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

Lixia Li,Ying Long,Xiaoming Wu,Hao Li

doi:10.3389/fgene.2019.01275

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.

Highlights

Plasmodiophora brassicae Wor. (P. brassicae), an obligate and biotrophic pathogen of Rhizaria (Schwelm et al, 2015), could infect over 3,700 species in Brassicaceae (Hwang et al, 2012), and lead clubroot which has caused significant economic losses every year (Dixon, 2009)
It was obvious that artificial inoculation in greenhouse can increase the disease index (DI) greatly compared with natural infection in field
Many studies focused on the middle or late phase/stage of clubroot course in Arabidopsis, B. rapa (Chinese cabbage), Brassica oleracea, and B. napus on the level of transcriptomics, proteomics, or others (Zhang et al, 2016; Hao et al, 2017; Irani et al, 2018; Ji et al, 2018; Prerostova et al, 2018; Su et al, 2018; Peng et al, 2019), while few studies were aimed at the early infection

Summary

Introduction

Plasmodiophora brassicae Wor. (P. brassicae), an obligate and biotrophic pathogen of Rhizaria (Schwelm et al, 2015), could infect over 3,700 species in Brassicaceae (Hwang et al, 2012), and lead clubroot which has caused significant economic losses every year (Dixon, 2009). (P. brassicae), an obligate and biotrophic pathogen of Rhizaria (Schwelm et al, 2015), could infect over 3,700 species in Brassicaceae (Hwang et al, 2012), and lead clubroot which has caused significant economic losses every year (Dixon, 2009). Once the conditions are suitable, primary zoospores are released from the resting spores to infect the root hairs when feel the stimulation of relevant signaling molecules secreted by host plants (Aist and Williams, 1971; Kageyama and Asano, 2009; Rolfe et al, 2016). The primary plasma mass is formed in the root hairs, and divided to form secondary sporangium, from which the secondary zoospores are released. The secondary plasma mass is divided to form mature resting spores, which are scattered in the soil and become the initial infection source in the coming year (McDonald et al, 2014). Only a few genes considering as the pathogenic factors in P. brassicae have been identified (Ando et al, 2006; Bulman et al, 2006; Feng et al, 2010)

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