Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world’s population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice’s response to environmental stress and to breed high-yield, high-quality and stress-resistant varieties. Over the past few decades, significant advancements in molecular biology have led to the widespread use of several omics methodologies to study all aspects of plant growth, development and environmental adaptation. Transcriptomics and proteomics have become the most popular techniques used to investigate plants’ stress-responsive mechanisms despite the complexity of the underlying molecular landscapes. This review offers a comprehensive and current summary of how transcriptomics and proteomics together reveal the molecular details of rice’s response to environmental stresses. It also provides a catalog of the current applications of omics in comprehending this imperative crop in relation to stress tolerance improvement and breeding. The evaluation of recent advances in CRISPR/Cas-based genome editing and the application of synthetic biology technologies highlights the possibility of expediting the development of rice cultivars that are resistant to stress and suited to various agroecological environments.

Goji berry ( Lycium barbarum L.), a nutritionally important fruit-bearing shrub in the Solanaceae family, possesses a distinctive carotenoid profile dominated by zeaxanthin esters, which contributes to its health benefits and stress resilience. However, the transcriptional networks governing carotenoid metabolism in Lycium remain incompletely understood across developmental stages and stress conditions. This review synthesizes recent multi-omics studies to propose a Lycium -centric regulatory framework for carotenoid biosynthesis and accumulation. We describe a ripening-associated transcriptional reprogramming that appears to activate core biosynthetic genes (PSY1, ZDS16) while modulating the expression of catabolic genes (CCD4, ZEP), although the precise regulatory mechanisms underlying this switch remain to be fully elucidated. We emphasize the potential role of transcription factor families — including R2R3-MYB, BBX, WRKY, NAC, ERF as candidate integrators of development and abiotic stress signals, with functional evidence available for key modules such as LbNAM2-LbZDS (drought response) and LbERF5.1-LbCCD4.1 (degradation control). A Solanaceae-wide comparison suggests conserved regulatory architecture alongside putative goji-specific adaptations, although comprehensive cross-species validation remains incomplete. We identify major knowledge gaps — including functional validation of candidate TFs, integration of multi-stress signaling, and characterization of epigenetic and post-transcriptional regulation — and propose key directions for future research. Overall, this synthesis provides a mechanistic framework for understanding carotenoid regulation in goji berry and may inform strategies for breeding nutritionally enhanced and climate-resilient Lycium cultivars, pending further experimental validation.