Comparative Transcriptome Analysis Reveals Key Pathways and Hub Genes in Rapeseed During the Early Stage of Plasmodiophora brassicae Infection

Abstract

Rapeseed (Brassica napus L., AACC, 2n = 38) is one of the most important oil crops around the world. With intensified rapeseed cultivation, the incidence and severity of clubroot infected by Plasmodiophora brassicae Wor. (P. brassicae) has increased very fast, which seriously impedes the development of rapeseed industry. Therefore, it is very important and timely to investigate the mechanisms and genes regulating clubroot resistance (CR) in rapeseed. In this study, comparative transcriptome analysis was carried out on two rapeseed accessions of R-(resistant) and S-(susceptible) line. Three thousand one hundred seventy-one and 714 differentially expressed genes (DEGs) were detected in the R-and S-line compared with the control groups, respectively. The results indicated that the CR difference between the R-and S-line had already shown during the early stage of P. brassicae infection and the change of gene expression pattern of R-line exhibited a more intense defensive response than that of S-line. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of 2,163 relative-DEGs, identified between the R-and S-line, revealed that genes participated in plant hormone signal transduction, fatty acid metabolism, and glucosinolate biosynthesis were involved in regulation of CR. Further, 12 hub genes were identified from all relative-DEGs with the help of weighted gene co-expression network analysis. Haplotype analysis indicated that the natural variations in the coding regions of some hub genes also made contributed to CR. This study not only provides valuable information for CR molecular mechanisms, but also has applied implications for CR breeding in rapeseed.

Transcriptome and Coexpression Network Analyses Reveal Hub Genes in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) During Different Stages of Plasmodiophora brassicae Infection

“…In our study, the expressions of BraA06g001760.3C and BraA06g001780.3C ( AOP1 ) at 5, 13, and 22 dai were found to be highly upregulated in DH40R relative to DH199S. Lipid metabolism indirectly involves or influences plant immunity, which might affect the energy flux from pathway to pathway or act as a physical barrier to impact the plant disease resistance response ( Li et al, 2020 ). The expression level of BraA03g027950.3C(lipid transfer protein EARLI 1) was upregulated in DH40R vs. DH199S at 5, 13, and 22 dai.…”

“…In this study, to better distinguish DEGs, the concept of relative period differentially expressed genes (rDEGs) was proposed; that is, when a gene was identified as a DEG between the R- and S-lines, but also identified as a DEG in the R-line compared with the R-previous period line at the corresponding time points, the gene was defined as a rDEG ( Li et al, 2020 ). GO enrichment analysis, KEGG pathway analysis and heatmap generation were performed using TBtools ( Chen C. et al, 2018 ).…”

Soil microbiota influences clubroot disease by modulatingPlasmodiophora brassicaeandBrassica napustranscriptomes

“…Concerning the plant, P. brassicae infection altered likewise primary and secondary metabolism, as pathways involved in lipid, carbohydrate, cell wall synthesis, lignification‐related genes, arginine and proline metabolism (Ludwig‐Müller, 2008; Gravot et al ., 2011; Gravot et al ., 2012; Chen et al ., 2015; Li et al ., 2020), producing a sink of plant metabolites assimilated by the pathogen and corresponding to a metabolic cost for the infested plant. Clubroot infection also modified plant hormone homeostasis and defence responses, such as cytokinin biosynthesis, auxin homeostasis, salicylic acid and jasmonic acid metabolism (Siemens et al ., 2006; Ludwig‐Müller, 2008; Agarwal et al ., 2011; Schuller et al ., 2014; Chen et al ., 2015; Lemarie et al ., 2015; Malinowski et al ., 2016; Li et al ., 2020).…”

Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization

“…Phenotypic and molecular event-based RNA-Seq transcriptome analysis and WGCNA are powerful research methods [ 21 – 23 ]. WGCNA is a progressive analysis method in which variable genes are divided into co-expression modules through an unsigned network based on the gene expression patterns identified by RNA-Seq.…”