European Journal of Sustainable Agroecosystems

Background: Salinity stress is an escalating threat to global food security, severely limiting the growth, development, and productivity of rice (Oryza sativa L.), a staple food for more than half of the world's population. Between 2015 and 2025, research on rice salinity tolerance has advanced significantly, transitioning from descriptive transcriptomics to functional genomics through the integration of RNA sequencing (RNA-seq), CRISPR/Cas genome editing, Genome-Wide Association Studies (GWAS), and multi-omics approaches. Despite these technological advances, translating laboratory discoveries into field-level applications remains a major challenge.

Objective: This critical review aims to comprehensively synthesize evidence published between 2015 and 2025 on the molecular and physiological mechanisms underlying salinity tolerance in rice. It seeks to evaluate key regulatory pathways, identify methodological limitations and knowledge gaps, and propose future research directions for accelerating the development of climate-resilient, high-yielding salt-tolerant rice cultivars.

Method: A systematic evidence synthesis was conducted using peer-reviewed literature published between 2015 and 2025. The review critically analyzed studies investigating ion transporter systems (OsHKT, OsNHX, and OsSOS1), transcription factor networks (NAC, MYB, bZIP, and WRKY families), MAPK- and phytohormone-mediated signaling pathways, as well as epigenetic regulation and post-translational modifications. Comparative analyses were performed to assess methodological differences between controlled hydroponic experiments and field-based studies while evaluating emerging technologies such as single-cell RNA sequencing (scRNA-seq), machine-learning-assisted phenotyping, and prime editing.

Results: The evidence indicates that salinity tolerance in rice is governed by highly coordinated molecular networks involving ion homeostasis, transcriptional regulation, signaling cascades, and epigenetic modifications. Functional genomics has substantially improved the identification of candidate genes and regulatory pathways associated with salt tolerance. However, considerable inconsistencies persist between laboratory and field studies, limiting the practical deployment of identified loci. Significant knowledge gaps remain regarding cell-type-specific responses, spatial regulation of stress adaptation, and the energetic costs associated with engineered tolerance traits. Emerging technologies demonstrate strong potential to overcome these limitations by enabling more precise functional characterization and breeding strategies.

Conclusion: Recent advances in functional genomics and multi-omics have considerably enhanced the understanding of salinity tolerance mechanisms in rice, providing valuable targets for molecular breeding and genome editing. Nevertheless, bridging the gap between laboratory discoveries and field performance requires integrated validation under realistic environmental conditions, deeper investigation of cellular-level regulatory mechanisms, and adoption of next-generation technologies. Future research combining scRNA-seq, artificial intelligence-assisted phenotyping, and precision genome editing will be essential for developing resilient, high-yielding rice cultivars capable of sustaining productivity under increasing soil salinity and changing climatic conditions.