Search Results (162)

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

Developing early-heading wheat cultivars is an important breeding strategy to utilize light and heat resources, facilitate multiple-cropping systems, and enhance annual grain yield. Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) possesses numerous agronomically beneficial traits for wheat improvement, such as early maturity and resistance to biotic and abiotic stresses. In this study, we found that a cytogenetically stable wheat–P. huashanica 7Ns disomic addition line showed (9–11 days) earlier heading and (8–10 days) earlier maturation than its wheat parents. Morphological observations of spike differentiation revealed that the 7Ns disomic addition line developed distinctly faster than its wheat parents from the double ridge stage. To explore the potential molecular mechanisms underlying the early heading, we performed transcriptome analysis at four different developmental stages of the 7Ns disomic addition line and its wheat parents. A total of 10,043 differentially expressed genes (DEGs) were identified during spike development. Gene Ontology (GO) enrichment analysis showed that these DEGs were linked to the carbohydrate metabolic process, photosynthesis, response to abscisic acid, and the ethylene-activated signaling pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were involved in plant hormone signal transduction (ARF, AUX/IAA, SAUR, DELLA, BRI1, and ETR), starch and sucrose metabolism (SUS1 and TPP), photosynthetic antenna proteins (Lhc), and circadian rhythm (PRR37, FT, Hd3a, COL, and CDF) pathways. In addition, several DEGs annotated as transcription factors (TFs), such as bHLH, bZIP, MADS-box, MYB, NAC, SBP, WRKY, and NF-Y, may be related to flowering time. Our findings reveal spike development-specific gene expression and critical regulatory pathways associated with early heading in the wheat–P. huashanica 7Ns addition line, and provide a new genetic resource for further dissection of the molecular mechanisms underlying the heading date in wheat. Full article

Vanillin, the principal aromatic compound in vanilla, is primarily derived from mature pods of vanilla (Vanilla planifolia Andrews). Although the biosynthetic pathway of vanillin has been progressively elucidated, the specific key enzymes and transcription factors (TFs) governing vanillin biosynthesis require further comprehensive investigation via combining transcriptomic and metabolomic analysis. For this study, V. planifolia (higher vanillin producer) and V. imperialis (lower vanillin producer) were selected. Time-series metabolomics analysis revealed 160–220 days after pollination (DAPs) as the critical phase for vanillin biosynthesis. Combined time-series transcriptome analysis revealed 984 upregulated differentially expressed genes (DEGs) in key periods, 2058 genes with temporal expression, and 4326 module genes through weighted gene co-expression network analysis (WGCNA), revealing six major classes of TFs: No Apical Meristem (NAC), Myb, WRKY, FLOWERING PROMOTING FACTOR 1-like (FPFL), DOF, and PLATZ. These TFs display strong regulatory relationships with the expression of key enzymatic genes, including P450s, COMT, and 4CL. The NAC TF family emerged as central regulators in this network, with NAC-2 (HPP92_014056) and NAC-3 (HPP92_012558) identified as key hub genes within the vanillin biosynthetic gene co-expression network. The findings of this study provide a theoretical foundation and potential target genes for enhancing vanillin production through genetic and metabolic engineering approaches, offering new opportunities for sustainable development in the vanilla industry and related applications. Full article

Madhuca longifolia (M. longifolia), a tropical tree valued for its medicinal, nutritional, and industrial applications, exhibits severe sensitivity to low-temperature stress in subtropical regions, particularly during seedling establishment. To address this challenge, this study systematically identified 109 NAC genes in M. longifolia and characterized their functional roles in cold adaptation via multi-omics analyses. All NAC proteins were hydrophilic. Key members (e.g., MlNAC026, MlNAC077, MlNAC076) were localized in the nucleus. Phylogenetic analysis grouped them with ANAC072 (RD26), a homolog involved in leaf senescence and ABA-regulated cold stress responses. The NAC family expanded primarily through segmental duplication. And low Ka/Ks ratios (<1) indicated purifying selection. Promoter analysis highlighted the prevalence of dehydration-responsive DRE and LTR cis-acting elements. Transcriptomic profiling under cold stress identified five continuous differentially expressed genes (MlNAC026, MlNAC040, MlNAC059, MlNAC077, and MlNAC078) linked to regulatory functions. Homology modeling predicted 3D structures of cold-responsive NAC proteins, and STRING network analysis indicated independent regulatory mechanisms due to the absence of prominent interaction nodes. These findings advance our understanding of NAC-mediated cold tolerance and offer genetic targets to enhance M. longifolia resilience in subtropical climates. Full article

Soil salinization has emerged as a significant global threat to agricultural productivity. Rice is susceptible to salinity stress at the seedling stage. However, the mechanisms underlying rice responses to salinity stress remain incompletely characterized. In this study, we have characterized a transfer DNA (T-DNA) insertion mutant line of rice, designated OsVPS16 (Os12g0594200), to elucidate its functional role in salt stress tolerance. A real-time quantitative PCR (RT-qPCR) analysis revealed that salt stress inhibited the expression of OsVPS16, with the vps16 mutant showing negligible expression levels. A phenotypic analysis showed that the loss of OsVPS16 enhanced primary root elongation, and increased the survival rate to improve salt stress tolerance. Compared to the wild type (DJ), the vps16 mutant accumulated less Na⁺ and more K⁺ in the shoots under salt stress. Furthermore, the vps16 mutant displayed decreased malondialdehyde (MDA) accumulation and enhanced the activities of superoxide dismutase (SOD) and peroxidase (POD) under salt stress. Transcriptomic profiling identified 1236 differentially expressed genes (DEGs) between vps16 and DJ roots under salt stress. A functional enrichment analysis revealed that DEGs were enriched in protein serine/threonine kinase activity, Ca²⁺ signal pathways, and the MAPK signaling pathway. Notably, the up-regulation of critical protein kinases (PKs) and transcription factors (TFs), including OsSRK1, OsCDPK21, and OsNAC45, probably adds to the effect of OsVPS16 mutation to account for salt stress tolerance. Collectively, comprehensive physiological and molecular analyses demonstrated that the loss of OsVPS16 improves rice salt tolerance through multiple mechanisms, including the regulation of K⁺/Na⁺ homeostasis, the modulation of antioxidant enzyme activities, and the transcriptional reprogramming of stress-responsive genes. This study not only elucidates the function of a novel salt stress response gene in rice, but also provides valuable genetic resources for developing salt-tolerant rice cultivars through molecular breeding approaches. Full article

Phytoalexins are specialized metabolites that are synthesized by plants in response to pathogens. A paradigm in transcription factor (TF) biology is that conserved TFs have dedicated roles across plant lineages in regulating specific branches of specialized metabolism. However, the Arabidopsis (Arabidopsis thaliana) NAC family TF ANAC042 (a.k.a. JUNGBRUNNEN1 or JUB1) regulates the synthesis of camalexin, a Trp-derived phytoalexin specifically produced by several Brassicaceae species, whereas its homolog in soybean (Glycine max) regulates the synthesis of glyceollins, which are Phe-derived phytoalexins specific to soybean. The question addressed by this research is whether ANAC042 broadly regulates phytoalexin biosynthetic pathways in Arabidopsis. Using a novel matrix-assisted laser desorption ionization high-resolution mass spectrometry (MALDI-HRMS) method, we found that the Arabidopsis loss-of-function mutant anac042–1 elicited with bacterial flagellin (Flg22) is deficient in lineage-specific Trp- and conserved Phe-derived phytoalexins—namely camalexin and 4-hydroxyindole-3-carbonyl nitrile (4OH-ICN), and pathogen-inducible monolignols and scopoletin, respectively. Overexpressing ANAC042 in the anac042-1 mutant restored or exceeded wildtype amounts of the metabolites. The expression of phytoalexin biosynthetic genes in mutant and overexpression lines mirrored the accumulation of metabolites. Yeast-one hybrid and promoter-reporter assays in Nicotiana benthamiana found that the ANAC042 protein directly binds and activates the promoters of CYP71B15, CYP71A12, and PAL1 genes for the synthesis of camalexin, 4OH-ICN, and pathogen-inducible monolignol/scopoletin, respectively. Our results demonstrate that ANAC042 regulates conserved and lineage-specific phytoalexin pathways in Arabidopsis. The latter suggests that it is an opportunistic TF that has coopted lineage-specific genes into phytoalexin metabolism, thus providing an exception to the current paradigm. Full article

Drought stress is a significant environmental factor that can impede plant growth and ornamental quality. Hemerocallis middendorffii, a drought-tolerant garden plant, has attracted attention for its ornamental value and application prospects. To investigate the molecular mechanism of drought stress resistance of H. middendorffii, this study employed 20% polyethylene glycol (PEG) 6000 to simulate drought stress. Leaves and roots of H. middendorfii were subjected to 24 h treatment and followed by transcriptome sequencing. Analysis revealed 8796 and 3401 differentially expressed genes (DEGs) in leaves and roots. The major biological processes and key molecular pathways activated under drought stress in H. middendorffii were revealed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The focus of this analysis was on the gene expression changes within plant hormone signal transduction pathway. Additionally, drought-associated transcription factor families such as AP2/ERF, WRKY, MYB, bHLH, NAC, and bZIP were identified among DEGs. Furthermore, potential regulatory relationships of the above transcription factors (TFs) with functional genes in the abscisic acid (ABA) and jasmonic acid (JA) signalling pathways were analysed using correlation network prediction. This research establishes the groundwork for subsequent exploration of drought-responsive gene expression and regulatory patterns in H. middendorfii and provides an importance for the systematic study of its drought-resistant molecular mechanism. Full article

Plants constantly encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Phytohormones such as abscisic acid, jasmonic acid, salicylic acid, and ethylene serve as crucial regulators, integrating internal and external signals to mediate stress responses while also coordinating key developmental processes, including seed germination, root and shoot growth, flowering, and senescence. Transcription factors (TFs) such as WRKY, NAC, MYB, and AP2/ERF play complementary roles by orchestrating complex transcriptional reprogramming, modulating stress-responsive genes, and facilitating physiological adaptations. Recent advances have deepened our understanding of hormonal networks and transcription factor families, revealing their intricate crosstalk in shaping plant resilience and development. Additionally, the synthesis, transport, and signaling of these molecules, along with their interactions with stress-responsive pathways, have emerged as critical areas of study. The integration of cutting-edge biotechnological tools, such as CRISPR-mediated gene editing and omics approaches, provides new opportunities to fine-tune these regulatory networks for enhanced crop resilience. By leveraging insights into transcriptional regulation and hormone signaling, these advancements provide a foundation for developing stress-tolerant, high-yielding crop varieties tailored to the challenges of climate change. Full article

Drought stress represents a prevalent environmental challenge that significantly impedes plant growth. The Chinese hog-peanut (Amphicarpaea edgeworthii Benth.), an amphicarpic legume, can produce both aerial seeds (ASs) and subterranean seeds (SSs). However, it is largely unknown whether there are differences between the seedlings from ASs and SSs in response to drought stress. In this study, the 30-day old AS and SS seedlings of A. edgeworthii are subjected to drought stress by withholding watering for five or ten days. Then, we identify the morphological and physio-biochemical characteristics of seedlings from both ASs and SSs under drought stress. Following ten days of drought treatment, the contents of proline (PRO) and malondialdehyde (MDA), the root shoot ratio, and the rate of water loss were significantly increased, whereas the chlorophyll content and the relative water content were significantly decreased in both AS and SS seedlings. Moreover, compared to AS seedlings, SS seedlings accumulated more hydrogen peroxide (H₂O₂) while exhibiting significantly lower peroxidase (POD) and superoxide dismutase (SOD) activities after exposure to ten days of drought stress. These findings indicate that SS seedlings are more susceptible to drought stress. To identify drought-associated genes and reveal the mechanisms underlying drought adaptability in AS and SS seedlings, we performed an RNA-seq-based transcriptomic analysis in AS and SS seedlings exposed to drought stress. We identified 1317 and 2029 differentially expressed genes (DEGs) in AS seedlings five and ten days post-drought treatment, respectively, and 1793 DEGs in SS seedlings ten days post-drought treatment compared to the normal treatment (CK). These DEGs were commonly enriched in response-related GO terms. Furthermore, hundreds of transcription factor (TF) genes were identified among the DEGs in AS and SS seedlings after drought treatment. Notably, the ERF, bHLH, NAC, and C2H2 families were predominant in AS seedlings five days following drought treatment, while the bHLH, ERF, MYB-related, and WRKY families were prevalent in both AS and SS seedlings ten days following drought treatment. These findings suggest that the identified TFs may play crucial roles in the response of AS and SS seedlings of A. edgeworthii to drought stress. Full article

Flowers are one of the most important organs in plants. Their development serves as a key indicator of the transition from vegetative to reproductive growth and is regulated by various internal signals and environmental factors. NAC (NAM, ATAF, CUC) transcription factors (TFs) play a crucial regulatory role in floral organ development; however, research on the analysis and identification of the NAC TF family in Chinese cabbage (Brassica rapa L.) remains limited. In this study, we performed a comprehensive genome-wide analysis of NACs in B. rapa and identified 279 members of the BrNAC gene family. Their physicochemical properties, domain structure, collinearity relation, and cis-regulatory elements were evaluated. Phylogenetic analysis indicates that NAC proteins from Arabidopsis, B. rapa, B. oleracea, and B. nigra can be classified into seven distinct clades. BrNACs exhibit a tissue-specific expression, and nine BrNACs being specifically expressed in the inflorescence. Furthermore, nine flower-related BrNACs were selected for RT-qPCR analysis to validate their expression profiles. BrNAC2s has been cloned to investigate their subcellular localization, and examine the expression patterns of their promoters in Arabidopsis inflorescences. BrNAC2a and BrNAC2c are highly expressed in stamens while BrNAC2b exhibits elevated expression in pistils and pedicel. Collectively, our findings enhance the understanding of the BrNAC family and provide a foundation for future studies on the molecular mechanisms of BrNACs in floral development. Full article

Hydrangea (Hydrangea macrophylla) is distinguished by having sepals instead of real petals, a trait that facilitates color diversity. Floral color is largely predetermined by structural genes linked to anthocyanin production, but the genetic factors determining floral hue in this non-model plant remain unclear. Anthocyanin metabolites, transcriptome, and the CIEL*a*b* hue system were employed to elucidate the biochemical and molecular mechanisms of floral color formation in three hydrangea cultivars: ‘DB’ (deep blue), ‘LB’ (light blue), and ‘GB’ (green blue). UPLC-MS/MS identified 47 metabolites, with delphinidin, cyanidin, malvidin, petunidin, pelargonidin, and peonidin being prominent. Delphinidins were 90% of the primary component in ‘DB’. The dataset identifies 51 and 31 DEGs associated with anthocyanin, flavonoid, and chlorophyll biosynthesis, with CHS, CHI, F3H, F3′5′H, DFR, ANS, BZ1, and 3AT displaying the highest expression in ‘DB’. Notably, DFR (cluster-46471.3) exhibits high expression in ‘DB’ while being down-regulated in ‘LB’ and ‘GB’, correlating with higher anthocyanin levels in floral pigmentation. Comparative analyses of ‘LB’ vs. ‘DB’, ‘DB’ vs. ‘GB’, and ‘LB’ vs. ‘GB’ revealed 460, 490, and 444 differentially expressed TFs, respectively. WRKY, ERF, bHLH, NAC, and AP2/ERF showed the highest expression in ‘DB’, aligning with the color formation and key anthocyanin biosynthesis-related gene expression. The findings reveal the molecular mechanisms behind floral pigmentation variations and lay the groundwork for future hydrangea breeding programs. Full article

Dimocarpus longan Lour. is an evergreen tree of the genus Longan in the Sapindaceae family, native to tropical and subtropical regions. Longan embryonic development is closely related to fruit set and fruit quality. An in-depth study of the mechanism of longan embryonic development could therefore contribute to the development of the longan industry. DIMBOA is the principal compound representing benzoxazinoids (BXs), and is closely linked to auxin biosynthesis and signal transduction. Auxin is one of the crucial hormones for inducing somatic embryogenesis (SE) in plants. Previous research has shown that DIMBOA promotes morphogenesis in the early somatic embryogenesis of longan, but the specific regulatory mechanism has not yet been clarified. To elucidate the molecular mechanism by which DIMBOA affects early somatic embryogenesis in longan, we chose longan embryogenic cultures grown under 0 mg/L DIMBOA as the control group (the check, CK), and longan embryogenic cultures grown under 0.1 mg/L DIMBOA as the treatment group (D) to be analyzed by transcriptomic sequencing. A total of 478 differentially expressed genes (DEGs) are detected in check vs. D, of which 193 are upregulated and 285 are downregulated. These DEGs are significantly enriched in the biosynthetic and metabolic functions of various substances such as vitamin B₆ (VB₆) biosynthesis, phenylpropanoid pathways, and carbohydrate metabolism. DIMBOA affects SE processes in longan via TFs, including MYB, ZF, bHLH, LBD, NAC, WRKY, etc. After DIMBOA treatment, the expression of most of the key genes for IAA synthesis was significantly downregulated, VB₆ content was significantly reduced, and H₂O₂ content was significantly increased. Therefore, it is suggested that DIMBOA directly or indirectly affects the H₂O₂ content through the VB₆ metabolic pathway, thereby regulating the endogenous IAA level to modulate the early SE morphogenesis of longan. Full article

Abscisic acid (ABA) is not only important for plant responses to abiotic stresses, but also plays a key and multifaceted role in plant immunity. In this work, we analyzed the role of ABA in the development of resistance/susceptibility in the wheat (Triticum aestivum L.)–Stagonospora nodorum Berk. pathosystem, which includes the recognition of the necrotic effectors (NEs) of a pathogen by the corresponding wheat susceptibility genes. We studied the interaction of the S. nodorum SnB isolate, which produces two NEs, SnToxA and SnTox3, with three wheat genotypes having different combinations of the corresponding host susceptibility genes (Tsn1 and Snn3-B1). The results of this work on the gene expression and redox status of resistant and sensitive wheat genotypes treated with ABA show that ABA signaling is directed at inducing the resistance of wheat plants to S. nodorum SnB isolate through the activation of the early post-invasive defense genes TaERD15 and TaABI5. The induction of the expression of these genes leads to reactive oxygen species (ROS) accumulation during the early stage of infection, with the subsequent limitation of the pathogen’s growth. In the presence of a compatible interaction of SnTox3–Snn3-B1, ABA signaling is suppressed. On the contrary, in the presence of a compatible interaction of SnToxA–Tsn1, ABA signaling is activated, but the activity of the early post-invasive defense genes TaERD15 and TaABI5 is inhibited, and the expression of the NAC (NAM, ATAF1/2, and CUC2) transcription factor (TF) family genes TaNAC29 and TaNAC21/22 is induced. The TF genes TaNAC29 and TaNAC21/22 in the presence of SnToxA induce the development of the susceptibility of wheat plants to S. nodorum SnB, associated with a decrease in the oxidative burst during the early stage of infection. Thus, our study provides new data on the role of the NEs SnTox3 and SnToxA in manipulating ABA signaling in the development of the susceptibility of wheat to S. nodorum. Deepening our knowledge in this area will be instrumental for developing new strategies for breeding programs and will contribute to the development of environmentally friendly sustainable agriculture. Full article

Brassica napus is a member of the cruciferous family with rich glucosinolate (GSL) content, particularly glucobrassicin (3-indolylmethyl glucosinolate, I3M), that can be metabolized into indole-3-carbinol (I3C), a compound with promising anticancer properties. To unravel the genetic mechanism influencing I3C content in rapeseed seedlings, a comprehensive study was undertaken with a doubled haploid (DH) population. By quantitative trait loci (QTL) mapping, seven QTL that were located on A01, A07, and C04 were identified, with the most significant contribution to phenotypic variation observed on chromosome A07 (11.78%). The genes within the QTL confidence intervals (CIs) include transcription factors (TFs) and glycosyltransferases. After co-expression analysis, GSL-related regulatory network of TFs-targets was constructed and two TFs, BnaA07.ERF019 and BnaA07.NAC92, were identified as possible regulators in GSL biosynthesis. Three IGMT (glucosinolate methyltransferases) genes were found within the CIs that expressed higher in seedlings with more I3C, indicating their roles in I3C synthesis regulation. Molecular docking studies validated the binding capability of I3M to IGMTs, and those within the I3C QTL CIs have the strongest binding energy. These new discoveries offer critical insights into the genetic regulation of I3C content in rapeseed seedlings and establish a foundation for breeding high-I3C rapeseed varieties with potential health-promoting properties. Full article