Bin Zhang, Jiajun Xin, Wei Luo, Zeyu Zheng, Youlin Peng, Mingliang Guo, Ye Jin, Ge Gao, Zhenyu Gao, Jiang Hu, Guosheng Xiong, Kang Chong, Qian Qian, Lianguang Shang, Xiaoming Zheng

Vita; 2026

DOI: 10.15302/vita.2026.09.0073

Abstract

Rice improvement often requires simultaneous enhancement of tolerance to abiotic stress and resistance to disease, yet these traits can be constrained by unfavorable genetic linkage. Here, we identify RESISTANCE TO BIOTIC AND ABIOTIC STRESS 1 (RBA1), a wild-rice-derived locus that underlies an antagonistic relationship between seedling chilling tolerance and blast resistance. Fine mapping and genome comparison revealed that RBA1 is a structurally variable, supergene-like region characterized by a 25.7-kb presence–absence variation. The insertion haplotype contains three atypical NLR-related genes, ORF1, ORF2 and ORF3. Functional analyses showed that all three genes contribute to chilling sensitivity: knockout of any single ORF in the indica background improved survival after chilling, whereas their introduction or overexpression in japonica reduced chilling tolerance. By contrast, blast resistance was mainly associated with ORF1, whose overexpression enhanced resistance and whose loss increased susceptibility, while ORF2 and ORF3 had little detectable effect on disease resistance. These results demonstrate that the RBA1 trade-off is caused by functionally distinct but tightly linked components within a structural haplotype. Population analyses further indicated contrasting distributions of the insertion and deletion haplotypes across rice groups and cultivation environments, consistent with context-dependent adaptive value. Importantly, dissection of the locus enabled ecology-specific breeding strategies. Introduction of ORF1 improved blast resistance in elite japonica rice, targeted knockout of ORF2 enhanced chilling tolerance in an elite indica cultivar without an obvious penalty in blast resistance or agronomic performance, and replacement with the favorable RBA1^GX2 allele improved chilling tolerance in a hybrid-rice background. Together, these findings show that a long-standing trade-off between chilling tolerance and blast resistance can be genetically uncoupled by resolving and reconfiguring a structural-variation locus. RBA1 therefore provides both a valuable genetic resource and a general framework for precision breeding of complex adaptive traits in crops.