Common wild rice (Oryza rufipogon Griff.) is invaluable genetic resource for rice resistance breeding. Whole-genome re-sequencing was conducted to systematically analyze the variations in two new inbred lines (Huaye 3 and Huaye 4) developed from a common wild rice. A total of 4,841,127 SNPs, 1,170,479 InDels, 24,080 structural variations (SVs), and 298 copy number variations (CNVs) were identified in three materials. Approximately 16.24 and 5.64% of the total SNPs and InDels of Huaye 3 and Huaye 4 were located in genic regions, respectively. Together, 12,486 and 15,925 large-effect SNPs, and 12,417 and 14,513 large-effect InDels, which affect the integrity of the encoded protein, were identified in Huaye 3 and Huaye 4, respectively. The distribution map of 194 and 245 NBS-LRR encoding homologs was constructed across 12 rice chromosomes. Further, GO enrichment analysis of the homologs with identical genotype variations in Huaye 3 and Huaye 4 revealed 67, 82, and 58 homologs involved in cell death, response to stress, and both terms, respectively. Comparative analysis displayed that 550 out of 652 SNPs and 129 out of 147 InDels were present in a widely used blast-susceptible rice variety (LTH). Protein-protein interaction analysis revealed a strong interaction between NBS-LRR candidates and several known R genes. One homolog of disease resistance protein (RPM1) was involved in the plant-pathogen interaction pathway. Artificial inoculation of disease/insect displayed resistance phenotypes against rice blast and brown planthopper in two lines. The results will provide allele-specific markers for rice molecular breeding.

中文翻译：

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遗传变异的全基因组分析和常见野生稻品系 NBS-LRR 编码基因丰富变异的检测

普通野生稻（Oryza rufipogon Griff.）是水稻抗性育种的宝贵遗传资源。进行全基因组重测序以系统分析从普通野生稻开发的两个新近交系（华野3号和华野4号）的变异。在三种材料中总共鉴定出 4,841,127 个 SNP、1,170,479 个 InDels、24,080 个结构变异 (SV) 和 298 个拷贝数变异 (CNV)。花野 3 号和花野 4 号的总 SNP 和 InDels 分别约有 16.24% 和 5.64% 位于基因区。在花叶 3 和花叶 4 中分别鉴定了 12,486 和 15,925 个大效应 SNP，以及 12,417 和 14,513 个影响编码蛋白完整性的大效应 InDels。在 12 条水稻染色体上构建了 194 和 245 NBS-LRR 编码同源物的分布图。更多，对花叶 3 和花叶 4 中具有相同基因型变异的同源物的 GO 富集分析揭示了分别涉及细胞死亡、应激反应和这两个术语的 67、82 和 58 个同源物。比较分析显示，652 个 SNP 中的 550 个和 147 个 InDel 中的 129 个存在于广泛使用的稻瘟病敏感水稻品种 (LTH) 中。蛋白质-蛋白质相互作用分析揭示了 NBS-LRR 候选者和几个已知 R 基因之间的强相互作用。抗病蛋白 (RPM1) 的一个同源物参与植物-病原体相互作用途径。病虫害的人工接种在两个品系中显示出对稻瘟病和褐飞虱的抗性表型。该结果将为水稻分子育种提供等位基因特异性标记。