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Intron retention and down-expression of defense response-related genes together affect the susceptibility of mutants pls4 to rice sheath bligh

ABSTRACT: Pls4 is a gene encoding a β -ketoacyl carrier protein reductase (KAR), which is mainly involved in biological processes such as cell membrane formation. However，the role of pls4 in rice sheath blight remains unclear. Our preliminary studies showed that rice pls4 mutants were highly susceptive to sheath blight in early development stage, and insensitive in adulthood. To explore the role of this gene in the occurrence of rice sheath blight, we compared the transcriptome profiles of rice pls4 mutant and wild-type by RNA-seq. The results showed that, 2569 differentially expressed genes (DEGs), and down-regulated genes were significantly enriched in defense response related biological stress. The expression pattern significantly changed in genes related to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), which were the main two innate immunity pathways in plants. The chitinase-related genes were mainly down-regulated, while both the disease-related genes and the related genes of the WRKY gene family were significantly up-regulated. Furthermore, 467 genes had significantly alternative splicing (AS) events. Among them, intron retention (IR) affected the gene expression levels and functions in vitamin B6 (VB6) metabolism pathway, which was related to sheath blight. This suggested that IR played an important role in sheath blight resistance of mutant pls4. In conclusion, these studies suggested that pls4 might be involved in the biological stress process of sheath blight by DEGs and the fine-tuning of IR, which would provide a molecular basis for the study of rice sheath blight resistance.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE203661 | GEO | 2022/05/27

REPOSITORIES: GEO

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Project description:Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice. The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races. To identify other genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 hours post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively. A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated Differentially expressed Genes), were identified. Based on their functional annotations, the XDGs were assigned to 14 categories some of which encode resistance/defense related proteins and signaling regulators. Interestingly, most signaling-related genes were down-regulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response. Moreover, a number of pathogenesis-related genes were induced at 72 and 120 hpi. Comparison of expression profiles mediated by other resistance genes revealed an interesting common responses in the plant immune system. Comparison analyses also suggest possible overlaps with hormone signaling pathways and with defense systems including basal defense and hypersensitive responses. We investigated the transcriptional characteristics of Xa21-mediated defense responses in rice using whole-genome oligonucleotide microarray, by comparing the expression profiles between incompatible interactions and mock treatments at five time-points and between incompatible and compatible interactions at 4 hours post inoculation. Microarray hybridization at each time point was carried out in three replications including two biological replications and one technological replication. To detect the genes that are significantly regulated and to eliminate those that have inconsistent expression data among replicated experiments, a cutoff of 1.5 fold change and 1.96 for intensity-dependent Z-scores were required in at least two experimental samples.

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Intron retention and down-expression of defense response-related genes together affect the susceptibility of mutants pls4 to rice sheath bligh

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