Search Results (521)

‘Hainan Qingyou’ (Citrus maxima) Pomelo is one of the predominant local cultivars cultivated in Hainan Province, renowned for its high economic value and strong market competitiveness. However, during cultivation, it was observed that the fruit quality of ‘Hainan Qingyou’ grafted onto a ‘Sanhong’ interstock deteriorated, predominantly manifesting as vesicle granulation. This study was therefore conducted to investigate this phenomenon using ‘Sanhong’ Honey Pomelo as the interstock. Fruit quality indicators were measured, and pulp transcriptomic analysis was performed during the expansion and maturation stages. The results indicated that fruits grafted onto ‘Sanhong’ interstock (SHZ) exhibited increased peel thickness, yellower peel, reduced edible rate, higher pulp firmness, decreased total soluble solids (TSS), increased total acid content, and reduced total antioxidant capacity at maturity, all contributing to diminished fruit quality. Additionally, SHZ fruit accumulated higher lignin content in the pulp, leading to vesicle granulation, which severely compromised marketability. Transcriptomic analysis identified 42 structural genes involved in lignin biosynthesis in ‘Hainan Qingyou’ pulp, including 5 PAL, 2 C4H, 2 4CL, 6 CAD, 15 PER, 2 HCT, 1 C3′H, 1 CCoAOMT, 1 CCR, 1 COMT, 2 CSE, and 1 F5H genes. Most of these genes were highly expressed in SHZ fruit at maturity, with expression levels significantly higher than those in fruit grafted onto ‘Hainan Qingyou’ interstock (QYZ). The interstock also affected hormone signaling pathways. Weighted gene co-expression network analysis (WGCNA) identified transcription factors such as MYB, MIKC, ERF, and bZIP as key regulators involved in pulp lignin biosynthesis. This study provides insights into the effects of rootstocks on citrus fruit quality and offers valuable information for cultivar improvement in pomelo orchards. Full article

To elucidate the molecular mechanisms underlying salt tolerance in rice (Oryza sativa L.), this study investigated differential transcriptional responses during the tillering stage. Salt-tolerant (N14) and salt-sensitive (N6) varieties were subjected to 0.3% and 0.6% NaCl treatments for 72 h, and their transcriptomes were analyzed via RNA-Seq. The results revealed distinct response strategies: 372 differentially expressed genes (DEGs) were identified in N14 and 393 in N6, with only 17 genes responding similarly. Gene Ontology (GO) analysis showed the tolerant N14 activated protein phosphorylation and lipid transport, primarily in the membrane and extracellular regions (e.g., ATP binding), whereas the sensitive N6 activated photosynthesis and protein folding, localized to chloroplasts and peroxisomes. KEGG analysis highlighted the activation of “Plant-pathogen interaction” in N14 versus “Metabolic pathways” in N6. Differential transcription factor activation was also observed, with N14 mobilizing 52 TFs (mainly WRKY and MYB) and N6 mobilizing 36 TFs (mainly MYB and b-ZIP). This study demonstrates that N14 and N6 utilize significantly different molecular pathways to cope with salinity, providing a crucial theoretical foundation for identifying novel salt tolerance genes and developing molecular breeding strategies. Full article

Background: Despite considerable advances to improve colorectal cancer (CRC) survival over the last decade, therapeutic challenges remain due to the rapid metastatic dissemination of primary tumors. This study revealed the apoptotic and anti-growth mechanism of VTD, a previously used anti-hypertensive supplement, can elevate UBXN2A, a known tumor suppressor protein in CRC, and simultaneously enhance intrinsic and extrinsic apoptosis in metastatic cancer cells. Methods and Results: An AOM/DSS mouse model of CRC showed that UBXN2A haplosufficient (UBXN2A +/−) mice treated with VTD had less tumor burden than mice with the full UBXN2A gene treated with vehicle. We have previously shown that casein-coated mesoporous silica nanoparticles (MSNs) offer an effective local delivery of drugs at tumor sites. Our findings demonstrate that the high rate of extracellular release of matrix metalloproteinases (MMPs), particularly MMP-7, by metastatic colon cancer cells, triggers the release of VTD from casein-coated mesoporous MSNs. This shows the “Zip Code” mechanism for the local enrichment of VTD at the tumor sites. After in vitro drug release verification, two independent mouse experiments, a xenograft and a splenolepatic metastatic mouse model of CRC, were used to evaluate the therapeutic efficacy of VTD-loaded and casein-coated carboxylated mesoporous silica nanoparticles, MSN-COOH/VTD/CAS (VTD, 0.2 mg/kg). Animal experiments revealed that MSN-COOH/VTD/CAS (VTD, 0.2 mg/kg) slows down the progress of tumors. Mass spectrometry (MS) revealed improved pharmacokinetics (PK) profile as MSN-COOH/VTD/CAS had less VTD accumulation in non-cancerous organs compared to pure VTD. We further improved nanoparticle targeting and drug release by shifting to calcium-based particles (CBPs). The engineered CBPs demonstrated higher drug-releasing performance. Without the MMPs trigger, MSNs show slow and continuous “drug leak” over longer period of time whereas CCSMPs stops leakage within an hour. Additionally, CBPs showed higher sensitivity to MMP-7 than MMP-9, enhancing the targetability of CBPs for CRC metastatic tumors with excessive extracellular MMP-7. Conclusions: This study introduces a new platform utilizing nanoparticle-based site-specific delivery of a plant-based anti-metastatic molecule, veratridine, with enhanced safety and therapeutic efficacy for the treatment of metastatic CRC. Full article

Mikania micrantha, commonly known as mile-a-minute weed, is listed among the world’s top 10 worst weeds. Although native to humid regions of South America, it has recently been found to colonize arid habitats as well. Despite pronounced seasonal hydroclimatic variations in South China and increasing drought due to global climate change, the mechanisms underlying M. micrantha’s drought tolerance remain poorly understood. In this study, we compared the photosynthetic responses of M. micrantha leaves and stems between the dry (June) and wet (December) seasons through field experiments. We measured changes in phenotype, photosynthetic characteristics, and the content of antioxidant and osmotic adjustment substances, using the co-occurring native vine Paederia scandens as a control. The results revealed that during the dry season, M. micrantha leaves exhibited wilting, along with significant reductions in relative water content (RWC), chlorophyll (Chl), soluble sugar (SS), and soluble protein (SP). In contrast, the stems of M. micrantha maintained relatively stable phenotypes and chlorophyll levels compared to those of P. scandens. Notably, M. micrantha stems exhibited significant increases in vessel wall thickness, vessel density, total phenol content, and the activities of peroxidase (POD) and ascorbate peroxidase (APX). Furthermore, compared to P. scandens, M. micrantha stems displayed a greater increase in cortex proportion, flavonoid content, and soluble protein content. Expression analysis of bZIP transcription factors further revealed drought-responsive upregulation of specific genes (bZIP60, ZIP42-1), suggesting their potential involvement in drought response. These results indicate that although the leaves of M. micrantha are susceptible to prolonged drought, the stems exhibit considerable resilience, which may be attributed to a combination of traits including structural modifications in stem anatomy, enhanced antioxidant capacity, and osmotic adjustment. These insights suggest that stem-specific adaptations are key to its drought tolerance, providing a theoretical foundation for understanding the habitat distribution of M. micrantha and informing effective management strategies. Full article

Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused on resource materials, identified an A/C SNP mutation at position 5486185 on chromosome D06 within the heat tolerance interval through genome-wide association studies (GWAS) of natural Gossypium hirsutum populations. Results: A total of 308 resource materials were identified and evaluated for their heat tolerance phenotypes over two years of field research. Kompetitive allele-specific PCR (KASP) molecular markers were developed on the basis of the D06-5486185 SNP to characterize the heat tolerance phenotypes of these 308 resource materials. Genotyping for heat tolerance-related traits and agronomic traits was also performed. Materials with the C/C haplotype at position D06-5486185 presented increased heat tolerance (higher pollen viability (PV), leaf area (LA), chlorophyll (Chl) and number of bolls on the third fruit branch (FB3) and a lower number of dry buds (DBs) and drop rate (DR)) without negatively impacting key yield traits. This locus is located in the intergenic region of two adjacent bZIP transcription factor genes (GH_D06G0408 and GH_D06G0409). Expression analysis revealed that the expression levels of these two genes were significantly greater in heat-tolerant accessions (C/C type) than in sensitive accessions and that their expression levels were significantly correlated with multiple heat-tolerant phenotypes. Conclusions: In summary, this study developed a Kompetitive Allele Specific PCR (KASP) marker associated with heat tolerance in G. hirsutum and identified two key heat tolerance candidate genes. These results provide an efficient marker selection tool and important genetic resources for the molecular breeding of heat-tolerant G. hirsutum, laying an important foundation for further establishing a molecular marker-assisted breeding system for heat tolerance in G. hirsutum. Full article

Background: The TGACG-BINDING FACTORS (TGA) gene family, a key subgroup of bZIP transcription factors, mediates plant stress responses and developmental processes by binding to the as-1 cis-element in target gene promoters to regulate transcriptional activation or repression. Despite its functional significance, systematic characterization of TGA genes in cotton (Gossypium spp.) remains insufficient. Methods: In this study, we performed a comprehensive genome-wide identification and phylogenetic analysis of TGA members across 10 Gossypium species and verified the functions of candidate genes using VIGS technology. Results: A total of 74 TGA homologous genes with conserved DOG1 and bZIP domains were identified. Evolutionary analysis revealed that the cotton TGA gene family can be classified into five distinct branches, suggesting functional diversification. Functional prediction analyses indicated these genes in cotton growth regulation and stress adaptation, potentially through hormone-mediated signaling pathways. Expression profiling demonstrated both tissue-specific expression patterns and salt-stress responsiveness in Gossypium hirsutum TGA genes, and GhTGA2 exhibited the most significant up-regulated expression under salt stress. Virus-induced gene silencing (VIGS)-mediated GhTGA2 silencing significantly reduced the salt tolerance in cotton. Conclusions: The TGA gene family is involved in regulating cotton growth, development, and stress responses, and plays a critical role in mediating salt stress tolerance in cotton. Our results provide mechanistic insights into cotton stress adaptation and establish a valuable genetic resource for developing elite salt-tolerant cotton cultivars, with direct implications for sustainable cotton production. Full article

Efficient allocation of mineral nutrients and photoassimilates is essential for grain development in rice. However, the transcriptional programs governing nutrient transport at key reproductive stages remain largely unresolved. Here, we performed a comprehensive transcriptome analysis of rice (Oryza sativa L.) across spatial (nodes, roots, and five other tissues) and temporal (seven reproductive stages) dimensions to elucidate the molecular basis of nutrient transport and allocation. RNA-seq profiling of node I identified stage-specific gene expression patterns, with the grain filling stage marked by strong induction of transporters involved in mineral allocation (e.g., OsYSL2, OsZIP3, OsSULTR3;3, SPDT) and carbohydrate distribution (e.g., OsSWEET13, OsSWEET14, OsMST6). Comparative analysis with the neck-panicle node (NPN) and root revealed tissue-specific regulatory networks, including nitrate (OsNRT1.1A, OsNRT2.3) and phosphate (OsPHT1;4, OsPHO1;3) transporters enriched at the grain filling stage. Root expression of Cd/As-related transporters (OsNRAMP5, OsCd1, OsLsi1, OsLsi2, OsLsi3) during grain filling highlights the contribution of belowground uptake to grain metal accumulation. Together, our study establishes a spatiotemporal atlas of nutrient transporter gene activity during rice reproductive development and identifies candidate genes regulating upward and lateral nutrient allocation. These findings provide insights into improving nutrient use efficiency and reducing toxic metal accumulation in rice grains through targeted manipulation of nodal and root transport systems. Full article

As the only harvest organ of pepper, fruit size is an important yield determinant. To elucidate the molecular mechanisms underlying pepper fruit size, we performed histological, physiological, and transcriptomic analyses on the pepper varieties QB6 (large fruit) and CXJ82 (small fruit). High contents of auxin and cytokinin in the early stage of fruit development promoted the rapid division of fruit cells in both varieties, which provided sufficient cells for subsequent fruit enlargement. High gibberellin accumulation induced the elongation and expansion of QB6 pericarp cells. Transcriptome analysis showed that genes related to cell division, cell wall polysaccharide degradation, and photosynthesis were highly expressed in QB6 fruit, likely contributing to its larger size. In the hormone–signal transduction factor–gene interaction network, GID6, GID1, IAA12, MYC30, and SAUR36 exhibited high correlations with numerous genes related to cell division, the cell wall, and photosynthesis, emerging as key signal transduction factors for the hormone-mediated regulation of pepper fruit size. Weighted gene co-expression network analysis identified the transcription factors OFP20, HD-ZIP6, and HD-ZIP13 as fundamental for pepper fruit size regulation. Our results expand the understanding of hormone regulation of pepper fruit size, providing a foundation for the breeding and improvement of excellent pepper varieties. Full article

Nitrogen is an essential macronutrient for crop growth. Although sorghum can tolerate poor soils, its low-nitrogen (LN) tolerance mechanisms remain underexplored. We conducted a genome-wide association study (GWAS) and RNA sequencing (RNA-seq) to dissect LN tolerance mechanisms in a diverse panel of 232 sorghum accessions. Phenotypic analyses revealed extensive variation in nitrogen-use efficiency traits, with shoot dry weight and shoot nitrogen accumulation in (SNAcc) showing the highest diversity. GWAS identified 10 quantitative trait loci harboring pleiotropic single-nucleotide polymorphisms (SNPs), including q1 (Chr3: 8.59–8.68 Mb), which is associated with biomass and nitrogen accumulation. Transcriptome profiling under LN stress revealed 6208 differentially expressed genes, with nitrate transporters showing genotype-specific regulation. Integration prioritized SORBI_3004G286700, where Hap2 accessions (14.66%) showed superior agronomic performance under LN conditions. We also identified pivotal transcription factors (TFs) that govern LN tolerance in sorghum, notably bHLH35 (SORBI_3007G051800) and three WRKY TFs, demonstrating constitutive upregulation in tolerant genotypes, whereas three previously uncharacterized TFs (MYB, bZIP, and B3) exhibited > 5-fold genotype-specific induction under LN. The integration of GWAS and transcriptome analyses offers an effective strategy for exploring candidate genes and elucidating nitrogen adaptation mechanisms in sorghum, while providing actionable molecular targets for precise breeding of nitrogen-efficient cultivars. Full article

In fish cells, light exposure elevates levels of reactive oxygen species (ROS) and stress-activated MAP kinase activity and thereby induces gene transcription. However, we lack a complete understanding of the function and evolution of this regulatory mechanism. Here, we reveal that a set of mitochondrial and heme metabolism genes is transcriptionally induced in zebrafish cells upon exposure to light or elevated ROS. The integrity of D-box and E-box enhancers in these gene promoters is essential for their transcriptional activation. Furthermore, light-induced transcription of mitochondrial and heme metabolism genes is absent in a cell line derived from the blind Somalian cavefish (Phreatichthys andruzzii). This fish species has evolved in perpetual darkness and lacks light-dependent circadian and DNA repair responses as well as D-box-mediated and light- and ROS-induced transcription. PAR-bZip transcription factors bind to and activate transcription via the D-box. Cavefish homologs of these factors share extensive homology with their zebrafish counterparts and lack the deletion mutations that characterize other light-dependent genes in this species. These results extend the role of the D-box as a key regulator of light- and ROS-driven transcription in fish, beyond the circadian clock and DNA repair systems, to also encompass metabolic and mitochondrial function. Full article

ATHB1, an Arabidopsis thaliana homeodomain-leucine zipper (HD-Zip) transcription factor, is involved in the control of leaf development and hypocotyl elongation under short-day conditions. As growth adaptation to environmental conditions is essential for plant resilience, we investigated the role of ATHB1 in the interaction between transcriptional regulatory networks and hormone signaling pathways. We found that wounding, flooding and ethylene induce ATHB1 expression. In addition, we found that the ethylene signal transduction pathway is also involved in an age-dependent ATHB1 expression increase in leaves. Conversely, methyl jasmonate (MeJA) application decreases the ATHB1 transcript level. By exploiting mutant and over-expressing (OE) lines, we also found that the ATHB1 level influences plant sensitivity to the inhibitory effect of MeJA treatment on growth. To gain deeper insights into the regulatory pathways affected by ATHB1, we performed a microarray analysis comparing the transcriptome of wild-type and athb1 mutant plants following exposure to MeJA. Remarkably, although the response to the MeJA treatment was not impaired in athb1, several genes involved in jasmonate and salycilic acid signaling were already downregulated in athb1 seedlings under normal conditions compared to the wild type. Thus, our study suggests that ATHB1 may integrate different hormone signaling pathways to influence plant growth under various stress conditions. Full article

Seed storage proteins (SSPs) play a pivotal role in determining the development, quality, and nutritional value of rice seeds. In this study, we conducted a transcriptome-based correlation analysis to identify novel transcription factors (TFs) potentially involved in the biosynthesis and accumulation of SSPs. Our analysis revealed nine TFs—OsGATA8, OsMIF1, OsMIF2, OsGZF1, OsbZIP58, OsS1Fa1, OsS1Fa2, OsICE2, and OsMYB24—that exhibit strong co-expression with key SSP genes, including those encoding glutelin and prolamin. Gene expression profiling using quantitative RT-PCR and GUS reporter assays revealed that these TFs are predominantly expressed during seed development, with peak expression observed at 10 days after flowering (DAF). Promoter analysis further demonstrated an enrichment of seed-specific and hormone-responsive cis-regulatory elements, reinforcing the seed-preferential expression patterns of these TFs. Collectively, our findings identify a set of candidate TFs likely involved in SSP regulation and seed maturation, providing a foundation for the genetic enhancement of rice seed quality and nutritional content through targeted breeding and biotechnological approaches. Full article

Phosphorus deficiency significantly limits soybean production across 74% of China’s arable land. This study investigated the molecular mechanisms enabling soybean to access insoluble phosphorus through transcriptome sequencing of the Heinong 48 variety across four developmental stages (Trefoil, Flower, Podding, and Post-podding). RNA-Seq analysis identified 2755 differentially expressed genes (DEGs), with 2506 up-regulated and 249 down-regulated genes. Notably, early developmental stages showed the most substantial transcriptional reprogramming, with 3825 DEGs in the Trefoil stage and 10,660 DEGs in the Flower stage, compared to only 523 and 393 DEGs in the Podding and Post-podding stages, respectively. Functional enrichment analysis revealed 44 significantly enriched GO terms in the Trefoil stage and 137 in the Flower stage, with 13 GO terms shared between both stages. KEGG pathway analysis identified 8 significantly enriched pathways in the Trefoil stage and 21 in the Flower stage, including key pathways related to isoflavonoid biosynthesis, alpha-linolenic acid metabolism, and photosynthesis. Among 87 differentially expressed transcription factors from 31 families, bHLH (8.08%), bZIP (7.18%), and WRKY (5.94%) were most prevalent. These findings provide genetic targets for developing soybean varieties with improved phosphorus acquisition capacity, potentially reducing fertilizer requirements and supporting more sustainable agricultural practices. Full article

Dendrobium officinale, an orchid of significant medicinal and ornamental value, exhibits poorly characterized hormonal regulation of flower bud differentiation. To address this knowledge gap, we employed an integrated multi-omics approach combining physiological, transcriptomic, metabolomic, and network analyses to elucidate the molecular mechanisms underlying the coordinated action of 6-Benzylaminopurine (6-BA) and Gibberellin A3 (GA₃) in this critical developmental process. Our key findings reveal that combined 6-BA and GA₃ treatment significantly enhances flower bud differentiation and induces stage-specific fluctuations in soluble sugar, protein, and starch levels. Transcriptomic profiling identified 11,994 differentially expressed genes (DEGs), with DEGs specific to the hormone-treated stage showing pronounced enrichment in plant hormone signal transduction and plant–pathogen interaction pathways. Metabolomic analysis uncovered 18 stage-specific differential metabolites (DAMs) during hormone treatment, including GA₃, 6-BA, and OPDA, whose accumulation dynamics were strongly correlated with the progression of differentiation. Weighted gene co-expression network analysis (WGCNA) pinpointed key hub genes within the yellow module, notably transcription factors from the C2H2, bZIP, and NAC families. Their interaction network demonstrated significant correlation with the transcriptional regulation of hormone-responsive genes. Significantly, this study establishes the first molecular framework for 6-BA and GA₃ regulation of flower bud differentiation in D. officinale. We demonstrate a metabolomic–transcriptomic coordination network driven by these hormones, where key hub genes form regulatory modules with transcription factors. Dynamic shifts in endogenous hormones reinforce the flowering signal. These findings provide crucial molecular targets for precision flowering control and molecular breeding strategies in orchids. 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