Traditional rice blast resistance breeding largely depends on utilizing typical resistance (R) genes. However, the lack of durable R genes has prompted rice breeders to find new resistance resources. Susceptibility (S) genes are potential new targets for resistance genetic engineering using genome-editing technologies, but identifying them is still challenging. Here, through the integration of genome-wide association study (GWAS) and transcriptional analysis, we identified two genes, RNG1 and RNG3, whose polymorphisms in 3′-untranslated regions (3′-UTR) affected their expression variations. These polymorphisms could serve as molecular markers to identify rice blast-resistant accessions. Editing the 3′-UTRs using CRISPR/Cas9 technology affected the expression levels of two genes, which were positively associated with rice blast susceptibility. Knocking out either RNG1 or RNG3 in rice enhanced the rice blast and bacterial blight resistance, without impacting critical agronomic traits. RNG1 and RNG3 have two major genotypes in diverse rice germplasms. The frequency of the resistance genotype of these two genes significantly increased from landrace rice to modern cultivars. The obvious selective sweep flanking RNG3 suggested it has been artificially selected in modern rice breeding. These results provide new targets for S gene identification and open avenues for developing novel rice blast-resistant materials.

中文翻译：

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通过关联分析和转录分析与基因编辑技术相结合鉴定两个新的水稻S基因

传统的稻瘟病抗性育种很大程度上依赖于利用典型的抗性（R）基因。然而，持久R基因的缺乏促使水稻育种者寻找新的抗性资源。易感性（S）基因是利用基因组编辑技术进行抗性基因工程的潜在新靶标，但识别它们仍然具有挑战性。在这里，通过全基因组关联研究（GWAS）和转录分析的结合，我们鉴定了两个基因RNG1和RNG3，它们在3'-非翻译区（3'-UTR）的多态性影响了它们的表达变异。这些多态性可以作为识别稻瘟病抗性种质的分子标记。使用 CRISPR/Cas9 技术编辑 3'-UTR 会影响两个基因的表达水平，这两个基因与稻瘟病易感性呈正相关。敲除水稻中的RNG1或RNG3可以增强稻瘟病和白叶枯病的抗性，而不影响关键的农艺性状。RNG1和RNG3在不同的水稻种质中具有两种主要基因型。从地方品种水稻到现代品种，这两个基因的抗性基因型频率显着增加。RNG3侧翼明显的选择性清除表明它在现代水稻育种中已被人为选择。这些结果为S基因鉴定提供了新靶点，并为开发新型稻瘟病材料开辟了途径。