyses using two parental lines, ‘M144’ (average FFFN: 6.3 ± 2.0) and ‘K55’ (average FFFN: 22.0 ± 4.5), along with their F₁ hybrid and an F₂ population consisting of 317 individuals. The results show that the low FFFN trait was incompletely dominant over the high FFFN trait. Using BSA-seq, we mapped a FFFN locus to an interval of 18.8–22.5 Mb on chromosome 4. Fine mapping with KASP markers narrowed the McFFFN4.1 to a 73.05 kb interval between markers 25QP334 and 26QP20, which contained seven predicted genes. Transcriptome analysis revealed that only Moc04g29650, which is annotated as cytochrome b-c1 complex subunit Rieske, was differentially expressed between the parents within this mapping interval. Sequence comparison identified a single SNP (C > A) in the promoter region of Moc04g29650, which was located within a putative YAB1/FIL-binding motif. Given the known role of FILAMENTOUS FLOWER (FIL) in regulating floral transition in Arabidopsis thaliana, Moc04g29650 is proposed as the most likely candidate gene for McFFFN4.1. The KASP marker 26QP20, located near Moc04g29650, showed the strongest association with FFFN in the F₂ population, with a maximum LOD score of 5.45, and thus represents a valuable tool for marker-assisted selection (MAS) breeding in bitter gourd. This study lays a foundation for cloning McFFFN4.1 and genetically improving early maturity in bitter gourd. Full article

Rice grain quality is strongly influenced by starch composition and structure, which differ between the two major cultivated Oryza sativa subspecies, indica and japonica. Although allelic variation in several key genes has been linked to these differences, it remains unclear whether subspecies divergence in starch metabolism is more strongly reflected in gene repertoire, structural organization, promoter composition, or transcriptional regulation. Here, we identified 52 starch metabolism-related genes representing 26 orthologous gene pairs in indica and japonica rice and compared their gene structures, predicted promoter cis-regulatory elements, and grain-filling expression patterns. The analyzed gene set was largely conserved between the two subspecies, with limited structural variation among orthologs. Although promoter analysis revealed differences in predicted cis-regulatory element composition, the strongest divergence was observed at the transcriptional level during grain filling. At 10 days after flowering (DAFs), RNA-seq profiling revealed relatively higher expression of several starch biosynthesis genes, including SSI, SSIIa, and BEI, in japonica than in indica. qRT-PCR further confirmed higher expression of SSI, SSIIa, BEIIb, and GBSSI in japonica, whereas AGPS2b was more highly expressed in indica during early grain filling. By 30 DAFs, expression of most tested genes had declined markedly in both subspecies. These findings indicate that divergence between indica and japonica is more clearly associated with transcriptional regulation during grain filling than with major differences in core starch metabolism gene content or structural organization. Full article

Cannabis sativa is a multipurpose dioecious species whose crop performance is governed by sex expression. Although sex is genetically determined by an X/Y chromosome system, plants can develop flowers of the opposite sex through sex reversion, commonly induced by manipulating endogenous hormone levels using plant growth regulators (PGRs). Here, we evaluated the effectiveness of PGRs that promote or inhibit major hormone pathways implicated in plant sex expression. Male and female clones from two accessions were treated with foliar applications of nine PGRs and four combinatory treatments to assess sex- and genotype-specific responses. Floral biomass and the proportion of each sex were recorded at harvest to assess treatment effectiveness. Ethylene emerged as the primary regulator of chemically modulated sex reversion in C. sativa, with its inhibition by silver thiosulfate inducing strong female-to-male reversion and its promotion by ethephon inducing equally strong male-to-female reversion in the inflorescences. Gibberellin promotion on its own resulted in female-to-male reversion at the axial nodes only, while its inhibition showed no reciprocal effects. The combination of silver thiosulfate and gibberellic acid resulted in the most complete female-to-male reversion, and all sex-reverted flowers were fertile. Together, the results indicated that flowers at axial nodes and at the terminal ends of inflorescences are under different hormonal control. Cytokinins, auxins, and jasmonates were found to exert minimal influence on sex reversion. All treatments exhibited pleiotropic effects, particularly gibberellic acid and paclobutrazol, which altered resource allocation, shifting biomass away from and towards floral tissue, respectively. These findings advance our understanding of the hormonal regulation of sex expression in C. sativa and identify optimized approaches for its manipulation. Full article

The development of rice flowers and panicles critically affects grain yield and quality. LEAFY HULL STERILE1/OsMADS1, a grass-specific SEPALLATA-like MADS-box transcription factor, is essential for rice floral development and floral meristem activity maintenance. However, the mechanism through which OsMADS1 interacts with other genes to regulate floral organ identity and meristem determinacy remains unclear. In this study, we first generated OsMADS1 knockout mutants using CRISPR/Cas9. The mutant florets exhibited obvious morphological defects, which were categorized into five phenotypic classes. Yeast two-hybrid screening identified two OsMADS1-interacting proteins: OsMADS22, an STMADS11-like protein, and OsYABBY5, a YABBY transcription factor. Their physical interactions were validated both in vitro and in vivo, and were important for floral organ specification and meristem maintenance. Transcriptomic analysis revealed that OsMADS1 regulates numerous genes involved in hormone signaling and panicle/flower development. Furthermore, OsMADS1 acts together with OsMADS22 and OsYABBY5 to modulate the expression of the downstream target OsMADS55, thereby controlling rice spikelet development. Together, our results reveal that OsMADS1 executes diverse regulatory functions in floral organ specification and meristem identity by interacting with multiple developmental regulators, providing new insights into the molecular mechanisms of plant flower development. Full article

To reveal how the characteristic flavor of jasmine tea is generated, this study analyzed the coordinated changes in sensory properties, chemical components, and aroma migration behavior during scenting. Sensory evaluation, biochemical assays, and headspace solid-phase microextraction–gas chromatography–mass spectrometry (HS-SPME-GC-MS) integrated with orthogonal partial least squares discriminant analysis (OPLS-DA) and relative odor activity value (rOAV) filtering were applied to tea samples before and after scenting. After scenting, aroma and taste scores increased significantly, and liquor color shifted from tender green to pale yellow. Amino acids and soluble sugars increased, while astringent substances such as tea polyphenols and catechins decreased. Key floral compounds, including cis-3-hexenyl benzoate and methyl anthranilate, were transferred from jasmine flowers to the tea base and enriched, likely contributing to the typical aroma profile. The retention rate of aroma in spent flowers was positively correlated with hydrophobicity (logP, r > 0.46, p < 0.01) and negatively with polarity (TPSA, r > −0.42, p < 0.05), suggesting regulation by hydrophobic partitioning. In contrast, aroma transfer to the tea base showed no simple correlation with any single physicochemical parameter, suggesting multi-factor regulation. This study provides insights into the scenting process and offers a theoretical reference for quality control in jasmine tea production. Full article

Background: Information on the autopolyploid of Gossypium herbaceum remains limited until now. Previously, the autotetraploid of G. herbaceum was successfully generated via colchicine-induced chromosome doubling from the diploid cultivar ‘Hongxing’ in our lab. Methods: To investigate the drought stress response mechanism of this tetraploid, the autotetraploid S4 was used as the experimental material. The plants were subjected to drought stress during the flowering stage, followed by measurements of physiological and biochemical indicators and transcriptomic sequencing analysis. Results: Under drought stress, MDA content increased, and cell membranes sustained oxidative damage. Photosynthetic parameters, such as net photosynthetic rate (Pn), were significantly suppressed, while the activity of osmotic regulators and key antioxidant enzymes increased significantly. After rehydration, all of the above physiological indicators showed varying degrees of recovery. Transcriptome analysis revealed that, when comparing the treatment group with the control group, a total of 5530 differentially expressed genes (DEGs) were identified, with 2714 up-regulated and 2816 down-regulated. Furthermore, this study investigated the drought resistance mechanism involving the interaction between the MAPK signaling pathway and other metabolic pathways in the autotetraploid. Nine drought-resistant genes, including MAPK3, bHLH47, GaRbohD, RIBA1, PIP1-3, RCA1, RbohD, CYP707A and HSP70, were selected and analyzed using real-time quantitative PCR; the results were generally consistent with the transcriptomic data. Conclusions: These findings substantially enhance our understanding of the molecular mechanisms underlying drought responses in autotetraploids. This novel autotetraploid genotype expands the available cotton germplasm resources and is expected to hold significant value for research on polyploidy evolution. Full article

Lycoris plants are known for their diverse flower colors, but the molecular mechanisms behind these variations remain unclear. In this study, we first used the CIELAB system to precisely measure flower color. We objectively defined the petals of Lycoris sprengeri as blue-purple (Bp) and compared them with the white petals of Lycoris longituba (W) and the red petals of Lycoris radiata var. pumila (R). Metabolomic analysis showed that specific kaempferol glycosides, including kaempferol-3-O-sophoroside and lonicerin, accumulated significantly in the blue-purple petals. Transcriptomic analysis revealed that genes related to flavonoid biosynthesis were generally more active in the colored petals (Bp and R). However, different expression patterns of key hydroxylase genes created a metabolic split. Specifically, the blue-purple petals showed high expression of LrF3′5′H (directing synthesis toward delphinidin) and LrFLS (promoting kaempferol accumulation), whereas the red petals mainly expressed LrF3′H (leading to cyanidin synthesis). Further investigation identified LrWRKY70 as a core transcription factor highly correlated with these flavonoid pathway genes. Crucially, we discovered a new long non-coding RNA, LncRNA401, located downstream of the LrWRKY70 antisense strand. It showed a strong positive correlation with LrWRKY70. Functional verification through transient overexpression demonstrated that LncRNA401 significantly increased the expression of LrWRKY70. This, in turn, broadly activated downstream flavonoid biosynthesis genes, including LrCHS, LrF3′5′H, LrFLS, and LrDFR. This cascade ultimately promoted the synthesis of anthocyanins and kaempferol derivatives, resulting in the unique blue-purple phenotype. Our results reveal a novel LncRNA401-LrWRKY70 regulatory module. This module plays a key role in metabolic reprogramming for flower color formation in Lycoris, providing important insights into plant secondary metabolism and valuable targets for breeding specific flower colors. Full article

This study aims to establish a time-resolved harvesting standard for Penthorum chinense. To achieve this, we systematically integrated growth phenology, phytochemical accumulation dynamics, and antioxidant activity across six key developmental stages. The contents of total phenolics, flavonoids, proanthocyanidins, and tannins exhibited a biphasic fluctuation pattern, which was closely correlated with variations in antioxidant capacity. Principal component analysis identified the optimal harvest windows: flowers achieved the highest integrated score at the full blooming stage, whereas leaves scored highest at the early fruiting stage. These periods also corresponded with greater fresh biomass, supporting favorable economic returns. Accordingly, we recommend the full blooming stage as the optimal harvest time for flowers and the early fruiting stage for leaves and stems. Future research should focus on elucidating how environmental factors regulate the accumulation of bioactive compounds, which will further refine cultivation and harvest strategies to enhance the quality of this medicinal herb. Full article

Soybean is a vital crop supporting global food, feed, and biofuel production. Soybean yields have surged, with record yields reaching 14,678 kg/ha⁻¹, though average farm yields remain stagnant at 2770–2790 kg ha⁻¹. The persistent yield gaps leave 44% of potential production unrealized due to climate change, threatening food security. To meet future caloric demands, which are projected to rise by 46.8% by 2050, soybean breeding must prioritize climate-resilient, high-yielding varieties with minimal ecological footprints. In this comprehensive and in-depth review, we synthesized existing literature and Google Patents and reviewed the multifaceted impacts of climate-change driven eCO₂ and stresses (heat, drought, flooding, salinity, and pathogens), revealing non-linear interactions where eCO₂ may not compensate yield losses under combined stresses. We then highlight key strategies for soybean breeding under climate-change scenario. To this regard, we provide a detailed trait-by-trait breeding roadmap covering seed number, seed size, seed weight, protein-oil balance and their metabolic trade-offs, above and below ground plant architecture, nitrogen fixation and nodulation dynamics, root system architecture, water use efficiency, canopy architecture, flowering time regulation, early maturity etc., in light of specific genes and validated strategies. We explicitly discuss the novel strategies including deeper understanding of traits, abiotic stress physiology, changing pathogen dynamics, phenomics, (multi-)omics, machine learning, and modern biotechnological techniques for developing future soybean varieties. We provide a future roadmap prioritizing specific actions, including engineering climate-resilient ideotypes through gene stacking, optimizing nitrogen fixation and nutrition under stresses leveraging omics data, pan-genome, wild soybean, speeding breeding hubs, and participatory farmer-network validation, while redefining the future soybean breeder would be a hybrid orchestrator of data and dirt. This review establishes a foundational framework for translating climate-adaptive morphological, biochemical, physiological, omics, agronomic, phenomics, and biotechnological insights into actionable breeding strategies, thereby guiding policy-driven investment in soybean improvement programs targeting 2050 and beyond. Full article

Background: Nymphaea atrans exhibits a gradual flower color transition from nearly white to rose-red during anthesis, yet the molecular mechanisms of this phenomenon remain unclear. In the present study, transcriptomic and metabolomic analyses were performed to systematically investigate anthocyanin accumulation patterns and regulatory mechanisms during the color transition of N. atrans. Methods: Petals were collected at three flowering stages: day 1 (D1), day 3 (D3), and day 5 (D5). Targeted metabolomics was performed using UPLC-ESI-MS/MS to profile anthocyanin and other flavonoid metabolites. Transcriptome analysis was conducted via RNA-seq. Differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were identified, followed by functional enrichment and integration analysis. Results: The results revealed significant accumulation of seven anthocyanins, including cyanidin-3-O-arabinoside, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, cyanidin-3-O-(6″-O-acetyl)-glucoside, at stages D3 (day 3 after flowering, light pink petals) and D5 (day 5 after flowering, deep pink petals), accompanied by the upregulation of key enzyme-encoding genes, chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, di-hydroflavonol 4-reductase, and anthocyanidin synthase in the anthocyanin biosynthetic pathway. Genes involved in JA biosynthesis and key regulatory genes in the JA signaling pathway were significantly up-regulated, indicating that the JA signaling pathway may play an important regulatory role in the synthesis of anthocyanins in N. atrans. Conclusions: This study unravels the metabolic and molecular underpinnings of flower color transition in N. atrans, thereby establishing a theoretical basis for the targeted regulation of floral pigmentation and molecular breeding of ornamental water lilies. Full article

Cerium dioxide (CeO₂) has emerged as a structurally versatile oxide for dye-wastewater purification because its architecture, porosity, and surface accessibility can be tuned over a wide range while maintaining good chemical stability and environmental compatibility. Recent studies show that template-free or low-template routes can generate porous, mesoporous, multilayered, and flower-like CeO₂ architectures with rapid dye uptake and, in some systems, adsorption-assisted photocatalytic removal. However, CeO₂-based dye removal has often been discussed either within broad surveys of environmental applications or from composition-centered viewpoints, whereas the more fundamental question is how synthesis route controls architecture formation and how architecture, in turn, governs adsorption and subsequent removal behavior. This mini-review addresses that question from a morphology-centered perspective. It first examines template-free and low-template routes for constructing structured CeO₂, then discusses how porosity, hierarchical assembly, and surface accessibility regulate adsorption kinetics and equilibrium capacity in dye-containing aqueous systems. It further considers adsorption-assisted photocatalytic removal and argues that dark adsorption should be regarded as the structural first step rather than a secondary contribution. On this basis, the review shows that rare-earth doping in these systems is most usefully understood as a secondary tuning strategy that refines an already favorable host architecture by modifying surface interaction, optical response, or reactive-species generation. Overall, the available evidence indicates that CeO₂-based dye-wastewater purification is most meaningfully interpreted through a route–architecture–function framework in which morphology defines the host, adsorption organizes the local reaction environment, and doping serves mainly as structure-assisted tuning. This perspective shifts the design logic of CeO₂ from empirical performance optimization toward rational structure-directed construction of integrated removal platforms. Full article

Excessive planting density and heavy rainfall weather threatens global agriculture, particularly affecting maize. Biochar is an environmentally friendly soil amendment that has a yield-increasing effect. However, the regulatory mechanism of biochar frequency on crop internode development and photosystem II photosynthetic efficiency remains unknown. A total of nine treatments were followed in this experiment. Three applications of biochar were as follows: no biochar application (B0); biochar application at 4.2 t ha⁻¹ year⁻¹ (B1); and biochar application at 8.4 t ha⁻¹ 2 year⁻¹ (B2), alongside three nitrogen (N) fertilizer rates (0, N0; 180 kg ha⁻¹, N1 and 225 kg ha⁻¹, N2). The results showed that the internode thickness of the 2nd to 5th nodes under N2B2 treatment increased by 17.7%, 16.0%, 19.7%, and 21.7%, respectively, compared to N0B0. Annual biochar application had a higher stem diameter coefficient for the 1st to 3rd nodes than no biochar (B0) and treatments applied every two years (B2). Annual biochar application had the highest dry weight of internodes and plant height compared with B0 and B2. The relative chlorophyll content of leaves was significantly increased by biochar combined with N fertilizer or by N fertilizer alone. Biochar combined with N fertilizer significantly reduced NPQt and ΦNPQ, which were reduced by 59% and 50%, respectively, under N2B1 treatment compared with N0B0. The N2B1 treatment increased ΦII by 30% compared to N0B0. Stem diameter coefficient was significantly negatively correlated with NPQt and ΦNPQ and significantly positively correlated with ΦII and Fv/Fm. Compared to B1, B2 increased the maize yield. Annual biochar application combined with N fertilizer reduced stem collapse and enhanced post-flowering photosynthesis. Overall, considering the yield traits, 8.4 t ha⁻¹ biochar application combined with 180 kg ha⁻¹ N fertilizer treatment was the best. This study will provide reference data for cultivation regulation to enhance maize’s resistance to collapse and maintain photosynthetic capacity. Full article

The plant-specific TCP transcription factor family plays crucial roles in morphogenesis and stress adaptation. While characterized in many species, this family remains unstudied in Punica granatum. We performed the first genome-wide analysis of the TCP family in pomegranate, identifying 24 PgTCP genes classified into the PCF, CIN, and CYC/TB1 subclades, supported by conserved gene structures and motifs. Evolutionary analysis indicated segmental duplication and purifying selection shaped this family. Expression profiling revealed distinct spatiotemporal patterns: PgTCP2/9/14/21 were highly expressed in flowers, with PgTCP21 also notably abundant in fruit tissues (seed coats and pericarp), suggesting roles in reproductive development. PgTCP19, an ortholog of the branching suppressor BRC1, showed dominant expression in dormant buds, implicating it in shoot architecture regulation. Furthermore, PgTCP5 and the miR319-targeted PgTCP22 were leaf-predominant, indicating a function in leaf development. Under abiotic stress, PgTCPs displayed dynamic, treatment-specific responses. A subset of genes was rapidly induced by cold, while PgTCP14 and PgTCP23 showed sustained upregulation during drought. Several light-responsive PgTCPs were suppressed under shading. This study provides a foundational resource, functionally classifies the PgTCP family, and identifies key candidates regulating organ development and stress resilience for future functional validation and molecular breeding in pomegranate. This work provides the first comprehensive overview of the TCP gene family in pomegranate and offers candidate genes for future functional studies related to development and stress responses. Full article