Search Results (175)

As a vital appearance quality trait of broccoli, curd-surface wax powder not only affects its commercial value but also plays a key role in plant resistance to abiotic stresses. However, its formation mechanism remains unclear. Using low-wax variety CK (‘QH18’) and high-wax variety T1 (‘QHMS4’) as materials, this study systematically elucidated the molecular mechanism of wax powder formation via physiological indexes, scanning electron microscopy (SEM), targeted metabolomics, and transcriptomics. Determination of fatty acid (FA) content in broccoli flower bud tissue showed a close association between FA content and wax deposition. SEM observation revealed that T1 had significantly denser wax crystals, mainly granular, than CK. Targeted metabolomics identified 25 fatty acids in the two varieties. And the linolenic and palmitic acids, with high content and significant differences, may be key metabolites regulating wax synthesis. Integrated transcriptomics and metabolomics indicated that BolfabG, BolLACS, BolKCS1, BolKCS2 and BolMAH1 genes are involved in wax biosynthesis. Moreover, AP2/ERF-ERF transcription factor (TF)-encoding genes (BolERF018, BolERF1F.1, BolERF1F.2 and BolERF1C) played the primary role in regulating wax biosynthesis, followed by NAC (BolNAC62.1), MYB (BolMYB44), and MADS-MIKC(BolPISTILLATA). These TFs may regulate BolfabG, BolLACS, BolKCS1, BolACOX2 and BolACAA1 to affect linolenic and palmitic acid balance, altering wax precursor synthesis and accumulation, and finally leading to differences in wax morphology and content. This study reveals a “Transcription Factors–Differentially Expressed Genes–Differentially Accumulated Metabolites–Fatty Acids” (TFs-DEGs-DAMs-FA) network, providing a basis for understanding broccoli wax formation. Full article

The System of Rice Intensification which promotes agro-ecological practices like alternate wetting and drying (AWD) to enhance root growth and resource efficiency, relies on the genotypic capacity of rice varieties to undergo physiological adaptation. This study elucidates the molecular basis of such adaptation by investigating the transcriptomic profile of four rice varieties to continuous flooding (CF) and AWD at 50 days after transplanting. Our analysis revealed distinct, organ-specific acclimation strategies. Roots underwent extensive transcriptional reprogramming, underscoring their role as the primary site of plasticity. Under CF, a conserved response involving cell wall reinforcement was accompanied by variety-specific strategies, ranging from sustained growth to enhanced anaerobic metabolism. Under AWD, roots shifted toward water stress management, with varieties employing distinct defensive (e.g., diterpenoid biosynthesis) and metabolic programs. Associated transcription factors (TFs) enriched under CF included Dof and MYB, whereas bZIP, HSF, and WRKY factors predominated under AWD. In leaves, acclimation to AWD involved more targeted adjustments, including modulation of nitric oxide signaling and photoprotective pathways, regulated by TFs such as WRKY, NAC, and HSF. Varieties with robust TF responses, such as IR64 and Hitachi hatamochi, showed comprehensive regulatory shifts, while others exhibited more constrained profiles. Overall, this study provides a molecular framework for understanding variety-specific adaptation to SRI-relevant water management practices and identifies key TFs as promising candidates for breeding climate-resilient rice. Full article

Background/Objectives: The screening and diagnosis of colon, ovarian, and prostate cancers are challenged by invasive procedures and lack of effective screening tests. To address these challenges, we developed an exosome-based liquid biopsy assay that utilized a new exosomal biomarker, α-linked Thomsen–Friedenreich glycoantigen (TF-Ag-α, Galβ1-3GalNAc-α). This assay provides a minimally invasive method with high sensitivity and specificity for the screening and diagnosis of colon, ovarian and prostate cancers. Methods: Exosomal TF-Ag-α levels in 10 μL serum samples were measured using a compact, surface plasmon resonance-based biosensor developed to facilitate clinical translation. The diagnostic performance of exosomal TF-Ag-α was initially evaluated in a training set consisting of normal controls (n = 80) and cancer patients (n = 120, 40 for prostate, 40 for colon, and 40 for ovarian cancer), and then validated in an independent test set including normal controls (n = 29) and cancer patients (n = 60, 20 for each cancer type). Receiver operating characteristic (ROC) analysis was performed to assess diagnostic sensitivity, specificity and area under the curve (AUC) of exosomal TF-Ag-α. Results: Serum samples from cancer patients showed significantly elevated levels of exosomal TF-Ag-α compared with normal controls. Exosomal TF-Ag-α distinguished all cancer patients from normal controls with a sensitivity of 99.2%, specificity of 100% and an overall accuracy of 99.5% at a cutoff value of 0.406. Conclusions: These findings demonstrated the clinical translational promise of exosomal TF-Ag-α as a liquid biopsy biomarker for the detection of colon, ovarian and prostate cancers. Full article

Understanding the molecular crosstalk between drought and iron (Fe) homeostasis is crucial for developing drought-tolerant wheat cultivars with enhanced nutrient quality. In this study, transcriptomic data mining identified 23,271 and 5933 differentially expressed genes (DEGs) under drought and Fe deficiency, respectively, with 2479 DEGs in response to both stresses. Notably, this overlapping set included significant numbers of genes encoding transcription factors (TFs) (149 genes), Fe homeostasis components (274 genes), and those involved in phytohormones pathways (245 genes), particularly the abscisic acid (ABA) pathway. Gene Ontology (GO) analysis revealed specific and commonly affected biological processes, such as response to abiotic stimulus and heme binding. Furthermore, co-expression network analysis revealed modules highly enriched with genes involved in transcriptional regulation and Fe uptake, enabling the identification of key hub regulatory genes, belonging to the MYB, NAC, BHLH, and AP2/ERF families, involved in the shared stress response. Finaly, the expression of a set of candidate TF-encoding genes was validated using qRT-PCR in durum wheat under drought and Fe starvation, providing a detailed overview of the possible shared regulatory mechanisms linking drought and Fe deficiency responses. Full article

Low-temperature stress severely restricts the growth, development, and yield of bitter gourd (Momordica charantia L.), a warm-loving crop with inherent low cold tolerance. NAC transcription factors (TFs) serve as crucial regulators in plant responses to abiotic stresses like cold, while their roles in coping with cold stress in bitter gourd remain unclear. This study identified cold-responsive genes in bitter gourd and characterized the candidate NAC TF McNAC087 through transcriptome analysis. Transcriptome sequencing of cold-tolerant (R) and cold-sensitive (S) bitter gourd inbred lines under 5 °C stress (0 h, 6 h, 12 h, 24 h) revealed 1157 co-expressed differentially expressed genes (DEGs), enriched via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in cold tolerance-related pathways (signal transduction, carbohydrate/amino acid metabolism). RT-qPCR showed higher McNAC087 expression in R than S under cold stress, and subcellular localization confirmed it as a nucleus-localized protein. McNAC087 overexpression in Arabidopsis enhanced cold tolerance after sequential stress (−14 °C for 1.5 h, 4 °C for 16 h, and 22 °C recovery for 2 days), with less damage compared to wildtype (WT). Physiologically, overexpressing lines had higher proline, elevated superoxide dismutase/peroxidase/catalase (SOD/POD/CAT) activities, lower malondialdehyde/hydrogen peroxide/superoxide anion (MDA/H₂O₂/O₂⁻) accumulation under cold stress, and upregulated ICE-CBF-COR pathway marker genes (CBF1, DREB2A, RD29A, COR47). In conclusion, McNAC087 enhances Arabidopsis cold tolerance by regulating physiology and activating cold-responsive genes, providing insights for bitter gourd cold tolerance mechanisms and crop breeding. Full article

Salinity is one of the key threats to food security and sustainability. To make saline soils productive again, we need to develop salt-tolerant crop varieties. Developing salt-tolerant wheat requires a detailed understanding of the molecular mechanisms underlying salt stress responses. In this study, we analyzed the Chinese Spring genome and identified 559 putative NAC transcription factors (TFs), which are recognized as key regulators of both abiotic and biotic stress. Protein family analysis revealed four distinct domain architectures, with more than 95% of the proteins containing a single NAC domain, consistent with their conserved regulatory role. Through in silico analyses, four salt stress-responsive TFs, NAC_1D, NAC_2D, NAC_4A, and NAC_5A, were highlighted, sharing nine of 13 DNA-binding residues. Promoter analysis of their putative target genes identified seven candidates, which, together with the NAC TFs, were subjected to RT-qPCR expression analysis in BARI Gom-25 plants exposed to 100 mM NaCl. The expression data revealed contrasting regulatory patterns between NAC TFs and their target genes. For example, Hsp70 was strongly upregulated in both shoots and roots, despite opposite patterns of NAC_1D expression between tissues. Similarly, bZIP expression mirrored the downregulation of NAC_2D, whereas HKT8 expression remained stable under salt stress. NAC_4A showed a root-specific pattern suggestive of positive regulation of a Non-specific serine/threonine protein kinase, while NAC_5A upregulation corresponded with downregulation of Plant cadmium resistance 2. Collectively, these results provide functional insights into four NAC TFs and identify potential molecular targets for improving wheat salt tolerance. By targeting key tolerance genes at the DNA level offers greater precision and can significantly reduce breeding time. Full article

Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared with conventional single-petal form. However, the molecular mechanisms underlying this floral trait remain largely undefined. In this study, RNA-based comparative transcriptomic analysis was performed between single- and double-petaled flowers of L. longituba at the fully opened flower stage. Approximately 13,848 differentially expressed genes (DEGs) were identified (6528 upregulated and 7320 downregulated genes). Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed several DEGs potentially involved in double-petal development. Six candidate genes, including the hub genes LlbHLH49, LlNAC1, LlSEP, LlTIFY, and LlAGL11, were identified based on DEG functional annotation and weighted gene co-expression network analysis (WGCNA). Transcription factors responsive to phytohormonal signaling were found to play a pivotal role in modulating double-petal development. Specifically, 123 DEGs were involved in phytohormone biosynthesis and signal transduction pathways, including those associated with auxin, cytokinin, gibberellin, ethylene, brassinosteroid, and jasmonic acid. Moreover, 521 transcription factors (TFs) were identified, including members of the MYB, WRKY, AP2/ERF, and MADS-box families. These results improve the current understanding of the genetic regulation of the double tepal trait in L. longituba and offer a base for future molecular breeding strategies to enhance ornamental characteristics. Full article

Leaf senescence, the terminal phase of leaf development, is governed by transcription factor (TF)-mediated genetic reprogramming events that significantly impact plant physiology and productivity. While TF-mediated senescence regulation has been demonstrated in various plant species, the underlying molecular mechanisms remain incompletely understood. This study investigated the regulatory roles of NAC family TFs in leaf senescence using two Clerodendrum japonicum lines exhibiting contrasting senescence phenotypes. Through integrated transcriptome sequencing, weighted gene co-expression network analysis (WGCNA), and functional enrichment approaches, we systematically analyzed temporal gene expression patterns during leaf senescence. Phenotypic characterization revealed distinct chlorophyll degradation dynamics between the lines, quantified by SPAD values. Transcriptomic analysis identified 232 consistently differentially expressed genes (DEGs) across senescence stages, among which 193 were annotated as NAC transcription factors. WGCNA delineated senescence-associated gene modules, with the turquoise and darkred modules showing particularly strong correlations with senescence progression. Further investigation identified 25 NAC genes exhibiting stage-specific expression patterns, and functional analysis revealed that 15 of these were significantly enriched in organ senescence-related pathways. qRT-PCR validation confirmed that the four core NAC regulators showed up to 5-fold higher expression in the early-senescing line during late senescence stages. These findings delineate the NAC-mediated regulatory network governing leaf senescence in C. japonicum, offering potential molecular targets for manipulating senescence progression, which warrants further functional characterization and practical application in plant improvement. Full article

Regulation of the phenylpropanoid pathway is critical for plant development and defense. This research investigates the transcriptional control of six Phenylalanine Ammonia-Lyase (PAL) gene homologs identified in the mulberry genome. A comprehensive in silico pipeline was employed to analyze the promoter architecture of these genes. Using the MEME suite, we identified three statistically significant conserved motifs within the 2000 bp upstream region. Subsequent TF binding prediction with FootprintDB for these motifs implicated the TCP, NAC, AP2/ERF, B3, and BBR-BPC families as potential regulators. A parallel analysis with PlantRegMap highlighted a high density of binding sites for the BBR-BPC and AP2/ERF families in the core promoter regions. A comparative analysis showed a weak correlation between the databases, underscoring the necessity of a multi-faceted predictive approach. Transcriptomic profiling under chitosan-induced conditions validated our in silico framework, suggesting the involvement of these TF families. Specifically, the data support NAC083 as a putative transcriptional activator and suggest a repressive function for members of the AP2/ERF and BBR-BPC families, providing a robust, experimentally supported model of PAL regulation. Full article

Rice (Oryza sativa), a crucial global staple, grapples with environmental stress and resource constraints, necessitating sustainable farming. This review explores the transformative role of transcription factors (TFs) in revolutionizing rice agriculture and their potential impact on global food security. It underscores TFs’ pivotal role in gene expression, particularly in responding to environmental stimuli, presenting a promising avenue for enhancing rice resilience. Delving into key TF families in rice, it highlights their multifaceted roles in abiotic stress responses, defense mechanisms, yield improvement, nutrient uptake, seed development, photosynthesis, and flowering regulation. Specific TFs, including DREB (Dehydration-Responsive Element-Binding), WRKY, NAC, MYB (Myeloblastosis), AP2/ERF (APETALA2/Ethylene Responsive Factor), and bHLH (basic Helix–Loop–Helix), are examined for their contributions to stress resilience, defense mechanisms, and yield enhancement. Concrete examples from cutting-edge research illustrate the tangible benefits of harnessing these molecular regulators. However, manipulating TFs presents challenges, necessitating innovative approaches such as predictive models, collaborative field testing, and transparent communication to navigate intricate regulatory networks and regulatory hurdles. Ultimately, a promising future emerges where manipulating rice TFs leads to the development of resilient, high-yielding, and nutritious varieties. Embracing research advancements and addressing existing challenges is imperative to unlock the full potential of these concealed regulators, ensuring sustainable food security for a growing global population. Full article

Dendrobium huoshanense, an endangered orchid species, is renowned for its polysaccharides with vast pharmacological significance in stems. Phosphomannomutase (PMM) critically regulates polysaccharide accumulation. Transcriptional regulation of DhPMM remains poorly characterized. This study employed a yeast one-hybrid (Y1H) system to identify upstream regulators of DhPMM. The 2.15 kb DhPMM promoter was cloned, revealing multiple stress- and hormone-responsive cis-elements (e.g., ABRE, MYC, ERF). A high-complexity Y1H library (3.60 × 10⁹ CFU) was constructed with insert sizes averaging 1–2 kb. Screening using aureobasidin A (AbA)-resistant Y1HGold [pAbAi-DhPMM] identified 11 candidate clones, including four transcription factor families (DOF, NAC, ERF, BES1). Interactions were rigorously confirmed by pairwise Y1H showing AbA-resistant growth and dual-luciferase assays demonstrating DhPMM activation. This represents the first functional cDNA library resource for D. huoshanense and identification of TFs interacting with DhPMM. The discovery of TFs belonging to DOF, NAC, ERF, and BES1 families as DhPMM regulators elucidated the transcriptional network underlying polysaccharide biosynthesis. This establishes a transcriptional framework for engineering polysaccharide biosynthesis in D. huoshanense. Full article

Most sweet cherry varieties exhibit typical gametophytic self-incompatibility (GSI) characteristics, necessitating careful configuration of pollination trees to ensure adequate yields. This requirement increases the costs associated with orchard labor, management, and other related expenses. Consequently, cultivating and developing sweet cherry cultivars with self-compatibility can effectively address these challenges. Research into the molecular mechanisms underlying GSI formation can provide vital theoretical support and genetic resources for breeding self-compatible sweet cherries. In this study, we assessed the fruit set rates of ‘Tieton’ following both self- and cross-pollination. Additionally, we conducted a transcriptome analysis of the ‘Tieton’ style (which includes the stigma) at 0, 12, 24, and 48 h post-pollination to identify key genes involved in the self-incompatibility process of sweet cherries. The results indicated that the self-fruiting rate of ‘Tieton’ was significantly lower than that of cross-pollination. We identified a total of 8148 differentially expressed genes (DEGs) through transcriptome analysis, with KEGG pathway analysis revealing that the plant-pathogen interaction, plant hormone signal transduction, and plant MAPK signaling pathways were primarily involved in sweet cherry GSI. Furthermore, we identified 13 core transcription factors (TFs) based on their differential expression patterns, including three ERFs, three NACs, three WRKYs, two HD-ZIPs, one RAV, and one MYB. Co-expression analysis identified 132 core DEGs significantly associated with these TFs. Ultimately, this study provides initial insights into the key genes within the sweet cherry GSI network, laying a theoretical foundation and offering genetic resources for the future molecular design breeding of new self-compatible varieties. Full article

Background/Objectives: Low-temperature stress during the grain-filling stage negatively affects rice grain quality and yield. Understanding the physiological and molecular mechanisms underlying cold tolerance is critical for breeding rice varieties with improved resilience. Methods: In this study, eight rice varieties with differential cold tolerance—LD1603, 13108, LD18, and 4-1021 (cold-tolerant) and LD3, LD4, LD121, and LD1604 (cold-sensitive)—were subjected to 17.5 °C low-temperature stress during grain filling in a naturally illuminated phytotron. Amylose and protein content, as well as taste quality, were analyzed. RNA sequencing was performed to identify differentially expressed genes and transcription factors associated with cold response. Results: Under low-temperature stress, amylose and protein content significantly increased in all eight varieties. The taste quality of cold-sensitive varieties declined markedly, whereas cold-tolerant varieties maintained higher and more stable taste quality values. Transcriptomic analysis revealed that key enzyme genes (INV, SUS, HXK, FRK, amyA, and TPP) in the starch and sucrose metabolism pathway were significantly upregulated in cold-tolerant varieties (LD18 and 4-1021), but suppressed in cold-sensitive varieties. Several cold-responsive transcription factors from the NAC, WRKY, AP2/ERF, MYB, and bZIP families were also identified. Weighted gene co-expression network analysis (WGCNA) further revealed hub TFs (OsWRKY1, OsWRKY24, OsWRKY53, and OsMYB4) and structural genes (OsPAL04 and OsCDPK7) potentially involved in cold tolerance during grain filling. Conclusions: This study enhanced our understanding of the molecular response to low temperature during rice grain filling and provided candidate genes for developing cold-tolerant rice varieties through molecular breeding. Full article

The main objective of this study was to reveal the molecular mechanism of the albinism in Schima superba and to identify the related functional genes to provide theoretical support for the optimization of S. superba seedling nursery technology. Combining third-generation SMRT sequencing with second-generation high-throughput sequencing technology, the transcriptomes of normal seedlings and albinism seedlings of S. superba were analyzed and the sequencing data were functionally annotated and deeply resolved. The results showed that 270 differentially expressed transcripts were screened by analyzing second-generation sequencing data. KEGG enrichment analysis of the annotation information revealed that, among the photosynthesis-antenna protein-related pathways, the expression of LHCA3 and LHCB6 was found to be down-regulated in S. superba albinism seedlings, suggesting that the down-regulation of photosynthesis-related proteins may affect the development of chloroplasts in leaves. Down-regulated expression of VDE in the carotenoid biosynthesis leads to impaired chlorophyll cycling. In addition, transcription factors (TFs), such as bHLH, MYB, GLK and NAC, were closely associated with chloroplast development in S. superba seedlings. In summary, the present study systematically explored the transcriptomic features of S. superba albinism seedlings, screened out key genes with significant differential expression and provide a reference for further localization and cloning of the key genes for S. superba albinism, in addition to laying an essential theoretical foundation for an in-depth understanding of the molecular mechanism of the S. superba albinism. The genes identified in this study that are associated with S. superba albinism will be important targets for genetic modification or molecular marker development, which is essential for improving the cultivation efficiency of S. superba. Full article

NAC (NAM, ATAF1/2, CUC1/2) is a plant-specific transcription factor (TF) family that plays important roles in various physiological and biochemical processes of plants. However, the NAC gene family in Lagerstroemia indica and its role in anthocyanin metabolism are still unexplored. In our study, a total of 167 NACs were identified in the L. indica genome via genome-wide analysis and bioinformatics techniques. Amino acid sequence analysis showed that all 167 NAC proteins contained a conserved NAM domain. This domain primarily comprised random coils, extended strands, and alpha helices. Most NACs were found on the nucleus and dispersed over 23 of the 24 plant chromosomes. Based on phylogenetic analysis, the NACs can be categorized into ten subgroups. Furthermore, the promoter homeotropic elements predicted the cis-acting elements in the promoters of these genes related to hormones, development, environmental stress response, and other related responses, demonstrating the diverse regulatory mechanisms underlying gene functions. In addition, a co-expression network was established through RNA sequencing. This network helped identify seven key LiNACs, genes related to anthocyanin expression (CHS) and transcription factors (MYB and bHLH). To identify potential anthocyanin regulatory factors present in L. indica petals, protein interaction prediction was performed, which revealed that LiNACs might participate in anthocyanin regulation by interacting with other proteins, such as MYB, ABF, ABI, bZIP, MYC, etc. Our results provided novel insights and could help in the functional identification of LiNACs in L. indica and the regulation of anthocyanin synthesis. Full article