Table_1_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中彻底根除，已成为威胁十字花科作物生产的全球性病害。本研究以优异抗病欧洲饲用芜菁ECD04为实验材料，通过转录组（transcriptome）、小RNA测序（sRNA-seq）、降解组（degradome）及基因编辑技术解析其抗病分子机制。研究共在病原菌侵染后的三个时间点中鉴定出1751个差异表达基因（Differentially Expressed Genes, DEGs），其中包含7个枢纽基因：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，本研究共鉴定出17个差异表达miRNA（Differentially Expressed miRNAs, DEMs），并预测得到15组miRNA-靶基因对（DEM-DEG）；通过降解组测序验证了其中2组调控组合：miR395-APS4与miR160-ARF。针对miR395-APS4调控轴，本研究开展了CRISPR-Cas9介导的基因编辑实验，结果显示敲除APS4可显著提升甘蓝型油菜（Brassica napus, B. napus）的根肿病抗性。综上，本研究获得的转录响应、microRNA及其靶基因相关数据，为芸苔属（Brassica）物种的根肿病抗性遗传改良提供了明确的研究方向与候选基因资源。