Functional and Regulatory Complexity: Challenges and Prospects for Understanding Rice WRKY Transcription Factors

WRKY Transcription factors (TFs) are central regulators of plant growth, development, and responses to biotic and abiotic stresses. In rice, the large size of this family, coupled with structural diversity, multifunctionality, redundancy, and extensive network integration, complicates efforts to define precise gene functions. While these features confer regulatory robustness, they limit the interpretability of single-gene analyses and obscure direct gene-trait relationships. This review examines the challenges underlying WRKY functional characterization in rice and highlights how they arise from the intrinsic properties of this gene family. We then present a challenge-centered framework in which experimental and computational approaches are mapped onto the four major barriers to WRKY functional resolution, such as context-dependent activity, functional redundancy, and target specificity. By emphasizing how these approaches resolve distinct layers of WRKY complexity, we provide a problem-driven synthesis of current methodologies. We further underscore the need for integrated WRKY-centric databases to support hypothesis generation and accelerate functional discovery. A systems-level understanding of WRKY TFs, grounded in their regulatory complexity, will be essential to harness their potential to improve stress resilience and productivity in rice.