Search Results (580)

Background/Objectives: Sweet potato is a tropical and subtropical crop and its growth and yield are susceptible to low-temperature stress. However, the molecular mechanisms underlying the low temperature stress of sweetpotato are unknown. Methods: In this work, combined transcriptome and metabolism analysis was employed to investigate the low-temperature responses of two sweet potato cultivars, namely, the low-temperature-resistant cultivar “X33” and the low-temperature-sensitive cultivar “W7”. Results: The differentially expressed metabolites (DEMs) of X33 at different time stages clustered in five profiles, while they clustered in four profiles of W7 with significant differences. Differentially expressed genes (DEGs) in X33 and W7 at different time points clustered in five profiles. More DEGs exhibited continuous or persistent positive responses to low-temperature stress in X33 than in W7. There were 1918 continuously upregulated genes and 6410 persistent upregulated genes in X33, whereas 1781 and 5804 were found in W7, respectively. Core genes involved in Ca²⁺ signaling, MAPK cascades, the reactive oxygen species (ROS) signaling pathway, and transcription factor families (including bHLH, NAC, and WRKY) may play significant roles in response to low temperature in sweet potato. Thirty-one common differentially expressed metabolites (DEMs) were identified in the two cultivars in response to low temperature. The KEGG analysis of these common DEMs mainly belonged to isoquinoline alkaloid biosynthesis, phosphonate and phosphinate metabolism, flavonoid biosynthesis, cysteine and methionine metabolism, glycine, serine, and threonine metabolism, ABC transporters, and glycerophospholipid metabolism. Five DEMs with identified Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were selected for correlation analysis. KEGG enrichment analysis showed that the carbohydrate metabolism, phenylpropanoid metabolism, and glutathione metabolism pathways were significantly enriched and played vital roles in low-temperature resistance in sweet potato. Conclusions: These findings contribute to a deeper understanding of the molecular mechanisms underlying plant cold tolerance and offer targets for molecular breeding efforts to enhance low-temperature resistance. Full article

Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. Using RNA sequencing (RNA-seq), we assembled 169,652 unigenes and identified differentially expressed genes (DEGs) at each stage compared to G0, increasing from 1708 in G1 to 10,250 in G4. Functional enrichment analysis revealed upregulation of genes associated with cell wall organization, glucan metabolism, and Photosystem II assembly. Key genes involved in cell wall remodeling, including cellulose synthase (CESA), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (COMT), and peroxidase (POD) showed progressive activation during germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed dynamic regulation of phenylpropanoid and flavonoid biosynthesis, photosynthesis, carbohydrate metabolism, and hormone signaling pathways. Transcription factors such as indole-3-acetic acid (IAA), ABA-responsive element binding factor (ABF), and basic helix–loop–helix (bHLH) were upregulated, suggesting hormone-mediated regulation of dormancy release and seedling development. Physiologically, cytokinin (CTK) and IAA levels peaked in G4, antioxidant enzyme activities were highest in G2, and starch content increased toward later stages. These findings provide new insights into the molecular mechanisms underlying seed germination in C. oleifera and identify candidate genes relevant to rootstock breeding and nursery propagation. Full article

Background/Objectives: Moso bamboo (Phyllostachys edulis), the most widely distributed bamboo species in China, is valued for both its shoots and timber. This species often faces challenges from high-temperature stress. To cope with this stress, Moso bamboo has evolved various adaptive mechanisms at the physiological and molecular levels. Although numerous studies have revealed that a large number of transcription factors (TFs) and genes play important roles in the regulatory network of plant heat stress responses, the regulatory network involved in heat responses remains incompletely understood. Methods: In this study, Moso bamboo was placed in a high-temperature environment of 42 °C for 1 h and 24 h, and transcriptome sequencing was carried out to accurately identify key molecules affected by high temperature and their related biological pathways. Results: Through a differential expression analysis, we successfully identified a series of key candidate genes and transcription factors involved in heat stress responses, including members of the ethylene response factor, HSF, WRKY, MYB, and bHLH families. Notably, in addition to traditional heat shock proteins/factors, multiple genes related to lipid metabolism, antioxidant enzymes, dehydration responses, and hormone signal transduction were found to play significant roles in heat stress responses. To further verify the changes in the expression of these genes, we used qRT-PCR technology for detection, and the results strongly supported their key roles in cellular physiological processes and heat stress responses. Conclusions: This study not only deepens our understanding of plant strategies for coping with and defending against extreme abiotic stresses but also provides valuable insights for future research on heat tolerance in Moso bamboo and other plants. 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

Hippeastrum, a perennial herbaceous plant belonging to the Amaryllidaceae family, is widely cultivated for its large, vibrant flowers with diverse petal colors, which have significant ornamental and economic value. However, the mechanisms underlying anthocyanin accumulation in Hippeastrum petals remain poorly understood. To fully explore the involved regulation mechanism was significant for the breeding of Hippeastrum and other Amaryllidaceae family plants. In this study, we selected six Hippeastrum cultivars with distinctly different petal colors. We used metabolomic profiling and high-throughput transcriptomic sequencing to assess varied anthocyanin profiles and associated expression of genes in their biosynthetic pathways. Four key anthocyanins were identified: cyanidin, cyanidin-3-O-rutinoside, delphinidin-3-glucoside, and delphinidin-3-rutinoside. Weighted gene co-expression network analysis (WGCNA) correlated the abundance of these four anthocyanins with transcriptomic data, to suggest three regulatory modules. Nine transcription factors families in these modules were identified and some of them were validated using qRT-PCR. Y2H assay isolated some transcription factors interacted with TTG1 (WD40 protein), including MYB3/39/44/306 and bHLH13/34/110, illustrating the possibility of forming MBW complexes. Our study provides a comprehensive characterization of anthocyanin composition. These findings laid a theoretical foundation for future research on the regulatory mechanisms of pigment accumulation and the breeding of Hippeastrum cultivars with novel petal colors. Full article

Floral pigmentation contributes directly to reproductive strategies and fitness by shaping pollinator behaviour, and its regulation therefore represents a critical aspect of flower development. Additionally, it is a major determinant of aesthetic and economic value in the ornamental plant industry. This review explores the genetic, biochemical, and ecological bases of floral colour change, focusing on the biosynthesis and regulation of the three major classes of plant pigments: carotenoids, flavonoids (particularly anthocyanins), and betalains. These pigments, derived from primary metabolism through distinct biosynthetic pathways, define the spatial and temporal variability of floral colouration. We discuss the molecular mechanisms underlying flower colour change from opening to senescence, highlighting pigment biosynthesis and degradation, pH shifts, metal complexation, and co-pigmentation. Additionally, we address the regulatory networks, including transcription factors (MYB, bHLH, and WDR) and post-transcriptional control, that influence pigment production. Finally, we provide a comprehensive survey of angiosperm species exhibiting dynamic petal colour changes, emphasizing how these mechanisms are regulated. Full article

Brain muscle ARNT-like1 (Bmal1) is a transcriptional factor, consisting of basic helix–loop–helix (bHLH) and PER-ARNT-SIM (PAS) domains, that plays a central role in circadian clock activity. However, the precise roles of the BMAL1-PAS domain, a circadian rhythm-regulating structure, remain unexplored in monocytes. Here, we highlight the BMAL1-PAS domain as a key structure in monocyte pleiotropic functions by using human monocytic cell line THP-1. THP-1 cells lacking the BMAL1-PAS-B domain (THP-1#207) abrogated the circadian expression of core clock genes. THP-1#207 cells exhibited less proliferation, glycolysis and oxidative phosphorylation activity, and LPS-induced IL-1β production, but exhibited more production of LPS-induced IL-10 than THP-1 cells. A quantitative proteomics analysis revealed significant expression changes in ~10% metabolic enzymes in THP-1#207 cells compared to THP-1 cells, including reduction in a rate-limiting enzyme hexokinase2 (HK2) in the glycolytic pathway. Importantly, treatment of THP-1 with 2-deoxy-D-glucose (2-DG), an HK2 inhibitor, largely recapitulated the phenotypes of THP-1#207 cells. These findings suggest that the BMAL1-PAS-B domain is an important structure for the regulation of proliferation, cellular energetics, and inflammatory response in THP-1 cells, at least in part, via the control of glycolytic activity. Thus, the BMAL1-PAS-B domain may become a promising pharmacological target to control inflammation. 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

Bract coloration in ornamental plants is a complex trait governed by diverse pigments (chlorophylls, anthocyanins, betalains, and carotenoids), their biosynthetic pathways, and regulatory networks. While previous research has primarily focused on floral pigmentation, studies on bract coloration—particularly in species where bracts serve as the primary ornamental feature—have received less attention until recent advances. This review synthesizes current understanding of bract color diversity, pigment biochemistry, and molecular regulation in key species including Bougainvillea, Euphorbia pulcherrima, Anthurium andraeanum, Curcuma alismatifolia, and Zantedeschia hybrida. Anthocyanins predominantly contribute to red-to-purple hues, while betalains generate red, purple, or yellow coloration through differential accumulation of betacyanins and betaxanthins. Developmental color transitions are mediated by chlorophyll degradation and carotenoid dynamics. The spatiotemporal regulation of pigment accumulation involves coordinated interactions between key structural genes (CHS, DFR, ANS for anthocyanins; DODA, CYP76AD1 for betalains), transcription factors (MYB, bHLH, WRKY), and plant growth regulators (BAP, GA, MeJA). Despite these advances, significant knowledge gaps remain in genetic inheritance patterns, epigenetic regulation, cross-pigment pathway crosstalk, and environmental modulation. Future research directions should integrate multi-omics approaches, wild germplasm resources, and gene-editing technologies to develop novel breeding strategies for bract color improvement. 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

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

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

Background: Pinus massoniana is a significant lipid-producing tree species in China and a susceptible host for both the pine wood nematode and its insect vector, Monochamus alternatus. The basic helix–loop–helix (bHLH) family of transcription factors play a crucial role in responding to both biotic and abiotic stresses. However, the role of bHLH in terpene-induced defense in P. massoniana remains poorly studied. Results: Transcriptome sequencing using DNA Nanoball Sequencing (DNBSEQ) and PacBio Sequel platforms was performed, revealing differences in gene expression in P. massoniana branch under the simulated feeding treatment of methyl jasmonate (MeJA) spraying. Fifteen bHLH genes were cloned and analyzed, among which eight highly upregulated PmbHLH genes showed similar temporal expression after MeJA treatment and M. alternatus adult feeding. Five highly upregulated bHLH genes with nuclear localization were highly expressed in P. massoniana after M. alternatus feeding and interacted with the promoter of the terpene synthase gene Pm TPS (−)-α-pinene, confirming their involvement in the defense response of P. massoniana against the M. alternatus adult feeding. Conclusions: Our results unveil the temporal changes and the regulation of the induced defense system in P. massoniana mediated by both MeJA signaling and M. alternatus feeding treatment. The potential application for transgenic experiments and the breeding of resistant species in the future were discussed. Full article

Maize (Zea mays L.) is one of the most important food crops. Salt stress can hinder crop growth and development, but the molecular mechanisms underlying maize’s response to salt tolerance remain unclear. In this study, we conducted comparative transcriptome, metabolome, and physiological analyses of a salt-tolerant maize inbred line (J1285) subjected to different NaCl concentrations during the seedling stage. The results demonstrated that, with increasing salt concentration, seedling growth parameters and antioxidant enzyme activities (SOD, POD, CAT) exhibited initially increases before subsequently decreasing, peaking at 50–150 mmol/L. Transcriptome data analysis revealed that the experimental groups subjected to 50, 100, 150, and 200 mmol/L treatments had 375, 1043, 2504, and 2328 differentially expressed genes (DEGs) compared to the control group, respectively. Additionally, through GO and KEGG analysis, we found that the DEGs were primarily enriched in the MAPK signaling pathway and plant hormone signal transduction, especially the abscisic acid (ABA) signaling pathway, both of which play instrumental roles in orchestrating the maize response to salt-induced stress. Transcription factors involved in the salt stress response, including WRKY, TIFY, bZIP, and bHLH, were identified. Metabolomic data analysis revealed that the experimental groups subjected to 50, 100, 150 and 200 mmol/L treatments had 44, 335, 278, and 550 differentially expressed metabolites (DEMs) compared to the control group, respectively. The DEMs were mainly enriched in metabolic pathways and the biosynthesis of secondary metabolites. Transcriptomics and metabolomics combined analysis were performed on J1285 seedling leaves, and it was found that the co-enrichment pathways included starch and sucrose metabolism, linoleic acid metabolism, α-linolenic acid metabolism, phenylpropanoid biosynthesis pathway, etc. Collectively, these results will aid in identifying resistance genes and elucidating the molecular mechanisms underlying salt tolerance for maize. Full article

Pea (Pisum sativum L.) is a significant source of dietary protein, starch, fiber, and minerals, offering health benefits and serving as both a green vegetable and dry grain. The pigment contents in pea pods with different colors and related genes are still unclear. We conducted an integrated transcriptome and metabolome analysis on three cultivars, including QiZhen (QZ) with green immature pods, FengMi (FM) with yellow immature pods, and ZiYu (ZY) with purple immature pods, to identify the key genes and metabolites involved in anthocyanin accumulation. ZY showed the highest total anthocyanin content compared with FM and QZ. Subsequent quantification revealed that four metabolites, including Delphinidin-3-O-galactoside, Delphinidin-3-O-(6″-O-xylosyl)glucoside, Cyanidin-3-O-galactoside, and Pelargonidin-3-O-(xylosyl)glucoside, were the most highly accumulated in the ZY cultivar, suggesting their role in the purple pigmentation of ZY pea pods. There were 49 differentially accumulated anthocyanidins in ZY vs. FM, 43 differentially accumulated anthocyanidins in ZY vs. QZ, and 21 differentially accumulated anthocyanidins in FM vs. QZ. These findings highlight the importance of the type and concentration of anthocyanin compounds, especially those based on delphinidin, cyanidin, and pelargonidin, in the development of purple pea pods. The transcriptomic analysis revealed that certain anthocyanin biosynthetic genes were expressed at higher levels in ZY than in FM and QZ. In ZY, the higher expression levels of five key genes (PAL, 4CL, CHS, F3H, and UFGT) resulted in elevated anthocyanin content compared to FM and QZ. Furthermore, the BSA-seq analysis identified a candidate region associated with purple color in pea pods, which is located on chromosome 6 and contains 21 DEGs. Sequence variation in KIW84_061698, which encodes a bHLH transcription factor, was identified as the key candidate gene controlling anthocyanin content. This study clarifies the molecular mechanisms behind pea pod coloration and identifies potential genetic engineering targets for breeding anthocyanin-rich sugar snap peas. Full article