Legume Genomics and Genetics 2025, Vol.16, No.2, 63-71 http://cropscipublisher.com/index.php/lgg 63 Feature Review Open Access Genome-Wide Identification of WRKY Transcription Factors in Chickpea and Their Roles in Stress Responses Deming Yu, Shengyu Chen Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: shengyu.chen@cuixi.org Legume Genomics and Genetics, 2025 Vol.16, No.2 doi: 10.5376/lgg.2025.16.0007 Received: 20 Jan., 2025 Accepted: 05 Mar., 2025 Published: 25 Mar., 2025 Copyright © 2025 Yu and Chen, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Yu D.M., and Chen S.Y., 2025, Genome-wide identification of WRKY transcription factors in chickpea and their roles in stress responses, Legume Genomics and Genetics, 16(2): 63-71 (doi: 10.5376/lgg.2025.16.0007) Abstract WRKY transcription factors play pivotal roles in regulating plant responses to various biotic and abiotic stresses. In this study, a comprehensive genome-wide identification and analysis of WRKY transcription factors were conducted in Cicer arietinum (chickpea), a key legume crop with growing importance in stress biology. Using advanced bioinformatics tools, we identified and annotated the complete set of WRKY genes in the chickpea genome, classifying them into groups I, II, and III based on conserved domains and structural features. The chromosomal distribution, gene structures, and phylogenetic relationships were analyzed to provide insights into their evolutionary patterns. Expression profiling under drought, salinity, and pathogen stress conditions (e.g., Fusarium and Ascochyta) revealed several stress-responsive WRKY genes with distinct tissue-specific and developmental expression patterns. We further explored their regulatory networks, including interactions with key signaling molecules (ABA, JA, SA) and crosstalk with other transcription factor families. A detailed case study highlighted the role of selected WRKY genes in drought tolerance, supported by phenotypic assessments under water-deficit conditions. Functional validation through overexpression, gene silencing, and omics approaches-such as transcriptomics and CRISPR/Cas-based editing-provided strong evidence for the functional roles of specific WRKYgenes. This study underscores the significance of WRKY transcription factors in stress adaptation and sets the foundation for their application in marker-assisted selection and breeding of stress-resilient chickpea varieties. Keywords Chickpea (Cicer arietinum); WRKY transcription factors; Abiotic and biotic stress; Gene expression profiling; Functional genomics 1 Introduction Chickpeas (Cicer arietinum L.) are not unfamiliar on people's dining tables, especially today when nutritional intake and food security are increasingly valued. This leguminous plant is not only rich in protein and minerals, but also thrives well in arid and semi-arid regions, which has drawn it worldwide attention. However, everything has two sides. Despite its drought resistance and strong adaptability, in actual production, it still frequently encounters challenges such as drought, saline-alkali land and diseases, and the problem of unstable yield has never been well solved. In fact, chickpeas are not only food crops; their value in scientific research is also constantly rising. As a "model student" among leguminous plants, it has been widely used to study the coping mechanisms of plants under adverse conditions. Especially in recent years, with the development of genomic and transcriptomic technologies, scientists have been able to identify a number of genes related to stress response, and the WRKY transcription factor is one of the more notable ones (Kumar et al., 2016). When it comes to transcription factors (TFS), they are almost ubiquitous in plants, just like sound engineers, controlling the "switches" of different genes. Among them, the WRKY family stands out particularly among plants due to its conservative WRKY domain and zinc finger domain. They have a distinct feature, that is, they can bind to the W-box element in the promoter of the target gene, thereby regulating those downstream genes related to plant development and stress response (Jiang et al., 2017; Cheng et al., 2021; Ma and Hu, 2024; Wang et al., 2024). However, this combination is not always an "activating" effect; it could also be an "inhibitory" one.
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