Table_6_Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism.xlsx

The clubroot disease has become a worldwide threat for crucifer crop production, due to its soil-borne nature and difficulty to eradicate completely from contaminated field. In this study we used an elite resistant European fodder turnip ECD04 and investigated its resistance mechanism using transcriptome, sRNA-seq, degradome and gene editing. A total of 1751 DEGs were identified from three time points after infection, among which 7 hub genes including XTH23 for cell wall assembly and two CPK28 genes in PTI pathways. On microRNA, we identified 17 DEMs and predicted 15 miRNA-target pairs (DEM-DEG). We validated two pairs (miR395-APS4 and miR160-ARF) by degradome sequencing. We investigated the miR395-APS4 pair by CRISPR-Cas9 mediated gene editing, the result showed that knocking-out APS4 could lead to elevated clubroot resistance in B. napus. In summary, the data acquired on transcriptional response and microRNA as well as target genes provide future direction especially gene candidates for genetic improvement of clubroot resistance on Brassica species.

根肿病（clubroot disease）因其土传特性且难以从受污染农田彻底根除，已成为全球十字花科作物生产的重大威胁。本研究选用优良抗源欧洲饲用芜菁ECD04，通过转录组、小RNA测序（sRNA-seq）、降解组测序（degradome）及基因编辑技术解析其抗根肿病机制。本研究在病原菌侵染后的三个时间点中共鉴定出1751个差异表达基因（DEGs），其中包含7个核心基因：分别为参与细胞壁组装的XTH23，以及模式触发免疫（Pattern-Triggered Immunity，PTI）通路中的2个CPK28基因。在microRNA层面，本研究鉴定出17个差异表达miRNA（DEMs），并预测得到15个miRNA-靶基因对（DEM-DEG）。借助降解组测序验证了其中两对调控组合：miR395-APS4与miR160-ARF。本研究利用CRISPR-Cas9介导的基因编辑技术对miR395-APS4调控轴展开深入研究，结果显示敲除APS4可提升甘蓝型油菜（Brassica napus，B. napus）的根肿病抗性。综上，本研究获取的转录响应、microRNA及其靶基因相关数据，可为芸苔属（Brassica）作物的根肿病抗性遗传改良提供关键研究方向，尤其是候选基因靶点。