Search Results (122)

Cinnamomum camphora is an ecologically and economically significant species, highly valued for its essential oil production and environmental benefits. Although a tissue culture system has been established for C. camphora, large-scale propagation remains limited due to the inconsistent formation of adventitious roots (ARs). This study investigated AR formation from callus tissue, focusing on associated physiological changes and gene expression dynamics. During AR induction, contents of soluble sugars and proteins decreased, alongside reduced activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and polyphenol oxidase (PPO). Levels of indole-3-acetic acid (IAA) and abscisic acid (ABA) decreased significantly throughout AR formation. Zeatin riboside (ZR) levels initially declined and then rose, whereas gibberellic acid (GA) levels displayed the opposite trend. Comparative transcriptomic and temporal expression analyses identified differentially expressed genes (DEGs), which were grouped into four distinct expression patterns. KEGG pathway enrichment indicated that 67 DEGs are involved in plant hormone signaling pathways and that 38 DEGs are involved in the starch and sucrose metabolism pathway. Additionally, protein–protein interaction network (PPI) analysis revealed ten key regulatory genes, which are mainly involved in auxin, cytokinin, GA, ABA, and ethylene signaling pathways. The reliability of the transcriptome data was further validated by quantitative real-time PCR. Overall, this study provides new insights into the physiological and molecular mechanisms underlying AR formation in C. camphora and offers valuable guidance for optimizing tissue culture systems. Full article

Dunaliella salina, a unicellular and eukaryotic alga, has been found to be one of the most salt-tolerant eukaryotes with a wide range of practical applications. To elucidate the underlying molecular mechanisms of D. salina in response to salinity stress, we performed transcriptome sequencing on samples under different stress conditions. A total of 82,333 unigenes were generated, 4720, 1111 and 2611 differentially expressed genes (DEGs) were identified under high salt stress, oxidative stress and hypertonic stress, respectively. Our analysis revealed that D. salina responds to salinity stress through a complex network of molecular mechanisms. Under high salt stress, starch degradation is regulated by AMY (α-amylase) and PYG (glycogen phosphorylase) with alternative expression patterns. This process is hypothesized to be initially constrained by low ATP levels due to impaired photosynthesis. The clustering analysis of DEGs indicated that starch and sucrose metabolism, as well as glycerol metabolism, are specifically reprogrammed under high salt stress. Glycerol metabolism, particularly involving GPDHs, plays a crucial role in maintaining osmotic balance under salinity stress. Key glycerol metabolism genes were up-regulated under salinity conditions, indicating the importance of this pathway in osmotic regulation. The G3P shuttle, involving mitochondrial GPDHs (c25199_g1 and c23777_g1), contributes to redox imbalance management under high salt, oxidative and hypertonic stresses. Notably, c23777_g1 is involved in the G3P shuttle under high salt, oxidative and hypertonic stresses, while c25199_g1 is specifically induced by hypertonic stress. The R2R3-MYB gene (c23845_g1) may respond to different effects of salinity stress by regulating the transcription of ROS-related genes. Our study provides a detailed understanding of the molecular responses of D. salina to salinity stress. We reveal the critical roles of starch and sucrose metabolism, glycerol metabolism and transcription factors in the D. salina adaptation to salinity. Full article

Background: F. hirta vahl is a famous Chinese medicinal plant. The root is the main organ accumulating bioactive compounds, and its development is directly related to the yield and quality of the harvested F. hirta. However, the molecular mechanisms underlying the bioactive compound biosynthesis occurring during the root development of F. hirta are unknown. Method: Transcriptome and widely targeted metabolome analyses were performed to investigate gene expression and metabolite variation during the development of F. hirta taproots. Results: A total of 3792 differentially expressed genes (DEGs) were identified between the one- and three-year-old F. hirta taproots; they are related to circadian rhythm–plant, phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant–pathogen interaction pathways. In total, 119 differentially accumulated metabolites (DAMs) were identified between the one- and three-year-old F. hirta taproots, including flavonols, phenolic acids, and coumarins compounds. Integrative transcriptome and metabolome analyses revealed a significant correlation between 172 DEGs and 21 DAMs; they were predominantly enriched for processes associated with phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and stilbenoid, diarylheptanoid, and ginerol biosynthesis. In addition, 26 DEGs were identified to be significantly correlated with the DAMs that accumulated in the phenylpropanoid biosynthesis pathway, and these DEGs may be the key genes for the biosynthesis of F. hirta active compounds. Conclusions: The phenylpropanoid biosynthesis pathway plays a dual role in both development and bioactive compound synthesis in F. hirta taproots. These findings provide a molecular regulatory network in the relationships between F. hirta taproot development and the accumulation of secondary metabolites. The identification of candidate genes and pathways provides a genetic resource for quality control and future molecular breeding in F. hirta. Full article

Tibetan hulless barley (qingke) grains are becoming more popular because of their high nutritional benefits. Comparative metabolomics and proteomics analyses of qingke grains (at 16, 20, 36, and 42 days after flowering) were conducted to explore the metabolic dynamics during grain filling and compare the differences in quality among three different varieties, Dulihuang, Kunlun 14, and Heilaoya. A total of 728 metabolites and 4864 proteins were identified. We first found that both the metabolite and protein profiles were more closely associated with the grain developmental stage in each cultivar than across different stages in a single cultivar. Next, we focused on the energy metabolism and biosynthesis pathways of key quality components, such as flavonoids, starch, and β-glucans in qingke grains. Quantitative analysis revealed significant variation in the abundance of cellulose synthase-like enzyme (CslF) among the three cultivars. Notably, Heilaoya displayed substantially lower CslF6 levels at 36 and 42 DAF than Kunlun 14 and Dulihuang did. These observed differences in CslF6 abundance may represent a key regulatory mechanism underlying the distinct β-glucan biosynthesis patterns among the three cultivars. Collectively, our results enhance the understanding of metabolic networks involved in qingke grain development and serve as a foundation for advancing breeding studies. Full article

Soybean [Glycine max (L.) Merr.] is a globally significant crop that provides essential meal protein and vegetable oil for human consumption. The protein content in soybean seeds is a critical factor that affects nutrition regarding human dietary needs as well as livestock feed. Therefore, identifying the key genes that affect the soybean seed protein content is one of the major goals in soybean research. To identify candidate genes and related pathways involved in soybean seed storage protein during seed development, an RNA-seq analysis was conducted in two soybean varieties that differ in protein content. A series of pathways related to seed protein metabolism, including “Photosynthesis”, “TCA cycle”, and “Starch and sucrose metabolism” pathways, were identified through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Seven candidate genes exhibiting two different gene regulation patterns were identified, six of which are directly related to the seed storage protein pathway, and one of which is related to the carbon binding pathway. An integrated analysis of transcriptomic and candidate gene expression trend suggested that 40 days after flowering (DAF) might be a crucial period for seed protein accumulation in soybean. Through a Weighted Gene Co-expression Network Analysis (WGCNA), two modules and two novel hub genes were found, which may be highly correlated with seed protein development. These findings might be valuable for a complete understanding of the genetic basis of seed protein content and lay a theoretical foundation for future gene functional identification and breeding efforts in soybean. Full article

To investigate the role of potassium in the regulation of potato growth, dynamic changes in starch–sugar metabolism, and processing quality. In this study, “Gannong Potato No. 9” was used as the test material, and five potassium concentration treatments of 0, 9.4, 23.5, 28.5, and 37.6 mmol/L were set. The results showed that moderate application of potassium (23.5 mmol/L) significantly enhanced plant height, stem thickness, and tuber yield. It also promotes starch accumulation in all tissues and reduces sucrose, fructose, and glucose content, thus optimizing processing quality. Dynamic analyses showed that potassium affects carbohydrate transport and partitioning among tissues by regulating the direction of carbon partitioning and the rate of conversion. Correlation analysis confirmed the synergistic effect of starch–sugar metabolism among tissues, forming a spatio-temporally linked carbon allocation network. This study reveals the pivotal role of potash in potato starch–sugar metabolism and provides a theoretical basis for precision potassium application and quality improvement. Full article

Dendrobium officinale holds significant value as a traditional medicinal plant, with its stems serving as the primary medicinal component and polysaccharides acting as the key active ingredients. To systematically analyze the biosynthetic pathways of polysaccharides and identify key genes involved in polysaccharide synthesis, this research assessed the water-soluble polysaccharide content and conducted transcriptome sequencing on stem tissues of D. officinale at different developmental stages. The findings revealed that the water-soluble polysaccharide level in D. officinale stems exhibited an increasing trend followed by a decrease, reaching its peak before flowering. Transcriptome analysis identified 5764, 6408, 4477, and 3809 differentially expressed genes (DEGs) in groups S1 vs. S2, S2 vs. S3, S3 vs. S4, and S4 vs. S5, respectively. The Kyoto Encyclopedia of Genes and Genomes Enrichment Analysis (KEGG) demonstrated that the DEGs in the S1 vs. S2, S2 vs. S3, and S3 vs. S4 groups were enriched in the starch and sucrose metabolism pathways. Based on the transcriptome sequencing results, expression heat maps of genes correlated with the polysaccharide synthesis pathways of D. officinale clearly showed changes in the expression of polysaccharide synthesis-related genes at five stages. Using weighted gene co-expression network analysis (WGCNA), three co-expression modules were identified, showing a significant positive correlation with fluctuations in the water-soluble polysaccharide content. From the light blue module with the highest correlation coefficient, 15 key genes potentially closely related to polysaccharide synthesis were identified. This study provides gene resources for the genetic improvement of D. officinale and detailed reference data for further elucidating the molecular mechanisms of polysaccharide biosynthesis. Full article

Daqu, a crucial fermentation starter for Chinese Baijiu, develops distinct microbial and physicochemical profiles depending on fermentation temperature, which significantly influence enzymatic activity and flavor formation. While high-temperature (HT-Daqu, 65 °C) and medium-temperature (MT-Daqu, 60 °C) variants are known to produce different liquor aromas, systematic comparisons of their microbial and physicochemical dynamics remain limited. This study integrated physicochemical assays (moisture, starch, acidity, enzymatic activity) with 16S rRNA and ITS (Internal Transcribed Spacer) sequencing to analyze HT-Daqu (HQ1–HQ3) and MT-Daqu (MQ1–MQ3) from Sichuan breweries. Results revealed that HT-Daqu exhibited significantly lower moisture (p < 0.05) and starch content (p < 0.05) but higher acidity (p < 0.05) compared to MT-Daqu. Enzymatic activities were generally reduced in HT-Daqu, except for neutral protease. Microbial profiling revealed distinct microbial dynamics between HT-Daqu and MT-Daqu: HT-Daqu harbored thermophilic Bacillus (40–60% relative abundance) with reduced fungal diversity, while MT-Daqu prioritized fungal consortia—Aspergillus dominated MQ1 (78%) and Saccharomyces transiently peaked in MQ2 (35%)—which correlated with enhanced saccharification enzyme activities and esterification potential. Alpha-diversity indices confirmed higher bacterial diversity in HT-Daqu and greater fungal richness in MT-Daqu. Correlation networks highlighted temperature-driven linkages, such as Bacillus positively associating with acidity. These findings elucidate the trade-offs between microbial stress adaptation and metabolic efficiency under different thermal regimes, providing actionable insights for optimizing Daqu production through targeted microbial management and temperature control to enhance liquor quality. Full article

To elucidate the molecular mechanisms that underlie jujube (Ziziphus jujuba) flavor synthesis, we integrated transcriptomic and metabolomic analyses on the ‘Lingwuchangzao’ cultivar across seven developmental stages. Our multi-omics approach detected 750 metabolites, categorized into 11 primary and 35 secondary classes, with K-means clustering revealing significant stage-specific variations in sugars, alcohols, and organic acids. KEGG enrichment analysis identified differentially expressed genes (DEGs) in key metabolic pathways, including carbohydrate metabolism and plant hormone signal transduction, showing dynamic changes during development. Weighted gene co-expression network analysis (WGCNA) further pinpointed gene networks related to starch/sucrose and carbon metabolism, and eight novel genes linked to starch and fatty acid metabolism. Notably, the white ripening stage (BS) emerged as the critical phase for flavor compound accumulation, offering new molecular insights and targets for quality improvement. Full article

Actinidia arguta (A. arguta) is valued for its nutritional richness, but physiological fruit abscission severely limits production efficiency in elite cultivars. To unravel the molecular basis of this process, we compared two cultivars: abscission-prone ‘KL’ and abscission-resistant ‘JL’. During fruit development, ‘KL’ exhibited an earlier decline in auxin (AUX) levels within the fruit abscission zone (FAZ), coupled with persistently higher ethylene (ETH) concentrations and polygalacturonase (PG) activity compared to ‘JL’. Comparative transcriptomics identified abscission-related genes enriched in plant hormone signaling (AUX, ETH, ABA, JA, BR), starch/sucrose metabolism, and photosynthesis pathways. AUX signaling diverged predominantly during early development, while ETH, BR, and JA pathways varied across multiple stages. Exogenous applications of plant growth regulators (ethephon, 2,4-D, methyl jasmonate, and 2,4-epibrassinolide) and transient overexpression of key genes (AaETR1, AaERF035, AaPME68, AaPP2C27, AaMYC1, and AaPMEI10) validated their roles in modulating hormone crosstalk and cell wall remodeling. Overexpression of AaERF035 and AaPME68 likely accelerated abscission by enhancing ETH biosynthesis and pectin degradation, while AaPMEI10 and AaMYC1 potentially delayed abscission via suppression of cell wall-modifying enzymes. This study elucidates the hormonal and transcriptional networks governing fruit abscission in A. arguta, providing insights for targeted breeding and cultivation strategies to mitigate yield loss. Full article

High-density planting is crucial for maximizing the genetic potential of soybean cultivars to achieve higher yields. However, increasing the planting density can lead to the risk of plant lodging. Therefore, the identification of gene loci associated with lodging resistance is considered critical for the development of high-yielding, lodging-resistant soybean cultivars. In this study, 338 natural soybean accessions from the similar latitude were used to identify candidate genes associated with lodging resistance. Based on 9,400,987 SNPs, the soybean population was classified into three subpopulations. Genome-wide association analysis revealed that under planting densities of 300,000 and 150,000 plants/ha, a total of 20 significant SNPs were repeatedly detected under both planting densities, distributed across 14 chromosomes of soybeans. A hotspot region was identified on chromosome 19, from which seven candidate genes were detected. Based on haplotype and gene expression analyses, Glyma.19g212800 (SUS3) and Glyma.19g212700 (GH9B13) were found to be associated with significant phenotypic variations and were identified as candidate genes. RNA-seq analysis showed that DEGs were primarily enriched in the starch and sucrose metabolism pathways. The differential expression of Glyma.19g212800 among soybean haplotypes was further validated by qRT-PCR. By participating in sucrose decomposition and polysaccharide metabolism processes, it regulated cellulose content, thereby affecting the soybean plant lodging. This study facilitated the dissection of genetic networks underlying lodging traits in soybean, which benefits the genetic improvement of high-yield soybean with dense planting. Full article

Desert shrubs play an important role in the stability of arid and fragile desert ecosystems. However, despite their significant ecological importance, limited research has been performed on shrub drought tolerance strategies at the morphological, physiological, and molecular levels. Therefore, this study focused on the typical desert shrub, Calligonum leucocladum, and analyzed its morphology, physiology, and protein expression under two different habitats: moist low-salt and arid low-salt. The results indicate that drought stress inhibited the growth of C. leucocladum, leading to significant reductions in its plant height, base diameter, and crown width by 14.93%, 49.57%, and 48.49%, respectively. Drought stress triggered a 30% decline in stomatal conductance, whereas homeostasis was observed in net photosynthesis, intercellular CO₂, and transpiration. The soluble sugar content significantly increased by 13.43%, while the starch, soluble protein, and proline content significantly decreased by 20.32%, 10.67%, and 55.61%, respectively. In addition, under drought stress, membrane peroxidation products, reactive oxygen species metabolites, and antioxidant enzyme activities significantly increased. Weighted gene co-expression network analysis revealed 40 proteins that were significantly enriched in the photosynthesis and oxidative phosphorylation pathways through KEGG enrichment analysis. In addition, C. leucocladum maintains photosynthetic homeostasis by enhancing PSII repair (PsbE, PsbL, PsbH) and electron transfer chain efficiency (PetD, nad 2, nad 9), thereby compensating for the insufficient carbon dioxide supply caused by stomatal limitation. This study integrated multidimensional data from morphology, physiology, and proteomics to reveal that C. leucocladum drives a coupled network of photosynthesis, antioxidant, and carbon metabolism through chloroplast translation reprogramming. It maintains photosynthetic homeostasis and osmotic balance under a 30% decrease in stomatal conductance, elucidating the cross-scale regulatory strategy of desert shrubs adapting to extreme drought. Full article

Low temperature is a major stress that severely affects tree growth and development. Despite the fact that the molecular mechanisms behind cold tolerance and associated regulatory networks in these trees remain largely unexplored, we conducted a study to examine the overall changes in metabolites and regulatory pathways of Populus ussuriensis kom. when exposed to cold stress, utilizing a comprehensive multi-omics approach. Transcriptomes exposed to cold stress reveal that most of the candidate genes related to the Calvin–Benson–Bassham cycle and flavonoid synthesis were upregulated. Joint analysis revealed that within 6–48 h of low-temperature treatment, differential genes (such as PAL and CHS) in the flavonoid biosynthesis pathway and metabolites (such as quercetin) were significantly upregulated, indicating a positive correlation under short-term stress. However, prolonged treatment (72 h) may trigger metabolic feedback, leading to a decrease in flavonoid content. In addition, the measurements of gas exchange and metabolite assays of P. ussuriensis showed that photosynthetic acclimation led to a change in the sugar accumulation and starch degradation in response to low temperature, indicating that extensive changes occurred due to the cold and improved tolerance in P. ussuriensis. This study provides a new basis for future studies on the molecular mechanism of cold tolerance at the transcriptional and metabolic levels. Full article

Reproduction and breeding are crucial to maintaining abalone aquaculture. Understanding the molecular underpinnings of sexual maturation is essential for advancing knowledge in reproductive biology. However, the molecular mechanisms of gonadal development in abalones remain poorly understood, particularly in microRNA (miRNA)-mediated regulation. Thus, this study conducted a comprehensive transcriptomic analysis of abalone Haliotis discus hannai (H. discus hannai) to identify genes and miRNAs associated with ovarian and testicular discovery. This study identified 685 differentially expressed (DE) genes between the H. discus hannai ovary (DD_ovary) and testis (DD_testis) groups, comprising 479 upregulated and 206 downregulated genes in the DD_ovary. Moreover, 137 miRNAs, including 83 novel and 54 known miRNAs, were detected, with 30 upregulated and 27 downregulated in the DD_ovary compared to the DD_testis. Bioinformatics analysis revealed that these miRNAs regulate key processes such as carbohydrate metabolic processes, kinase and hydrolase activity, and starch and sucrose metabolism, all potentially associated with reproductive traits. Further, key mRNA candidates, including Vitelline envelope sperm lysin receptor (Verl) and Testis-specific serine/threonine-protein kinase (Tssk) 1, and miRNAs such as novel_90 and novel_120, were identified as components of a functional miRNA-mRNA network associated with sexual maturity and sex determination. These key genes were verified using qRT-PCR and fluorescence in situ hybridization (FISH). These transcriptomic and miRNA datasets provide valuable resources for understanding abalone reproductive biology and may support molecular breeding strategies. Full article

Malformed coconut fruit occurrence exhibits dual impacts on agricultural productivity and economic returns, primarily through substantial yield reduction and compromised commercial value resulting from morphological defects. To elucidate the molecular determinants underlying this developmental anomaly, we conducted a systematic investigation integrating physiological profiling and transcriptomic sequencing on pulp tissues from malformed (MF) and normal (NF) coconut fruits. Notably, MF specimens displayed marked depletion in carbohydrate reserves, with soluble sugars (SS), reducing sugars (RS), starch (SH), soluble proteins (SP), and fat (FA) declining by 28.57%, 20.43%, 15.51%, 36.78%, and 50.18%, respectively, compared to NF controls. Conversely, a coordinated upregulation of phytohormones was observed, where indole acetic acid (IAA), abscisic acid (ABA), cytokinin (CK), gibberellic acid (GA), brassinosteroid (BR), jasmonic acid (JA), and salicylic acid (SA) levels increased by 31.82–92.97%, while ethylene (ETH) exhibited a paradoxical 30.09% reduction. Transcriptomic dissection revealed 6370 functionally annotated differentially expressed genes (DEGs), comprising 4235 upregulated and 2135 downregulated transcripts. These DEGs were predominantly enriched in critical pathways including plant hormone signal transduction, flavonoid/phenylpropanoid biosynthesis, and carbohydrate metabolic networks. Particularly noteworthy was the enhanced activity of cell wall remodeling enzymes—cellulase (CEL), polygalacturonase (PG), and pectinesterase (PE)—accompanied by differential expression of nine cell wall-associated gene families (CEL, PE, PG, PEL, URG, UTR, VTC2, EXP, XET/XTH) and eight phytohormone-related gene clusters. Functional stratification analysis further identified key transcriptional regulators, with MYB, ERF/AP2, BHLH, WRKY, bZIP, and MADS transcription factors demonstrating significant expression divergence, suggesting their pivotal regulatory roles in MF pathogenesis. This multi-omics integration not only deciphers the molecular choreography of coconut fruit malformation but also establishes a novel conceptual framework for developmental disorder research in perennial crops. Full article