Towards Understanding of Chickpea-Ascochyta rabiei Interaction: Transcriptome Profiling and QTL Analysis of Ascochyta Blight Resistance in Chickpea

Ascochyta blight caused by the fungus Ascochyta rabiei is one of the most devastating diseases of chickpea worldwide.  The use of resistant varieties is considered the most economical and sustainable approach for controlling this disease. Four RIL mapping populations were genotyped by GBS and were rated for their reaction to ascochyta blight under field and greenhouse conditions in 2013 and 2014. A total of 16 QTLs across eight chickpea chromosomes were identified to be associated with AB resistance across the four mapping populations. GWAS on a panel of diverse chickpea genotypes identified additional SNPs associated with ascochyta blight under field and/or greenhouse conditions.  These SNPs were located in 7 out of 8 chickpea chromosomes. To gain insight into the potential resistance mechanism, RNA-seq was done on tissues collected at different intervals after inoculation from the ascochyta blight partial resistance lines and from the highly susceptible genotype. More than 90% of chickpea transcriptome reads were mapped to the chickpea reference genome sequence. Differential expression analysis revealed that several pathogenesis-related genes, cell wall-mediated pathogen resistance genes, enzymes involved in defence mechanisms and different classes of stress responsive transcription factors were significantly up-regulated in Ascochyta rabiei inoculated chickpea samples. Sequence variants associated with AB resistance and differentially expressed genes in partially resistant chickpea varieties are currently being tested for assisted selections for improvement of AB resistance.