Comparative spatial transcriptomics reveals root dryland adaptation mechanism in rice and HMGB1 as a key regulator.

Drought severely threatens food security, and its detrimental effects will be exacerbated by climate change in many parts of the world. Rice production is water consuming and particularly vulnerable to drought stress. A special rice ecotype called upland rice specifically adapts to dryland mainly through its robust root system. However, the molecular and developmental mechanism underlying this adaption has remained elusive. Here, by comparing the root development between upland and irrigated rice phenotypically and cytologically, we identified key developmental phenotypes that distinguish upland rice. We further generate spatial transcriptomic atlases for coleoptilar nodes and root tips to explore the molecular differences in crown root formation and development between upland and irrigated rice, uncovering promising genes for enhancing drought resistance. Among the identified genes, HMGB1, a transcriptional regulator, functions as a key factor that elongates and thickens roots in upland rice and enhances drought resistance. Our study uncovered spatially resolved transcriptomic features in upland rice root that contribute to its adaptation to dryland conditions, providing valuable genetic resources for breeding drought resilient rice.