An Integrated Approach to Study Regulation of Gene Expression in Response to Ascochyta Blight in Chickpea

Ascochyta blight is one of the severe threats to chickpea production across all chickpea growing areas and understanding gene regulation mechanisms behind this disease would be helpful to develop stress tolerant chickpea genotypes. Recently, microRNAs (miRNAs) have emerged as one of the most versatile performers in regulation of gene expression in plants, both in abiotic and biotic stress conditions. Considering this, the present study utilises combination of genome-wide transcriptome, small RNA and degradome profiling to identify differentially expressed genes, miRNAs and their targets in chickpea in response to Ascochyta blight pathogen i.e. Ascochyta rabiei. A total of 20 samples from 5 (three resistant and two susceptible) genotypes across two stages (3rd and 7th day post inoculation (DPI)) were subjected to transcriptome and small RNA sequencing and 12 samples for degradome sequencing. Genome-wide transcriptome profiling generated a total of 817 million high quality reads and identified ~6K differentially expressed genes, while, small RNA sequencing generated 470 million reads and identified 446 differentially expressed miRNAs across various combinations. The majority of genes targeted by miRNAs were also found to be differentially expressed between susceptible and resistant genotypes under stress conditions. The present study also reveals a comprehensive set of genotype specific and stress responsive miRNAs along with their targets thus establishing a framework for understanding regulatory mechanism of Ascochyta blight resistance in chickpea. Functional validation of these genes could help to identify promising candidates for developing Ascochyta blight resistant chickpea genotypes.