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

Frontiers in Plant Science Pub Date : 2024-05-23 DOI:10.3389/fpls.2024.1396602

Xueqing Zhou, Ting Zhong, Meixiu Wu, Qian Li, Wenlin Yu, Longcai Gan, Xianyu Xiang, Yunyun Zhang, Yaru Shi, Yuanwei Zhou, Peng Chen, Chunyu Zhang

{"title":"Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism","authors":"Xueqing Zhou, Ting Zhong, Meixiu Wu, Qian Li, Wenlin Yu, Longcai Gan, Xianyu Xiang, Yunyun Zhang, Yaru Shi, Yuanwei Zhou, Peng Chen, Chunyu Zhang","doi":"10.3389/fpls.2024.1396602","DOIUrl":null,"url":null,"abstract":"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.","PeriodicalId":505607,"journal":{"name":"Frontiers in Plant Science","volume":"18 19","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in Plant Science","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3389/fpls.2024.1396602","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 0

Abstract

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.

查看原文本刊更多论文

对抗性欧洲萝卜 ECD04 在球根病感染期间的多组学分析揭示了抗性机制的关键枢纽基因

由于根瘤病由土壤传播，且很难从受污染的田地中完全根除，因此它已成为十字花科作物生产的一个全球性威胁。在这项研究中，我们使用了抗性欧洲饲料芜菁 ECD04，并利用转录组、sRNA-seq、降解组和基因编辑技术研究了其抗性机理。从感染后的三个时间点共鉴定出 1751 个 DEGs，其中有 7 个中枢基因，包括细胞壁组装的 XTH23 和 PTI 通路中的两个 CPK28 基因。在微小RNA方面，我们发现了17个DEM，并预测了15对miRNA-靶标（DEM-DEG）。我们通过降解组测序验证了两个配对（miR395-APS4 和 miR160-ARF）。我们通过 CRISPR-Cas9 介导的基因编辑对 miR395-APS4 进行了研究，结果表明敲除 APS4 可提高油菜的抗球根病能力。总之，所获得的转录反应和 microRNA 以及靶基因的数据为未来的研究提供了方向，特别是为遗传改良甘蓝类作物的抗球根病能力提供了候选基因。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Frontiers in Plant Science

自引率

0.00%

发文量