Abstract
BACKGROUND: Soil salinization threatens global rice production, driving the urgent need for salt-tolerant rice cultivars. Sea rice HD961, renowned for its exceptional salt tolerance, serves as an ideal model for elucidating molecular adaptations to salinity. RESULTS: In this study, we generated a high-quality, chromosome-level genome assembly of HD961 using Nanopore long-read sequencing, Illumina short-read polishing, and Hi-C-based scaffolding, providing a robust foundation for translatomic analysis. To explore translational responses to salt stress, we integrated ribosome profiling (Ribo-seq) with the QEZ-seq protocol and RNA sequencing (RNA-seq) under 150 mM NaCl conditions. Our results reveal that salt stress selectively enhances translational efficiency (TE) in genes critical for ion homeostasis, antioxidant defense, and cell wall remodeling, enabling HD961 to maintain cellular balance under stress. Especially, eukaryotic translation initiation factor 2B (eIF2B) emerged as a key regulator, with its upregulation and the formation of stress-induced eIF2B-containing bodies indicating a novel mechanism to optimize protein synthesis. Additionally, ribosome footprint profiling revealed codon-specific modulation of A-site dwell times, with the GCG codon showing a particularly pronounced shift under salt stress, suggesting fine-tuned translational control that prioritizes stress-responsive proteins. CONCLUSION: Together, these findings highlight eIF2B-mediated translational regulation as central to HD961's salt tolerance, offering valuable genomic and translatomic resources for breeding salt-tolerant rice and other crops.