| Bacterial blight,caused by Xanthomonas oryzae pv.oryzae(Xoo),is a devastating disease in most of the rice growing regions worldwide.Xoo injects the transcriptional activator-like effector TALE protein into the host cell to spread the disease.Among the 42 BB resistance(R)genes,Xa23 is an executor R gene,conferring broad-spectrum disease resistance to all naturally occurring biotypes of Xoo.Identifying the DEGs in resistant and susceptible genotypes of rice,different strains of Xoo,i.e.,PXO99~A,P99M2 and PH,were inoculated into the leaves of CBB23 and JG30 genotypes.PXO99~A is a wild type of Xoo;while P99M2 and PH strains are avrXa23 mutated and without TALE gene,respectively.1.Comparative transcriptomic profiling of two near isogenic lines(NILs),CBB23(harboring Xa23)and JG30(without Xa23),before and after infection of the Xoo strain PXO99~A was done by RNA-Sequencing.After high throughput sequencing,1,645 DEGs were identified between CBB23 and JG30 at different time point.GO analysis categorized the DEGs into the biological process,molecular function and cellular component.KEGG analysis categorized the DEGs into different pathways with the biosynthesis of phenylpropanoids was the most prominent pathway followed by biosynthesis of plant hormones,flavonoid biosynthesis,and glycolysis/gluconeogenesis.Further analysis led to the identification of differentially expressed transcription factors(TFs)and different kinase responsive genes in CBB23 than that in JG30.Besides TFs and kinase responsive genes,DEGs related to ethylene,Jasmonic acid,secondary metabolites were also identified in both genotypes after PXO99~A infection.The data of DEGs are precious resource for future applied breeding programs to combat the Xoo threat.2.CBB23 genotype was inoculated with wild PXO99~A and its mutant,P99M2,to retrieve the differentially expressed genes(DEGs).RNA-Seq analysis retrieved 1,235 DEGs(p-value?0.05)at 12,24,36,and 48 hours of post inoculation(hpi).Gene ontology(GO)analysis classified the DEGs functionally into biological process,cellular component and molecular function.KEGG pathway analysis categorized the DEGs into 11 different pathways,and the ribosome is a prominent pathway.Gene co-expression network analysis identified the clusters of TFs,which may be involved in PXO99~A resistance.Additionally,we retrieved 67 differentially expressed TFs and 26 peroxidase responsive genes which may be involved in disease resistance mechanism.DEGs involved in the host-pathogen interaction,e.g.,signaling mechanism,cell wall and plant hormones were identified.This data would be a valuable resource for researchers to identify the candidate genes associated with Xoo resistance.3.Leaves of JG30 genotype were inoculated with wild PXO99~A and its mutant PH,without any TALE,to retrieve the DEGs having a role in susceptibility.RNA-Seq data analysis showed that 1,143genes were significantly differentially expressed(p-value?0.05)at 12,24,36 and 48 hours of post inoculation(hpi).Expression patterns evaluated by quantitative real-time PCR(qRT-PCR)of randomly selected eight genes were similar to the RNA-Seq data.KEGG pathway classified the DEGs into photosynthesis and biosynthesis of phenylpropanoid pathway.We identified 43 differentially expressed TFs belonging to different families.Also,clusters of the DEGs representing kinase and peroxidase responsive genes were retrieved.MapMan pathway analysis representing the expression pattern of genes expressed highly in biotic stress and metabolic pathways after PXO99~A infection relative to PH.This study would be useful for the researchers to reveal the potential functions of genes involved in the rice susceptibility to PXO99~A infection.By transcriptomic study,DEGs were retrieved at different time periods.GO and KEGG pathway analysis were important to predict the role of identified DEGs at specified point in different pathways.These findings could be useful for researchers for functional analysis of DEGs to uncover the insight role in resistance and susceptibility. |
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