Differential gene expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race-4 using cDNA SCoT marker

The cDNA-based start codon targeted polymorphism (SCoT) (cDNA-SCoT) approach has gained significant importance in gene discovery and molecular mechanisms prediction. The cDNA-SCoT profiling was used for the first time in this work to identify differentially expressed genes during Fusarium oxysporum f. sp. ciceris race-4 infection of chickpea in resistant and susceptible cultivars. Pathogenicity test performed by root dip inoculation method showed 73.7% wilting in the susceptible cultivar at 16th day after inoculation. All SCoT primers were reproducible and expressed 77 amplicons including 63 polymorphic and 14 monomorphic. Functional characterization of DEFs was followed by Sanger sequencing and nBLAST homology search tool. Among the eight DEFs, two amplicons observed only in ‘WR-315’ showed 84% and 91% homology with Cicer arietinum cysteine rich PAK1 inhibitors like mRNA (LOC101498699) and annotated as a defensin-like peptide using other species information so far. This novel gene might be one of the key responsible genes in the activation of resistance against F. oxyporum in chickpea. In addition, string protein interaction revealed cysteine-rich PAK1 inhibitor-like mRNA interacted with Leucine-rich receptor protein kinase EXS-like, Chaperonin CPN60-2, Protein HOTHEAD and other proteins indicating that the defense mechanism regulation against F. oxyporum is governed by complex genetic factors. In summary, findings from this study are novel and would be used in the identification of candidate functional gene(s) in future chickpea research, which can be further employed in marker development, marker-assisted selection and to identify the genes’ regulatory functions.