Abstract Transposable elements (TEs), which were once relegated to the status of genomic parasites, are today accepted as important agents of plant genome evolution and adaptation. This review integrates evidence pointing to their dual function as drivers of genetic diversity and instability, with a focus on their contribution to phenotypic innovation, stress tolerance, and crop trait control. TEs create structural and regulatory diversity by insertional mutagenesis, cis ‐regulatory sequence donation, and epigenetic interactions, facilitating fast adaptation to environmental stress. Advances in omics technologies have unraveled TE dynamics, showing insertion bias toward genic and regulatory regions and stress‐responsive activation patterns. The influence of the mobilome on crop improvement is emphasized by TE‐derived molecular markers, clustered regularly interspaced short palindromic repeats‐mediated TE regulation, and epigenome editing that minimizes risks of genome instability while tapping TE‐driven diversity. Rice ( Oryza sativa L.) mPing and maize ( Zea mays L.) Hopscotch , for instance, demonstrate TE potential in trait enhancement and domestication. Moreover, multi‐omics integration has defined TEs’ input into stress response and genome plasticity, offering new targets for precision breeding. Challenges remain in modeling TE behavior and weighing adaptive potential against harmful effects, requiring sophisticated computational models and synthetic biology strategies. Interdisciplinary approaches integrating machine learning and synthetic TE design should be prioritized in future research to maximize TE‐mediated crop resilience. With the integration of TE biology and cutting‐edge biotechnologies, global food security issues, fueled by climate change, can be mitigated by the scientific community. This overview situates TEs not merely as genomic leftovers but as essential next‐generation crop requirements, necessitating their strategic location in sustainable agro‐innovation.
Medeiros et al. (Sun,) studied this question.