Genome-wide identification and expression analysis of chickpea U-box E3 ligases identifies CaPUB4 and CaPUB16 as candidate responsive genes for abiotic stress tolerance

Abstract

U-box E3 ubiquitin ligases play a crucial role in post-translational protein modification, stress signaling, and cellular adaptation in plants. In this study, 38 non-redundant CaPUB genes were identified from the chickpea (Cicer arietinum) genome and characterized for their phylogenetic relationships, domain architecture, gene structures, and expression profiles. Synteny and gene ontology analyses revealed evolutionary conservation with Lotus japonicus and Arabidopsis thaliana, and functional involvement in processes such as ubiquitination, signaling, and stress responses. RNA sequencing and qPCR analyses demonstrated distinct tissue-specific expression patterns. Specifically, CaPUB14 and CaPUB2 were predominantly expressed in particular organs, whereas CaPUB4 and CaPUB16 were upregulated under drought and salt stress in the stress-tolerant ICC4958 cultivar. Functional interaction network analysis revealed that CaPUB4 and CaPUB16 proteins interact with an identical set of partner proteins, supporting the hypothesis that these ligases may function collaboratively in stress adaptation. Collectively, these findings provide insights into the diversity, expression patterns, and potential regulatory roles of the CaPUB gene family, highlighting promising candidate genes for future functional characterization and their possible utility in improving crop stress resilience.