Transcriptome sequencing and differential expression analysis in bacterial wilt tolerant and susceptible clones of tomato (Solanum lycopersicum L.) following Ralstonia solanacearum infection

Two tomato clones (Vellayani Vijay (V) tolerant to bacterial wilt (BW) and Pusa Ruby (P), susceptible to BW) were used to understand the molecular mechanism of tomato in response to Ralstonia solanacearum infection through RNA-sequencing (RNA-seq) technology. We identified 164 differentially expressed genes (DEGs) between V and P before R. solanacearum inoculation. Among these DEGs, 81 were up-regulated while 83 were down-regulated. Six hours after the inoculation with R. solanacearum, 1374 DEGs were identified with 701 up regulated and 673 down regulated. Twelve hours after the post inoculation 95 up regulated and 179 down regulated. Twenty-four hours after inoculation, 565 upregulated and 229 down regulated. Forty-eight hours after inoculation, it was identified 1489 upregulated DEG's and 1588 down regulated DEG's. Gene Ontology (GO) enrichment analysis revealed DEG's were annotated with biological process, cellular component and molecular functions. A total of 824 regulated pathways were identified under various time instances during post inoculation. The majority of DEGs of biological process corresponds to protein modification process, response to stress, response to biotic stimulus and lipid metabolic process. These plays an integral role during bacterial infection. Circadian clock regulation altered the transcriptional activities, which further resulted in the reduction in upregulated and downregulated transcript. The top KEGG pathways enriched in the bacterial wilt tolerant and susceptible clones of tomato were biosynthesis of secondary metabolites, metabolic pathways, phenylpropanoid biosynthesis and plant pathogen interaction. Significant number of transcripts engaged in the synthesis of secondary metabolites at various time points of both tolerant and susceptible clones, confirming pathogen infection. Furthermore, quantitative RT-PCR analysis confirmed the expression patterns of selected DEG, which suggested that the RNA-seq results were reliable. The findings of this study provide profound insight into the potential mechanism of tomato in response to R. solanacearum infection, which lays an important foundation for future studies on management of bacterial wilt.