| Summary: | Pigeonpea (<i>Cajanus cajan</i> L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its high level of tolerance against biotic and abiotic stresses. In this regard, understanding the genes involved in stress tolerance has great importance. In the present study, identification, and characterization of WRKY, a large transcription factor gene family involved in numerous biological processes like seed germination, metabolism, plant growth, biotic and abiotic stress responses was performed in pigeonpea. A total of 94 <i>WRKY</i> genes identified in the pigeonpea genome were extensively characterized for gene-structures, localizations, phylogenetic distribution, conserved motif organizations, and functional annotation. Phylogenetic analysis revealed three major groups (I, II, and III) of pigeonpea <i>WRKY</i> genes. Subsequently, expression profiling of 94 <i>CcWRKY</i> genes across different tissues like root, nodule, stem, petiole, petal, sepal, shoot apical meristem (SAM), mature pod, and mature seed retrieved from the available RNAseq data identified tissue-specific <i>WRKY</i> genes with preferential expression in the vegetative and reproductive stages. Gene co-expression networks identified four <i>WRKY</i> genes at the center of maximum interaction which may play a key role in the entire <i>WRKY</i> regulations. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis of <i>WRKY</i> genes in root and leaf tissue samples from plants under drought and salinity stress identified differentially expressed <i>WRKY</i> genes. The study will be helpful to understand the evolution, regulation, and distribution of the <i>WRKY</i> gene family, and additional exploration for the development of stress tolerance cultivars in pigeonpea and other legumes crops.
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