Comparison of mRNA and protein expression levels of eleven representative genes. Quantitative real time PCR was performed using gene specific primers (Additional file 2). The log10 transformed fold change values (infected/control) of protein spot intensities and mRNA expression level were plotted at different time intervals (48 h, 72 h and 96 h) after infection with Foc1 for both chickpea genotypes. JG62 represented by grey color bars and WR315 represented by black color bars. The proteins selected are SOD (superoxide dismutase), PMIP (Pasma membrane intrinsic protein), ICDH (Isocitrate dehydrogenase), FLP (Fructokinase like protein), TIM (Triose phosphate isomerase), GNBP (Guanine nucleotide binding protein), PDI (Protein disulfide isomerase), EF1 (Elongation factor1), BGL2 (Glucan-endo-1, 3-beta-glucosidase), TLP (Thaumatin like protein), PR1 (Pathogenesis related protein1).