Cell‐Type‐Specific and Variety‐Specific Responses to Salt Stress in Wheat Root Revealed by Single‐Cell Transcriptomics

Soil salinization threatens the yield and quality of wheat. Roots are critical for the salt stress response, yet their cell-type-specific mechanisms remain unclear. We conducted the first single-nucleus RNA sequencing analysis of wheat root tips from salt-sensitive (CS) and -tolerant (DK) varieties under salt stress, profiling 188 270 high-quality root cells. Seventeen cell types were identified and validated using reported marker genes and reference atlases. Cell-type-specific analyses found that root hair cells exhibited the strongest association with salt stress, with variety-specific transcriptional changes potentially contributing to DK's superior salt tolerance. Comparative gene profiling of root hair cells highlighted that CS prioritized rapid stress signaling and osmolyte accumulation, whereas DK emphasized metabolic reprogramming and cellular repair mechanisms. Pseudotime analysis pinpointed TaGSTU1-5B as a key candidate for wheat salt tolerance, and it was validated as improving salt tolerance by mediating ROS scavenging by overexpression. Additionally, subgenomic analysis revealed that salt stress enhanced asymmetric expression of the homeologs in polyploid wheat roots, and A- and D-dominant homologs were more related to salt response. This study reports the first single-cell atlas of salt-stressed wheat roots, uncovering cell-type-specific and variety-specific salt responses, providing novel insights into the molecular basis of salt adaptation and tolerance in wheat.