Identification of Micro Ribonucleic Acids and Their Targets in Response to Plasmodiophora brassicae Infection in Brassica napus

Abstract

Clubroot disease, which is caused by the soil-borne pathogen Plasmodiophora brassicae War (P. brassicae), is one of the oldest and most destructive diseases of Brassica and cruciferous crops in the world. Plant microRNAs [micro ribonucleic acids (miRNAs)] play important regulatory roles in several developmental processes. Although the role of plant miRNAs in plant-microbe interaction has been extensively studied, there are only few reports on the specific functions of miRNAs in response to P. brassicae. This study investigated the roles of miRNAs and their targets during P. brassicae infection in a pair of Brassica napus near-isogenic lines (NILs), namely clubroot-resistant line 409R and clubroot-susceptible line 409S. Small RNA sequencing (sRNA-seq) and degradome-seq were performed on root samples of 409R and 409S with or without P. brassicae inoculation. sRNA-seq identified a total of 48 conserved and 72 novel miRNAs, among which 18 had a significant differential expression in the root of 409R, while only one miRNA was differentially expressed in the root of 409S after P. brassicae inoculation. The degradome-seq analysis identified 938 miRNA target transcripts, which are transcription factors, enzymes, and proteins involved in multiple biological processes and most significantly enriched in the plant hormone signal transduction pathway. Between 409R and 409S, we found eight different degradation pathways in response to P. brassicae infection, such as those related to fatty acids. By combining published transcriptome data, we identified a total of six antagonistic miRNA-target pairs in 409R that are responsive to P. brassicae infection and involved in pathways associated with root development, hypersensitive cell death, and chloroplast metabolic synthesis. Our results reveal that P. brassicae infection leads to great changes in miRNA pool and target transcripts. More interestingly, these changes are different between 409R and 409S. Clarification of the crosstalk between miRNAs and their targets may shed new light on the possible mechanisms underlying the pathogen resistance against P. brassicae.

Transgressive and parental dominant gene expression and cytosine methylation during seed development inBrassica napushybrids

“…Differential expression from targets of the aforementioned miRNA families was observed in our studies during seed development, and further target validation through degradome sequencing (German et al, 2008), precise isomiRs classification (Morin et al, 2008; Sablok et al, 2015; Yang et al, 2019), target knock-out experiments (Jain et al, 2018; Wei et al, 2018; Li et al, 2021) as well as gene co-expression networks (Schiessl et al, 2020) can prove beneficial for identifying their role in seed and embryo formation in B . napus .…”

Mapping of a novel clubroot disease resistance locus in Brassica napus and related functional identification

“…The miR172/TOE1-TOE2 is an important regulatory module in plants, involved in plant development regulation, morphogenesis and innate immunity (Zou et al, 2018;Werner et al, 2021). There has been reported that this module in response to P. brassicae infection in B. napus (Li et al, 2021a). In summary, the exploration of the CR mechanism involving ERF034 can be carried out from these three aspects: (i) hormone regulation associated with ERF034, including ethylene, SA, jasmonic acid (JA), etc.…”

What Can We Learn from -Omics Approaches to Understand Clubroot Disease?

“…Novel miRNAs were identified in the differentially regulated set of another important crop plant, Chinese cabbage ( B. rapa ) using similar experimental approaches [ 108 ]. Extending these findings to resistant and susceptible cultivars of B. napus to P. brassicae identified several specific miRNA–target RNA pairs for the resistant reaction [ 109 ]. Consequently, specific miRNAs were identified that regulate disease tolerance genes of the TIR-NBS family in B. napus [ 110 ].…”