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Reconfiguring the wild-rice RBA1 locus breaks the trade-off between chilling tolerance and blast resistance

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

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Vita > Correspondence > DOI: 10.15302/vita.2026.09.0073
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Reconfiguring the wild-rice RBA1 locus breaks the trade-off between chilling tolerance and blast resistance

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Rice adaptation is constrained by opposing selection on biotic and abiotic stress responses across agroecological environments1-3. Chilling stress limits seedling establishment and adaptation to different growing regions, particularly at high latitudes, during early-season cultivation, and in areas prone to spring cold spells. Rice blast also poses a major threat to yield stability, especially under warm and humid conditions4-7. Although substantial progress has been made in identifying and deploying loci for chilling tolerance8,9 and blast resistance10-12, improving both traits simultaneously remains challenging because of the uneven distribution of favorable alleles among rice subspecies, linkage drag, and complex genetic interactions13-15. Here, we identified RESISTANCE TO BIOTIC AND ABIOTIC STRESS 1 (RBA1) from wild rice as a key locus underlying the trade-off between chilling tolerance and blast resistance. Rather than representing a conventional single gene, RBA1 is a supergene-like region defined by structural variation, and its alternative haplotypes have been differentially maintained during rice domestication and ecological adaptation. This genetic architecture provides a framework for understanding why simultaneous improvement of chilling tolerance and blast resistance has been difficult in breeding, and it also offers a clear target for the rational dissection and redesign of this trade-off.
Through screening of wild rice germplasm resources, we identified a wild rice accession GX2 (accession number YD2-0636) with significantly enhanced chilling tolerance at the seedling stage (Fig. 1a, b). Further genetic analysis revealed a major chilling-tolerance QTL on chromosome 11, named RBA1 (Supplementary Fig. S1). Fine mapping together with high-quality genome assembly showed that the critical variation at this locus is not a conventional small sequence polymorphism, but a presence-absence variant in which chilling-sensitive indica rice variety PL (PERUBAK LUEY) carries an additional 25.7-kb insertion absent from GX2 (Fig. 1c). This insertion contains three predicted genes, ORF1, ORF2, and ORF3, all of which encode atypical NLR-related proteins (Supplementary Figs. S2, S3). Functional analyses demonstrated that these three genes jointly account for the chilling-sensitive phenotype associated with the insertion haplotype. Knocking out any one of them in the PL background significantly improved seedling survival after chilling treatment, whereas introducing or overexpressing them in a japonica background (ZH11) reduced chilling tolerance (Fig. 1d–g; Supplementary Figs. S4, S5). These results indicate that the core genetic effect of RBA1 is defined by the insertion itself, with the deletion haplotype being favorable for chilling tolerance and the insertion haplotype being unfavorable for seedling performance under low temperature. In this sense, RBA1 is best understood not as an acquired determinant of chilling tolerance, but as a structural module that suppresses low-temperature adaptation in specific genetic backgrounds, such that its absence becomes the favorable state for cold adaptation.
Importantly, the effect of RBA1 on blast resistance is not parallel to its effect on chilling tolerance. Blast inoculation assays showed that materials carrying the 25.7-kb insertion displayed stronger disease resistance (Supplementary Fig. S6). Overexpression of ORF1 enhanced blast resistance in a japonica background, whereas loss of ORF1 increased susceptibility, while ORF2 and ORF3 made little detectable contribution to blast resistance (Fig. 1h, i). Thus, the insertion haplotype contains a functionally asymmetric set of linked genes in which ORF1 is beneficial for blast resistance, while ORF1, ORF2, and ORF3 together reduce chilling tolerance. The long-recognized negative association between chilling tolerance and blast resistance therefore reflects not a diffuse physiological correlation, but a discrete and genetically tractable architecture encoded by a structurally defined haplotype. Together with the observed differences in reactive oxygen species accumulation and peroxidase activity under chilling stress and pathogen infection (Supplementary Figs. S6, S7), these results suggest that RBA1 may influence stress-associated redox responses under chilling stress and pathogen infection, and that the three ORFs at this locus function in a shared genetic pathway or convergent regulatory process, whereas the downstream molecular mechanisms remain to be resolved.
The contrasting population distributions of the two RBA1 haplotypes suggest that their relative adaptive values may differ among agroecological contexts (Fig. 2a, b; Supplementary Fig. S8). The insertion-bearing haplotype contains a component that contributes to blast resistance, whereas the deletion haplotype is associated with enhanced chilling tolerance. These contrasting effects may have influenced the distribution of the two haplotypes across both rice populations and cultivation regions. However, the current population data are correlative and do not directly demonstrate opposing natural selection or trait-driven maintenance and fixation during rice domestication. RBA1 is therefore better viewed as a structurally defined trade-off locus with context-dependent value, whose linked components have distinct effects on chilling tolerance and blast resistance.
From a breeding perspective, the greatest value of RBA1 lies in its separability and reconfigurability, and more specifically in the fact that it offers three distinct solutions for three different ecological settings. In warm and humid japonica-growing regions where blast pressure is high but chilling stress is relatively limited, ORF1 can be introduced as a favorable disease-resistance module into elite local cultivars to strengthen blast resistance. This strategy was validated in the elite japonica cultivar Nan-Jing 9108 (NJ9108), in which introduction of ORF1 with its native promoter significantly enhanced blast resistance, demonstrating that the beneficial disease-resistance component of RBA1 can be extracted and deployed independently to address the common problem of strong chilling tolerance but insufficient blast resistance in temperate-adapted japonica germplasm (Fig. 2c; Supplementary Fig. S9).
In contrast, in southern double-cropping systems or indica-growing regions characterized by high temperature and humidity but also by transient low-temperature episodes during early spring seedling establishment, ORF2 and potentially ORF3 can be knocked out by targeted editing to improve chilling tolerance while retaining the blast-resistance benefit conferred by ORF1. This strategy was demonstrated in the elite early-season indica cultivar Mei-Xiang-Zhan 2 (MXZ2), in which knockout of ORF2 significantly improved seedling chilling tolerance without an obvious penalty in blast resistance or agronomic performance, suggesting that this approach may be well suited for environments requiring both disease resistance and safe establishment under episodic chilling (Fig. 2d; Supplementary Fig. S9 and Table S4). A third strategy applies to regions where low-temperature adaptation is the primary breeding objective and the stability of hybrid rice parents and combinations under cold-prone conditions must be enhanced. In this case, the favorable RBA1GX2 allele can be introduced to replace or reconstruct the RBA1 region, thereby improving cold adaptation. Introgression of the RBA1GX2 allele into PA64s enhanced chilling tolerance in the sterile line, and the resulting hybrid combination also exhibited stronger low-temperature adaptation while maintaining stable yield-related traits (Fig. 2e; Supplementary Fig. S9 and Table S4). This result shows that RBA1 is useful not only for improving varieties but also for optimizing hybrid rice parents and combinations, particularly for higher-latitude rice-growing areas or regions exposed to low-temperature risk. Taken together, these results establish three breeding routes centered on RBA1: introducing ORF1 improves blast resistance in japonica regions prone to disease; editing ORF2 balances blast resistance and chilling tolerance in southern early-season indica systems; and substituting the RBA1GX2 allele enhances chilling tolerance in hybrid rice, though this particular approach is not designed to confer blast resistance. This ecology-oriented deployment of different genetic components highlights RBA1 not merely as a locus explaining natural variation and domestication history, but as a practical breeding target that can be configured to address production constraints (Fig. 2f). However, broader validation across additional germplasm and field environments will be required before general breeding recommendations can be made.
Overall, RBA1 reveals how a structurally defined supergene-like locus can simultaneously shape low-temperature adaptation and disease resistance in rice, and explains why it is difficult to improve these traits together through conventional breeding. More importantly, our results show that this trade-off is not immutable. Once the internal functional components of the locus are resolved, unfavorable linkage can be converted into a designable breeding target. Favorable wild rice alleles are underutilized in breeding, not because they lack value, but because their beneficial effects are genetically linked to undesirable components. RBA1 illustrates that when the genetic composition, functional partitioning, and background-dependent utility of such loci are clearly defined, targeted improvement can be achieved through introgression, allele substitution, or genome editing. RBA1 therefore provides not only a new genetic resource for the coordinated improvement of chilling tolerance and blast resistance, but also a broader framework for the molecular design of complex adaptive traits in crop breeding. More generally, this study suggests that many trait combinations long regarded as difficult to reconcile may similarly be determined by structural variants or tightly linked modules, and that once these modules are accurately identified and functionally dissected, long-standing breeding barriers can be overcome for precision improvement.

DATA AVAILABILITY

The authors declare that the data supporting the findings of this study are available within the paper and its supplementary information files. The genomic information of PL has been uploaded to the National Genomics Data Center (BioProject accession number: PRJCA069795, ngdc.cncb.ac.cn). The gene accession numbers for ORF1, ORF2, and ORF3 are PL_Os11gG020480, PL_Os11gG020490, and PL_Os11gG020500, respectively.

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RIGHTS & PERMISSIONS

The Author(s) 2026. Published by Higher Education Press. This is an Open Access article distributed under the terms of the CC BY license (https://creativecommons.org/licenses/by/4.0/).

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Zhang, B. et al.  Reconfiguring the wild-rice RBA1 locus breaks the trade-off between chilling tolerance and blast resistance  Vita https://doi.org/10.15302/vita.2026.09.0073 ()
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