Transcriptome analysis for the identification of spot blotch responsive  genes and miRNAs in wheat
Spot blotch caused by Bipolaris sorokiniana is one of the most devastating foliar diseases of wheat particularly in South Asian countries including India, Nepal, Bangladesh etc. In the present study, using whole genome transcriptome sequencing data from two contrasting genotypes for spot blotch disease (one resistant and the other susceptible), at three time points after inoculation, we identified a large number of differentially expressed genes (DEGs) and many micro RNAs (miRNAs) with their target genes (in silico). The mean reads in six libraries were 39.8 millions with a range of 32.1 to 44.9 million reads per library. The DEGs included 5294 upregulated and 4383 downregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included photosynthesis-antenna proteins, MAPK signaling pathways, plant-pathogen interactions, circadian rhythm-plant, etc. These DEGs mainly encoded proteins with leucine rich repeat (LRR) domain, F-box-like domain, non-specific serine/threonine-protein kinases, wall-associated receptor kinases (WAKs), etc. Many DEGs also belonged to the following families of transcription factors (TFs): AP2/ERF, NAC, WRKY, GRAS, MYB etc.