Brown stem rot (BSR) reduces soybean [Glycine max (L.) Merr.] yield by up to 38%. The BSR causal agent is Phialophora gregata f. sp. sojae, a slow‐growing, necrotrophic fungus whose life cycle includes latent and pathogenic phases, each lasting several weeks. Brown stem rot foliar symptoms are often misdiagnosed as other soybean diseases or nutrient stress, making BSR resistance especially difficult to phenotype. To shed light on the genes and networks contributing to P. gregata resistance, we conducted RNA sequencing (RNA‐seq) of a resistant genotype (PI 437970, Rbs3). Leaf, stem, and root tissues were collected 12, 24, and 36 h after stab inoculation with P. gregata, or mock infection, in the plant stem. By using multiple tissues and time points, we could see that leaves, stems, and roots use the same defense pathways. Our analyses suggest that P. gregata induces a biphasic defense response, with pathogen‐associated molecular pattern (PAMP) triggered immunity observed in leaves at 12 and 24 h after infection (HAI) and effector triggered immunity detected at 36 h after infection in the stems. Gene networks associated with defense, photosynthesis, nutrient homeostasis, DNA replication, and growth are the hallmarks of resistance to P. gregata. While P. gregata is a slow‐growing pathogen, our results demonstrate that pathogen recognition occurs hours after infection. By exploiting the genes and networks described here, we will be able to develop novel diagnostic tools to facilitate breeding and screening for BSR resistance.

中文翻译：

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表征大豆早期褐变病抗性信号的新工具

褐腐病（BSR）使大豆[ Glycine max（L.）Merr。]的产量降低多达38％。BSR的病因是Phialophora gregata f。sp。大豆，一种生长缓慢的坏死性真菌，其生命周期包括潜伏期和致病期，每期持续数周。褐茎腐烂的叶状症状通常被误诊为其他大豆疾病或营养胁迫，这使得BSR抗性尤其难以表型。为了阐明有助于聚合酶抗性的基因和网络，我们进行了抗性基因型（PI 437970，Rbs3）的RNA测序（RNA-seq ）。在用P. gregata刺伤接种后12、24和36小时收集叶，茎和根组织或植物茎中的模拟感染。通过使用多个组织和时间点，我们可以看到叶，茎和根使用相同的防御途径。我们的分析表明，聚合假单胞菌诱导双相防御反应，在感染（HAI）后12和24 h在叶片中观察到病原体相关分子模式（PAMP）触发免疫，在茎中感染后36 h观察到效应子触发免疫。 。与防御，光合作用，营养稳态，DNA复制和生长相关的基因网络是对聚合球菌抗性的标志。而P. gregata是一种生长缓慢的病原体，我们的结果表明病原体识别发生在感染后数小时。通过利用此处描述的基因和网络，我们将能够开发新颖的诊断工具，以促进BSR抗性的育种和筛选。