Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum

Jin-Qi Ma,Jia-Na Li,Wei Sun,Kun Lu,Fei Xu,Li-Juan Wei,Wen Xu,Huan-Huan Jiang,Ai Lin

doi:10.3390/genes11070784

Abstract

Alternative splicing (AS) is a post-transcriptional level of gene expression regulation that increases transcriptome and proteome diversity. How the AS landscape of rapeseed (Brassica napus L.) changes in response to the fungal pathogen Sclerotinia sclerotiorum is unknown. Here, we analyzed 18 RNA-seq libraries of mock-inoculated and S. sclerotiorum-inoculated susceptible and tolerant B. napus plants. We found that infection increased AS, with intron retention being the main AS event. To determine the key genes functioning in the AS response, we performed a differential AS (DAS) analysis. We identified 79 DAS genes, including those encoding splicing factors, defense response proteins, crucial transcription factors and enzymes. We generated coexpression networks based on the splicing isoforms, rather than the genes, to explore the genes’ diverse functions. Using this weighted gene coexpression network analysis alongside a gene ontology enrichment analysis, we identified 11 modules putatively involved in the pathogen defense response. Within these regulatory modules, six DAS genes (ascorbate peroxidase 1, ser/arg-rich protein 34a, unknown function 1138, nitrilase 2, v-atpase f, and amino acid transporter 1) were considered to encode key isoforms involved in the defense response. This study provides insight into the post-transcriptional response of B. napus to S. sclerotiorum infection.

Highlights

Rapeseed (Brassica napus L.), the second largest oilseed crop in the world [1], is vulnerable to the necrotrophic ascomycete pathogen Sclerotinia sclerotiorum, which targets over 400 host species [2,3], including soybean (Glycine max), peanut (Arachis hypogaea), and sunflower (Helianthus annuus) [4].S. sclerotiorum infects the leaves and stem of its host plants and causes Sclerotinia stem rot (SSR), known as white mold, in rapeseed, resulting in yield losses of up to 94% in severe SSR outbreak seasons in the major growing areas such as Canada, China and the USA [5,6]
The raw data were downloaded from two datasets, one of which comprised single-end reads and the other paired-end reads
We aimed to identify genetic factors and specific response mechanisms that influence resistance to SSR by analyzing the RNA sequencing (RNA-seq) data of infected and mock-treated resistant and susceptible cultivars

Summary

Introduction

S. sclerotiorum infects the leaves and stem of its host plants and causes Sclerotinia stem rot (SSR), known as white mold, in rapeseed, resulting in yield losses of up to 94% in severe SSR outbreak seasons in the major growing areas such as Canada, China and the USA [5,6]. Despite this huge economic impact, no highly resistant B. napus varieties have been developed. Current research into SSR is mainly focused on the pathogenicity and resistance mechanisms involved.

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