Natural Variation of a Specific NLR Gene RGA4L Confers Strong Chilling Tolerance in Rice

Low temperature limits rice geographical distribution. However, japonica rice, characterised by its chilling tolerance, can be planted in high-altitude and temperate regions, and the molecular mechanisms underlying this adaptation remain partially understood. Here, we identified a novel major chilling-tolerant QTL, qCSS12, through map-based cloning using a chromosome segment substitution line (CSSL) previously developed from a cross between the chilling-tolerant japonica rice Koshihikari and the indica rice Nona Bokra. Its causal gene RGA4L (Disease Resistance Gene Analog 4-Like) encodes a specific NLR protein. RNAi lines of the Koshihikari allele RGA4L^jap exhibit increased sensitivity to cold, whereas overexpression lines enhance chilling tolerance of both the vegetative and reproductive stages in rice. Further, we found that RGA4L physically interacts with both OsHSP90 and OsLEA5. These interactions may facilitate the proper assembly of an RGA4L protein complex and then sense and transduce chilling signals to downstream pathways involving OsLEA5, thereby conferring chilling tolerance. Moreover, we demonstrate that RGA4L has been a major target of artificial selection for low-temperature acclimation during japonica rice domestication. This work shows that RGA4L confers chilling tolerance throughout all growth stages and holds potential for breeding cold-resistant elite rice varieties.