Search Results (720)

Sea buckthorn is a vital woody oil species valued for its role in soil conservation and its bioactive seed oil, which is rich in unsaturated fatty acids and other compounds. However, low seed oil content and small seed size are the main bottlenecks restricting the development and utilization of sea buckthorn. In this study, we tested the seed oil content and seed size of 12 sea buckthorn cultivars and identified the key genes and transcription factors involved in seed development and lipid biosynthesis via the integration of UID RNA-seq (Unique Identifiers, UID), WGCNA (weighted gene co-expression network analysis) and qRT-PCR (quantitative real-time PCR) analysis. The results revealed five cultivars (CY02, CY11, CY201309, CY18, CY21) with significantly higher oil contents and five cultivars (CY10, CY201309, CY18, CY21, CY27) with significantly heavier seeds. A total of 10,873 genes were significantly differentially expressed between the S1 and S2 seed developmental stages of the 12 cultivars. WGCNA was used to identify five modules related to seed oil content and seed weight/size, and 417 candidate genes were screened from these modules. Among them, multiple hub genes and transcription factors were identified; for instance, ATP synthase, ATP synthase subunit D and Acyl carrier protein 1 were related to seed development; plastid–lipid-associated protein, acyltransferase-like protein, and glycerol-3-phosphate 2-O-acyltransferase 6 were involved in lipid biosynthesis; and transcription factors DOF1.2, BHLH137 and ERF4 were associated with seed enlargement and development. These findings provide crucial insights into the genetic regulation of seed traits in sea buckthorn, offering targets for future breeding efforts aimed at improving oil yield and quality. Full article

SnRK kinases, central regulators of plant stress response, remain uncharacterized in Taxus—an ancient gymnosperm valued for paclitaxel production. This study aimed to identify the Taxus SnRK family and elucidate its functional roles. Specifically, we identified SnRK genes through genomic analysis and assessed tissue-specific expression via transcriptomics, while regulatory networks were deciphered using WGCNA. To overcome experimental constraints, a PEG-mediated protoplast transient expression system was developed using calli, followed by dual-luciferase assays. Consequently, 19 SnRK genes (2 SnRK1, 4 SnRK2, 13 SnRK3) were identified, with tissue-specific expression revealing TaSnRK1.2 upregulation under methyl jasmonate (MeJA) and in stress-resilient tissues (bark/root). Subsequently, WGCNA uncovered a bark/root-specific module containing TaSnRK1.2 with predicted TF interactions (TaGRAS/TaERF). Critically, homologous dual-luciferase assays demonstrated TaSnRK1.2 activates TaGRAS and TaERF promoters (4.34-fold and 3.11-fold induction, respectively). This study establishes the Taxus SnRK family and identifies TaSnRK1.2 as a hub integrating stress signals (e.g., MeJA) to modulate downstream TF networks, while the novel protoplast system enables future functional studies in this medicinal plant. Full article

The soil-borne fungal pathogen Verticillium dahliae causes devastating vascular wilt disease in numerous crops, including cotton. In this study, we reveal that VdSOX1, a highly conserved sarcosine oxidase gene, is significantly upregulated during host infection and plays a multifaceted role in fungal physiology and pathogenicity. Functional deletion of VdSOX1 leads to increased fungal virulence, accompanied by enhanced microsclerotia formation, elevated carbon source utilization, and pronounced upregulation of effector genes, including over 50 predicted secreted proteins genes. Moreover, the VdSOX1 knockout strains suppress the expression of key defense-related transcription factors in cotton, such as WRKY, MYB, AP2/ERF, and GRAS families, thereby impairing host immune responses. Transcriptomic analyses confirm that VdSOX1 orchestrates a broad metabolic reprogramming that links nutrient acquisition to immune evasion. Our findings identify VdSOX1 as a central regulator that promotes V. dahliae virulence by upregulating effector gene expression and suppressing host immune responses, offering novel insights into the molecular basis of host–pathogen interactions and highlighting potential targets for disease management. Full article

Chromosomal microarray analysis (CMA) was performed for 40 patients with B-ALL undergoing treatment according to the ALL-2016 protocol to investigate the copy number alterations (CNAs) and copy neutral loss of heterozygosity (cnLOH) associated with minimal residual disease (MRD)-positive remission. Aberrations involving over 20,000 genes were identified, and a random forest approach was applied to isolate a subset of genes whose CNAs and cnLOH are significantly associated with poor therapeutic response. We have assembled the triple matched healthy population data and used that data as a reference, but not as a matched control. We identified a recurrent cluster of cnLOH in the 19q13.2–19q13.31 region, significantly enriched in MRD-positive patients (70% vs. 47% in the reference group vs. 16% in MRD-negative patients). This region includes the pregnancy-specific glycoprotein (PSG) gene family and the oncogene ERF, suggesting a potential role in leukemic persistence and treatment resistance. Additionally, we observed significant deletions involving 7p22.3 and 16q13, often as part of large-scale losses affecting almost the entire chromosomes 7 and 16, indicative of global chromosomal instability. These findings highlight specific genomic regions potentially involved in therapy resistance and may contribute to improved risk stratification in B-ALL. Our findings emphasize the value of high-resolution CMA in diagnostics and risk stratification and suggest that PSG genes and other candidate genes could serve as biomarkers for predicting treatment outcomes. Full article

Apomixis-mediated fixation of heterosis could transform hybrid breeding in alfalfa (Medicago sativa), a globally important forage crop. The parthenogenesis-inducing morphogenetic regulator BABY BOOM (BBM) represents a promising candidate for enabling this advancement. Here, we identified BBM homologs from three alfalfa genomes, characterized their promoter regions, and cloned a 2082 bp MsBBM gene encoding a 694-amino acid nuclear-localized protein. Three alfalfa BBM gene promoters primarily contained light- and hormone-responsive elements. Phylogenetic and conserved domain analyses of the MsBBM protein revealed a high sequence similarity with M. truncatula BBM. Expression profiling demonstrated tissue-specific accumulation of MsBBM transcripts, with the highest expression in the roots and developing pods. Hormonal treatments differentially regulated MsBBM. Expression was upregulated by GA₃ (except at 4 h) and SA, downregulated by NAA, MeJA (both except at 8 h), and ABA (except at 4 h), while ETH treatment induced a transient expression peak at 2 h. As an AP2/ERF family transcription factor showing preferential expression in young embryos, MsBBM likely participates in reproductive development and may facilitate apomixis. These findings establish a molecular framework for exploiting MsBBM to enhance alfalfa breeding efficiency through heterosis fixation. Full article

Anthocyanins are important phenolic compounds in grape skins, affecting the color, oxidation resistance, and aging ability of red wine. In recent years, global warming has had a negative effect on anthocyanin biosynthesis in grape berries. Ethylene serves as a crucial phytohormone regulating the development and ripening processes of fruit; however, the specific molecular mechanism and the regulatory network between ethylene signaling and the anthocyanin biosynthesis pathway remain incompletely understood. In this study, 400 mg/L ethephon (ETH) solution was sprayed onto the surface of grape berries at the lag phase (EL-34), and the changes in anthocyanin-related genes and metabolites were explored through transcriptomic and metabolomic analysis. The results showed that ETH treatment increased Brix and pH in mature berries. In total, 35 individual anthocyanins were detected, in which 21 individual anthocyanins were enhanced by ETH treatment. However, the anthocyanin profile was not affected by exogenous ethylene. Transcriptomics analysis showed that there were a total of 825 and 1399 differentially expressed genes (DEGs) 12 h and 24 h after treatment. Moreover, key structural genes in the anthocyanin synthesis pathway were strongly induced, including VvPAL, VvCHS, VvF3H, VvF3′5′H, VvDFR and VvUFGT. At the maturity stage (EL-38), the expression levels of these genes were still higher in EHT-treated berries than in the control. ETH treatment also influenced the expression of genes related to hormone biosynthesis and signal transduction. The ethylene biosynthesis gene (VvACO), ethylene receptor genes (VvETR2, VvERS1 and VvEIN4), ABA biosynthesis gene (VvNCED2), and ABA receptor gene (VvPYL4) were up-regulated by ETH treatment, while the auxin biosynthesis gene (VvTAA3) and seven genes of the auxin-responsive protein were inhibited by exogenous ethylene. Meanwhile, ETH treatment promoted the expression of the sugar transporter gene (VvEDL16) and two sucrose synthase genes (VvSUS2 and VvSUS6). In EHT-treated berries, 19 MYB and 23 ERF genes were expressed differently compared with the control (p < 0.05). This study provides the theoretical foundation and technical support for the regulation of anthocyanin synthesis in non-climacteric fruit. Full article

The rapid evolution of pathogens and the limited genetic diversity of hosts are two major factors contributing to the plant pathogenic phenomenon known as the loss of disease resistance in maize (Zea mays L.). It has emerged as a significant biological stressor threatening the global food supplies and security. Based on previous cross-species homologous gene screening assays conducted in the laboratory, this study identified the maize disease-resistance candidate gene ZmNLR-7 to investigate the maize immune regulation mechanism against Bipolaris maydis. Subcellular localization assays confirmed that the ZmNLR-7 protein is localized in the plasma membrane and nucleus, and phylogenetic analysis revealed that it contains a conserved NB-ARC domain. Analysis of tissue expression patterns revealed that ZmNLR-7 was expressed in all maize tissues, with the highest expression level (5.11 times) exhibited in the leaves, and that its transcription level peaked at 11.92 times 48 h post Bipolaris maydis infection. Upon inoculating the ZmNLR-7 EMS mutants with Bipolaris maydis, the disease index was increased to 33.89 and 43.33, respectively, and the lesion expansion rate was higher than that in the wild type, indicating enhanced susceptibility to southern corn leaf blight. Physiological index measurements revealed a disturbance of ROS metabolism in ZmNLR-7 EMS mutants, with SOD activity decreased by approximately 30% and 55%, and POD activity decreased by 18% and 22%. Moreover, H₂O₂ content decreased, while lipid peroxide MDA accumulation increased. Transcriptomic analysis revealed a significant inhibition of the expression of the key genes NPR1 and ACS6 in the SA/ET signaling pathway and a decrease in the expression of disease-related genes ERF1 and PR1. This study established a new paradigm for the study of NLR protein-mediated plant immune mechanisms and provided target genes for molecular breeding of disease resistance in maize. Overall, these findings provide the first evidence that ZmNLR-7 confers resistance to southern corn leaf blight in maize by synergistically regulating ROS homeostasis, SA/ET signal transduction, and downstream defense gene expression networks. Full article

Tomato (Solanum lycopersicum) is a globally important crop, and enhancing its fruit quality and phenotypic traits is a key objective in modern breeding. This study investigates the role of the LEAFY-COTYLEDON1-LIKE4 (L1L4), an NF-YB subunit of the nuclear factor Y (NF-Y) transcription factor, in tomato fruit development using RNA-sequencing data from zinc-finger nuclease (ZFN)-targeted disruption lines. Differential gene expression (DEG) analyses of two independent l1l4 mutant lines compared to the wild-type line revealed significant alterations in key metabolic pathways and regulatory networks that are implicated in fruit ripening. Specifically, L1L4 disruption impacted the genes and pathways related to the fruit’s color development (carotenoid and flavonoids), texture (cell wall modification), flavor (sugar and volatile organic compound metabolism), and ripening-related hormone signaling. The analyses also revealed multiple differentially expressed histones, histone modifiers, and transcription factors (ERFs, MYBs, bHLHs, WRKYs, C2H2s, NACs, GRAS, MADs, and bZIPs), indicating that L1L4 participates in a complex regulatory network. These findings provide valuable insights into the role of L1L4 in orchestrating tomato fruit development and highlight it as a potential target for genetically improving the fruit quality. Full article

Konjac glucomannan (KGM), derived from Amorphophallus konjac, is increasingly utilized in food and pharmaceutical applications. However, inconsistent KGM production across cultivars jeopardizes its quality and market viability. Lanthanum (La) has been shown to promote KGM levels, but the underlying mechanism remains unclear. In this study, 20~80 mg L⁻¹ La significantly stimulated KGM accumulation compared with the control group. We performed a transcriptome analysis and found 21,047 differentially expressed genes (DEGs), predominantly enriched in carbohydrate and glycan metabolism pathways. A total of 48 DEGs were linked to KGM biosynthesis, with 20 genes (SuSy, INV1/3/5/6, HK1/2, FPK2, GPI3, PGM3, UGP2, GMPP1/4, CslA3~7, CslH2, and MSR1.2) showing significant positive correlations with KGM content. Interestingly, three key terminal pathway genes (UGP1, UGP3, and CslD3) exhibited strong upregulation (log2 fold change > 3). Seven DEGs were validated with qRT-PCR, aligning with the transcriptomic results. Furthermore, 12 hormone-responsive DEGs, including 4 ethylene-related genes (CTR1, EBF1/2, EIN3, and MPK6), 6 auxin-related genes (AUX/IAA1-3, SAUR1-2, and TIR1), and 2 gibberellin-related genes (DELLA1-2), were closely linked to KGM levels. Additionally, the transcription factors bHLH and AP2/ERF showed to be closely related to the biosynthesis of KGM. These results lay the foundation for a model wherein La (Ш) modulates KGM accumulation by coordinately regulating biosynthetic and hormonal pathways via specific transcription factors. Full article

We study a novel Doubly penalized ERror Function regularized Quantile Regression (DERF-QR) in this paper. This is a method of variable selection by ERror Function (ERF) regularization in the linear effects model. We introduce a two-stage iterative algorithm combining the iterative reweighted $L_1$ approach and the alternating direction method of multipliers (ADMM) to estimate the model parameters. Numerical simulations show that by using this method we remove redundant variables effectively and obtain accurate coefficient estimations. Our method outperforms two existing penalized quantile regression methods in various error conditions by comparison. Finally, we apply the methodology in a financial dataset and showcase its practicality. Full article

The APETALA2/ethylene response factor (AP2/ERF) is a class of plant-specific transcription factors, among which the dehydration-responsive element-binding protein (DREB) subfamily has been widely reported to enhance plant resistance to abiotic stresses. A high-temperature-related gene, Apium graveolens DREBA6b (AgDREBA6b; accession number: OR727346), was previously cloned from a heat-tolerant celery variety. In this study, we transformed this gene into Arabidopsis thaliana using an Agrobacterium rhizogenes-mediated method to explore its function. The results showed that overexpressing AgDREBA6b in Arabidopsis thaliana significantly improved plant growth under high-temperature stress (38 °C) compared to the dreb mutant and wild-type (WT) plants. The anatomical structure of the leaves revealed that the number and degree of stomatal openings in the overexpressed plants were significantly higher than those in the WT and dreb plants, suggesting that AgDREBA6b enhances stomatal opening. Additionally, the chlorophyll content, chlorophyll fluorescence properties, proline (Pro), malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities were higher in the transgenic plants, indicating better stress tolerance. qPCR analysis showed that four heat tolerance-related genes (AtHSP98.7, AtHSP70-1, AtAPX1, and AtGOLS1) were upregulated in the transgenic plants, with higher expression levels than in WT and mutant plants. This study provides valuable genetic resources for understanding the molecular mechanisms of celery’s heat tolerance and offers insights for breeding heat-tolerant celery varieties. Full article

Melatonin (MT) has been reported to alleviate chilling injury (CI) in postharvest tomato fruit during low-temperature storage. In the present study, the DNA methylation profile changes in the CpG islands of ethylene signaling genes regulated by MT in postharvest tomato fruit during low-temperature storage were detected. The MT treatment increased the content of total soluble solids (TSS) and enhanced the ethylene production of tomato fruit. Moreover, it decreased titratable acidity (TA) content, inhibited the activity of polygalacturonase (PG), and kept the firmness of tomato fruit under low-temperature storage. In the MT-treated tomato fruit, significant changes in DNA methylation of CpG island of SlACS10, LeCTR1, LeEIN3, SlERF-A1, and LeERT10 genes were induced; the expression of LeCTR1 was inhibited; and the expression of SlACS10, LeEIN3, and SlERF-A1 genes was increased, by which the ethylene signaling might be influenced and the CI was alleviated. The present results provide evidence that the CI of postharvest tomato fruit alleviated by MT might be related to the changes in DNA methylation of ethylene-signaling genes. Full article

Background: γ-Aminobutyric acid (GABA) is a non-proteinogenic amino acid with key roles in plant metabolism, stress responses, and fruit nutritional quality. In tomato (Solanum lycopersicum), GABA levels are dynamically regulated during fruit development but decline in the late ripening stages. Methods: To enhance GABA accumulation, we used CRISPR/Cas9 to edit the calmodulin-binding domain (CaMBD) of SlGAD2 and SlGAD3, which encode glutamate decarboxylases (GADs). The resulting truncated enzymes were expected to be constitutively active. We quantified GABA content in leaves and fruits and performed transcriptomic analysis on edited lines at the BR+7 fruit stage. Results: CaMBD truncation significantly increased GABA levels in both leaves and fruits. In gad2 sg1 lines, GABA levels increased by 3.5-fold in leaves and 3.2-fold in BR+10 fruits; in gad3 sg3 lines, increases of 2.8- and 2.5-fold were observed, respectively. RNA-seq analysis identified 1383 DEGs in gad2 #1−5 and 808 DEGs in gad3 #3−8, with 434 DEGs shared across both lines. These shared DEGs showed upregulation of GAD, GABA-T, and SSADH, and downregulation of stress-responsive transcription factors including WRKY46, ERF, and NAC. Notably, total free amino acid content and fruit morphology remained unchanged despite elevated GABA. Conclusions: CRISPR/Cas9-mediated editing of the CaMBD in SlGAD genes selectively enhances GABA biosynthesis in tomato without adverse effects on development or fruit quality. These lines offer a useful platform for GABA-centered metabolic engineering and provide insights into GABA’s role in transcriptional regulation during ripening. Full article

Polyembryonic maize, capable of producing multiple seedlings from a single kernel, holds great potential value in agricultural and industrial applications, but the seedling quality needs to be improved. In this study, seedlings of two waxy maize (Zea mays L. sinensis Kulesh) inbred lines, D35 (a polyembryonic line with twin shoots) and N6110 (single-shoot), exhibited similar relative growth rates during 1 to 5 days post-germination. UPLC-MS/MS profiling of 3- to 5-day-old seedling roots and shoots revealed that H2JA, MeSAG, and IAA-Val-Me were the common differentially accumulated metabolites (DAMs) of the 3-day-old vs. 5-day-old seedlings of D35 and N6110 in the same tissues, and MeSAG, tZ9G, cZROG, and DHZROG were identified in D35 vs. N6110 across the same tissues and the same periods. RNA-seq analyses showed various processes involved in seedling development, including DNA replication initiation, rhythmic processes, the cell cycle, secondary metabolic processes, and hormone biosynthetic regulation. The differentially expressed genes (DEGs) between D35 and N6110 were significantly enriched in organic hydroxy compound biosynthetic, alcohol biosynthetic, organic hydroxy compound metabolic, abscisic acid biosynthetic, and apocarotenoid biosynthetic processes. The KEGG-enriched pathways of DAMs and DEGs identified that AUX1, AHP, A-ARR, JAR1, SIMKK, ERF1, and GID2 might be conserved genes regulating seedling growth. The integrated analyses revealed that 98 TFs were potentially associated with multiple hormones, and 24 of them were identified to be core genes, including 11 AP2/ERFs, 4 Dofs, 2 bZIPs, 2 MADS-box genes, 2 MYBs, 1 GATA, 1 LOB, and 1 RWP-RK member. This study promotes a valuable understanding of the complex hormone interactions governing twin-shoot seedling growth and offers potential targets for improving crop establishment via seedling quality. Full article

Poplar (Populus spp.) is an economically and ecologically important temperate tree species known for its rapid growth. Clonal propagation has facilitated genetic advancements, but it remains challenging due to substantial variations in rooting capacity among poplar species and clones. Poplar clones were divided into two groups based on their rooting ability (high or low), and their transcriptome was analyzed for 3 weeks following stem-cutting propagation to investigate the rooting mechanisms of a hybrid of two fast-growing poplar species (Populus alba × P. tomentiglandulosa). The root length and area of the high-rooting group were 668.7% and 198.4% greater than those of the low-rooting ability group, respectively (maximum p < 0.001). Compared to week 0, genes involved in auxin signaling, cell wall organization, and secondary metabolite biosynthesis were consistently upregulated at 1, 2, and 3 weeks after planting, respectively. The expression of genes associated with cell wall differentiation and flavonoid biosynthesis was greater in the high- than in the low-rooting group at week 2. MYB and AP2/ERF transcription factors, which regulate flavonoid biosynthesis, as well as chalcone isomerase, a key enzyme in early flavonoid biosynthesis and root formation, were upregulated in the high-rooting group. The flavonoid biosynthesis pathway is important in rooting after stem cutting of Populus alba × P. tomentiglandulosa hybrids. Full article