Integrated Transcriptomic and Metabolomic Analysis Reveals the Mechanism of Gibberellic acid Regulates the Growth and Flavonoid Synthesis in Phellodendron chinense Schneid Seedlings

Galactinol synthase 4 influences plant height by affecting phenylpropanoid metabolism and the balance of soluble carbohydrates in tomato

Plant height is a key trait that significantly influences plant architecture, disease resistance, adaptability to mechanical cultivation, and overall economic yield. Galactinol synthase (GolS) is a crucial enzyme involved in the biosynthesis of raffinose family oligosaccharides (RFOs). It plays a significant role in carbohydrate transport and storage, combating abiotic and biotic stresses, and regulating plant growth and development. The present study employed CRISPR/Cas9 gene-editing technology to create the gols4 mutant in tomato (Solanum lycopersicum), which exhibits a semi-dwarf phenotype. Results showed that glucose, sucrose, myo-inositol, galactinol, and raffinose levels were significantly reduced in the slgols4 mutant, impairing material transport and affecting the balance of soluble carbohydrates. Integration of transcriptomics and metabolomics data indicated not only a decrease in the expression of synthesis genes related to phenylpropanoid biosynthesis but also a significant reduction in the content of lignin and flavonoids, which are byproducts of phenylpropanoid metabolism. This may be a key factor contributing to dwarfism. Overall, these findings provide evidence for the role of SlGolS4 in regulating sugar metabolism and phenylpropanoid metabolism, offering new insights into tomato dwarfing cultivation and germplasm resources.

Intercropping improves the yield by increasing nutrient metabolism capacity and crucial microbial abundance in root of Camellia oleifera in purple soil

Intercropping system influences the endophytic microbial abundance, hormone balance, nutrient metabolism and yield, but the molecular mechanism of yield advantage in Camellia oleifera intercropping with peanut is not clear. In this study, the C. oleifera monoculture (CK) and C. oleifera-peanut intercropping (CP) treatments in purple soil were conducted, and the physicochemical properties, gene expressions, signal pathways and crucial microbial abundances were investigated to reveal the molecular mechanism of the yield advantage of intercropped C. oleifera. The results showed that the intercropping system increased in contents of pigment, carbohydrate, available nitrogen and phosphorus in leaf and root, as well as the abundances of Burkholderia, Ralstonia, Delftia, Pseudoalteromonas and Caulobacter, enhanced the relative expression levels of CoSPS, CoGBE, CoGlgP, CoGBSS/GlgA genes to promote sugar metabolism, decreased the relative expression levels of CoASA, CoTSB, CoPAI, CoTDC and CoCYP71A13 genes for inhibiting IAA biosynthesis and signal transduction, as well as microbial diversity, Fusarium, Albifimbria and Coniosporium abundances in root, ultimately improved the fruit yield of C. oleifera. These findings indicate that intercropping system improves the fruit yield by enhancing the nutrient metabolism capability and crucial microbial abundances in root of C. oleifera in purple soil.

Quantitative Proteomics Analysis of ABA- and GA3-Treated Malbec Berries Reveals Insights into H2O2 Scavenging and Anthocyanin Dynamics

Abscisic acid (ABA) and gibberellic acid (GA3) are regulators of fruit color and sugar levels, and the application of these hormones is a common practice in commercial vineyards dedicated to the production of table grapes. However, the effects of exogenous ABA and GA3 on wine cultivars remain unclear. We investigated the impact of ABA and GA3 application on Malbec grapevine berries across three developmental stages. We found similar patterns of berry total anthocyanin accumulation induced by both treatments, closely associated with berry H2O2 levels. Quantitative proteomics from berry skins revealed that ABA and GA3 positively modulated antioxidant defense proteins, mitigating H2O2. Consequently, proteins involved in phenylpropanoid biosynthesis were downregulated, leading to decreased anthocyanin content at the almost ripe stage, particularly petunidin-3-G and peonidin-3-G. Additionally, we noted increased levels of the non-anthocyanins E-viniferin and quercetin in the treated berries, which may enhance H2O2 scavenging at the almost ripe stage. Using a linear mixed-effects model, we found statistical significance for fixed effects including the berry H2O2 and sugar contents, demonstrating their roles in anthocyanin accumulation. In conclusion, our findings suggest a common molecular mechanism by which ABA and GA3 influence berry H2O2 content, ultimately impacting anthocyanin dynamics during ripening.

Genome-wide profiling of WRKY genes involved in flavonoid biosynthesis in Erigeron breviscapus

The transcription factors of WRKY genes play essential roles in plant growth, stress responses, and metabolite biosynthesis. Erigeron breviscapus, a traditional Chinese herb, is abundant in flavonoids and has been used for centuries to treat cardiovascular and cerebrovascular diseases. However, the WRKY transcription factors that regulate flavonoid biosynthesis in E. breviscapus remain unknown. In this study, a total of 75 EbWRKY transcription factors were predicted through comprehensive genome-wide characterization of E. breviscapus and the chromosomal localization of each EbWRKY gene was investigated. RNA sequencing revealed transient responses of 74 predicted EbWRKY genes to exogenous abscisic acid (ABA), salicylic acid (SA), and gibberellin 3 (GA3) after 4 h of treatment. In contrast, the expression of key structural genes involved in flavonoid biosynthesis increased after 4 h in GA3 treatment. However, the content of flavonoid metabolites in leaves significantly increased at 12 h. The qRT-PCR results showed that the expression patterns of EbWRKY11, EbWRKY30, EbWRKY31, EbWRKY36, and EbWRKY44 transcription factors exhibited a high degree of similarity to the 11 structural genes involved in flavonoid biosynthesis. Protein-DNA interactions were performed between the key genes involved in scutellarin biosynthesis and candidate WRKYs. The result showed that F7GAT interacts with EbWRKY11, EbWRKY36, and EbWRKY44, while EbF6H has a self-activation function. This study provides comprehensive information on the regulatory control network of flavonoid accumulation mechanisms, offering valuable insights for breeding E. breviscapus varieties with enhanced scutellarin content.

Integrated Transcriptomic and Metabolomic Analyses Identify Critical Genes and Metabolites Associated with Seed Vigor of Common Wheat

Seed aging is a common physiological phenomenon during storage which has a great impact on seed quality. An in-depth analysis of the physiological and molecular mechanisms of wheat seed aging is of great significance for cultivating high-vigor wheat varieties. This study reveals the physiological mechanisms of wheat seed aging in two cultivars differing in seed vigor, combining metabolome and transcriptome analyses. Differences between cultivars were examined based on metabolomic differential analysis. Artificial aging had a significant impact on the metabolism of wheat seeds. A total of 7470 (3641 upregulated and 3829 downregulated) DEGs were detected between non-aging HT and LT seeds; however, 10,648 (4506 up and 6142 down) were detected between the two cultivars after aging treatment. Eleven, eight, and four key metabolic-related gene families were identified in the glycolysis/gluconeogenesis and TCA cycle pathways, starch and sucrose metabolism pathways, and galactose metabolism pathways, respectively. In addition, 111 up-regulated transcription factor genes and 85 down-regulated transcription factor genes were identified in the LT 48h group. A total of 548 metabolites were detected across all samples. Cultivar comparisons between the non-aged groups and aged groups revealed 46 (30 upregulated and 16 downregulated) and 62 (38 upregulated and 24 downregulated) DIMs, respectively. Network analysis of the metabolites indicated that glucarate O-phosphoric acid, L-methionine sulfoxide, isocitric acid, and Gln-Gly might be the most crucial DIMs between HT and LT. The main related metabolites were enriched in pathways such as glyoxylate and dicarboxylate metabolism, biosynthesis of secondary metabolites, fatty acid degradation, etc. However, metabolites that exhibited differences between cultivars were mainly enriched in carbon metabolism, the TCA cycle, etc. Through combined metabolome and transcriptome analyses, it was found that artificial aging significantly affected glycolysis/gluconeogenesis, pyruvate metabolism, and glyoxylate and dicarboxylate metabolism, which involved key genes such as ACS, F16P2, and PPDK1. We thus speculate that these genes may be crucial in regulating physiological changes in seeds during artificial aging. In addition, an analysis of cultivar differences identified pathways related to amino acid and polypeptide metabolism, such as cysteine and methionine metabolism, glutathione metabolism, and amino sugar and nucleotide sugar metabolism, involving key genes such as BCAT3, CHI1, GAUT1, and GAUT4, which may play pivotal roles in vigor differences between cultivars.