The combined transcriptome and metabolome analysis revealed that plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched in resistant rice varieties, providing valuable information on the molecular mechanisms by which rice defends against U. virens infection.
Abstract
Rice false smut caused by Ustilaginoidea virens is a major fungal disease of rice in rice-growing regions throughout the world. However, the key genes and key metabolites related to U. virens resistance in rice remain unclear. Here, we used transcriptomics and metabolomics to determine the gene expression and metabolite accumulation changes in rice at 5, 7, and 9 d after inoculation with U. virens. By comparing the transcriptomes of IR27 (resistant cultivar) and 9311 (susceptible cultivar) spikelets, variable transcriptional responses under control and infection conditions were revealed. In total, 11,235 and 13,453 differentially expressed genes (DEGs) were identified in IR27 and 9311, respectively. The results of Kyoto Encyclopedia of Genes and Genomes and co‑expression analyses showed that the DEGs involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction responded to disease resistance. Several WRKY transcription factors were also differentially regulated in the resistant and susceptible cultivars. The metabolome analysis identified 343 and 303 differentially accumulated metabolites in IR27 and 9311, respectively, including salicylic acid, jasmonic acid, gibberellin, d-pantothenic acid, and p-coumaric acid. Many of these are primarily involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways. Furthermore, the combined transcriptome and metabolome analysis revealed that plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched in resistant rice varieties. Therefore, these results provide valuable information on the molecular mechanisms by which rice defends against U. virens infection, and they will facilitate the development of disease‑resistant rice cultivars.
Rice (Oryza sativa L.) is a crucial global cereal crop, severely threatened by the brown planthopper (BPH), which causes extensive damage through direct feeding and virus transmission. To elucidate the resistance mechanism mediated by the BPH-resistance gene Bph6, metabolic responses to BPH infestation were compared between the resistant rice line G6 and the susceptible cultivar Nipponbare using LC-MS-based metabolomics combined with quantitative real-time PCR analysis. The Bph6 gene conferred both antixenotic and antibiotic resistance to BPH. A total of 673 metabolites were identified across all samples. BPH infestation induced more pronounced metabolic alterations in susceptible Nipponbare than in the resistant G6 line. Compared with Nipponbare, G6 exhibited a more coordinated defense response characterized by enhanced accumulation of amino acid-derived metabolites, flavonoids, and serotonin-associated compounds. Consistently, the expression levels of key biosynthetic genes, including TDC and CYP71A1 involved in serotonin biosynthesis and CHS and F3H associated with flavonoid biosynthesis, were significantly upregulated in G6. These findings demonstrate that Bph6 mediates a more stable and effective defense metabolism in rice through coordinated regulation of primary and secondary metabolism, particularly flavonoid- and serotonin-related pathways.
Jiajiao Zhang, Qian Zhang, Yinhua Ma et al.· Functional Plant Biology· 0 citations
Tobacco is a model plant as well as an important economic crop. Black shank disease, caused by Phytophthora nicotianae, severely undermines tobacco yield and quality, yet the molecular basis of differential cultivar resistance remains incompletely understood. Here, we compared the resistant cultivar, 'Xiangyan 7' (X7) and the susceptible cultivar 'Honghuadajinyuan' (HD), after inoculation with P. nicotianae race 0. Disease evaluation showed that X7 had a significantly lower disease index than HD. Transcriptomic and metabolomic analyses were performed on leaves collected at 0, 1, 2, 4, 8, and 12 days post-inoculation (dpi). RNA-seq identified extensive transcriptional responses in both cultivars; the inter-cultivar differentially expressed gene (DEG) number peaked at 8 dpi with 14,160 DEGs (7057 up-regulated and 7103 down-regulated). Widely targeted metabolomics detected 1092 metabolites, and the inter-cultivar differentially accumulated metabolite (DAM) number peaked at 12 dpi with 355 DAMs (95 up-regulated and 260 down-regulated). Weighted Gene Co-expression Network Analysis (WGCNA) identified 593 hub genes from three resistance-associated modules (Coral3, Lightblue3, and Lavender). Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis revealed that phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, and plant hormone signal transduction were common transcriptional-metabolic pathways enriched in X7, together with early calcium-related signaling in the plant-pathogen interaction pathway. These results suggest that the stronger resistance to P. nicotianae by X7 is associated with rapid coordination of defense-related transcription, phenylpropanoid and flavonoid metabolism, hormone signaling, and suppression of photosynthesis and primary metabolism. Our study provides multi-omics resources and candidate genes, including Nitab4.5_0000101g0110, Nitab4.5_0000101g0120, Nitab4.5_0001915g0140, and Nitab4.5_0002942g0040, for improving tobacco resistance to black shank disease.
Guo Li, Changjiang Zhang, Bei Yu et al.· Plant physiology and biochem...· 0 citations
Tomato mottle mosaic virus (ToMMV) is an emerging tobamovirus causing severe losses in tomato production. To elucidate host resistance mechanisms, we compared two tomato cultivars with contrasting responses to ToMMV using integrated transcriptomic, metabolomic, and functional analyses. The resistant line (R) carried resistance gene Tm‑2² at extremely low levels, while the susceptible line (S) did not; both lines highly expressed susceptibility gene tm-2. R plants exhibited minimal viral accumulation and maintained chlorophyll levels, whereas S plants showed high viral load and chlorophyll degradation. Multi-omics revealed that in S, ToMMV primarily disrupted chlorophyll biosynthesis and photosynthesis, while activating multiple defense pathways, including plant-pathogen interaction, phenylpropanoid/flavonoid biosynthesis, and MAPK signaling. In R, a broader activation of plant-pathogen interaction and phosphatidylinositol signaling pathways was observed, alongside early upregulation of SlSN2. The abundance of phenolic acids, notably caffeic acid, ferulic acid, and sinapic acid, was significantly higher in R than in S. Integrated transcriptomic and metabolomic analyses showed that both differential genes and metabolites were co-enriched in the phenylpropanoid biosynthesis pathway. Functional assays demonstrated that SlSN2 overexpression suppressed ToMMV accumulation and infection, likely via enhanced lignin biosynthesis. These findings suggest a potential role for SlSN2 in contributing to ToMMV resistance, independent of the known Tm‑2² pathway. This work identifies SlSN2 as a candidate factor for further evaluation in the prevention of ToMMV.
The results suggest that the flavonoid biosynthesis pathway in potatoes plays a key role in responding to PVS infection and promotes the selection and utilization of disease-resistant varieties.
Kuo Wu, Xia Liu, Yu Li et al.· Frontiers in Microbiology· 0 citations
BACKGROUND
Natural plant metabolites, such as flavonoids and lignin, exhibited safe and environmentally friendly roles in defending against pathogen attack. However, their functional roles in the interaction between wheat and Puccinia triticina (Pt) remained poorly characterized.
RESULTS
In this study, we integrated transcriptomic and quasi-targeted metabolomic analyses to systematically characterize differentially expressed genes (DEGs) and metabolites associated with the compatible and incompatible interactions between wheat and Pt. In the wheat-Pt interaction system, a total of 1,242 metabolites were identified, predominantly classified into amino acids and derivatives, flavonoids, and related compound classes. In the flavonoid and lignin biosynthesis-related pathways-namely, Flavonoid biosynthesis and Phenylpropanoid biosynthesis-significant differences were observed in both the accumulation levels of key metabolites and the expression of genes associated with their biosynthetic pathways. Notably, in the incompatible interaction, the expression of TaCAD, a gene implicated in syringyl lignin (S-lignin) biosynthesis, was significantly up-regulated. Gene regulatory network (GRN) analysis further suggested that transcription factors (TFs) including ERF, LBD, BBR-BPC, and C2H2 may play critical regulatory roles in mediating wheat resistance to leaf rust. Moreover, the key flavonoid hesperetin was markedly enriched in the incompatible combination (TcLr24_120 h vs. TcLr24_0 h). Exogenous application of hesperetin significantly inhibited urediniospores germination in vitro. More importantly, it significantly reduced disease severity of wheat leaf rust in vivo.
CONCLUSIONS
These findings indicated that hesperetin may serve as a potential defense compound in wheat during the early stages of leaf rust infection, providing crucial insights for developing novel natural products and a theoretical foundation for genetic improvement in disease-resistant wheat breeding.
Yaqiong Zhao, Weiwei Gong, Ruimin Wang et al.· BMC Genomics· 0 citations
These findings provide the first comprehensive evidence that alkaloid metabolism, particularly the isoquinoline alkaloid pathway, are transcriptionally and metabolically reprogrammed during blister blight infection, suggesting a potential role in tea’s defense against this pathogen.
Yanglongyu Chen, Ping Li, Yuqing Ma et al.· Frontiers in Plant Science· 0 citations