<p>The underutilized protein-rich legume winged bean (<i>Psophocarpus tetragonolobus</i> (L.) DC.) bears an edible protein-rich tuber. The present study investigates and analyzes the transcriptome datasets of the tuber of <i>P. tetragonolobus</i>, resulting in the identification of the underlying molecular factors responsible for controlling the process of tuberization in <i>P. tetragonolobus</i>. Differential gene expression analysis of normal root and root tuber of <i>P. tetragonolobus</i> tissue was carried out. Eight putative genes were identified and selected for their involvement in the process of root tuberization in <i>P. tetragonolobus</i>. The key genes responsible for tuberization were validated through qRT-PCR. The expression of Ca²⁺/calmodulin-dependent protein kinase was found to be significantly higher in the tuber. Ca²⁺/calmodulin-dependent protein kinase 1 and Ca²⁺/calmodulin-dependent protein kinase 5 transcripts were highly expressed compared to other Ca²⁺/calmodulin-dependent protein kinase transcripts. A hypothetical model of the genetic regulatory network for tuberous root development of <i>P. tetragonolobus</i> is proposed, emphasizing specific signal transduction pathways like plant hormone signal transduction, Ca²⁺signal, and metabolic processes. In <i>P. tetragonolobus</i>, Ca²⁺ and the Ca²⁺ sensor protein calmodulin (CaM) function as signal molecules for tuber induction. The transcriptional regulators influenced by Ca²⁺ and CaM, and their importance in the tuberization-induced signal transduction in <i>P. tetragonolobus,</i> are also revealed. The knowledge gained will provide insights into elucidating the molecular mechanism of tuberization in the underutilized legume <i>P. tetragonolobus</i>.</p>