Root-knot nematodes (RKNs) are infamous plant pathogens in tomato production, causing considerable losses in agriculture worldwide. Mi-1 is the only commercially available RKN-resistance gene; however, the resistance is inactivated when the soil temperature is over 28 °C. Mi-9 in wild tomato (Solanum arcanum LA2157) has stable resistance to RKNs under high temperature but has not been cloned and applied. In this study, a chromosome-scale genome assembly of S. arcanum LA2157 was constructed through Nanopore and Hi-C sequencing. Based on molecular markers of Mi-9 and comparative genomic analysis, the localization region and candidate Mi-9 genes cluster consisting of seven nucleotide-binding sites and leucine-rich repeat (NBS-LRR) genes were located. Transcriptional expression profiles confirmed that five of the seven candidate genes were expressed in root tissue. Moreover, virus-induced gene silencing of the Sarc_034200 gene resulted in increased susceptibility of S. arcanum LA2157 to Meloidogyne incognita, and genetic transformation of the Sarc_034200 gene in susceptible Solanum pimpinellifolium conferred significant resistance to M. incognita at 25 °C and 30 °C and showed hypersensitive responses at nematode infection sites. This suggested that Sarc_034200 is the Mi-9 gene. In summary, we cloned, confirmed and applied the heat-stable RKN-resistance gene Mi-9, which is of great significance to tomato breeding for nematode resistance.

中文翻译：

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染色体规模基因组组装辅助鉴定茄属 LA2157 中的 Mi-9 基因，赋予对南方根结线虫的热稳定抗性

根结线虫（RKN）是番茄生产中臭名昭著的植物病原体，给全世界农业造成巨大损失。Mi-1是唯一市售的RKN抗性基因；但当土壤温度超过28℃时，抵抗力就会失活。野生番茄( Solanum arcanum LA2157)中的Mi-9在高温下对RKNs具有稳定的抗性，但尚未被克隆和应用。在本研究中，通过纳米孔和Hi-C测序构建了S.arcanum LA2157的染色体规模基因组组装。基于Mi-9的分子标记和比较基因组分析，定位区域和候选Mi-9定位了由七个核苷酸结合位点和富含亮氨酸重复序列（NBS-LRR）基因组成的基因簇。转录表达谱证实七个候选基因中有五个在根组织中表达。此外，病毒诱导的Sarc_034200基因沉默导致S.arcanum LA2157对南方根结线虫的敏感性增加，并且易感Solanum pimpinellifolium中Sarc_034200基因的遗传转化赋予了在25℃和30℃下对南方根结线虫的显着抗性。并在线虫感染部位表现出过敏反应。这表明Sarc_034200是Mi-9基因。综上所述，我们克隆、证实并应用了耐热RKN抗性基因Mi-9，对番茄抗线虫育种具有重要意义。