Comparative transcriptome analysis of resistant and susceptible wheat in response to Rhizoctonia cerealis

Abstract

Background: Sheath blight is an important disease caused by Rhizoctonia cerealis that affects wheat yields worldwide. No wheat varieties have been identified with high resistance or immunity to sheath blight. Understanding the sheath blight resistance mechanism is essential for controlling this disease. In this study, we investigated the response of wheat to Rhizoctonia cerealis infection by analyzing the cytological changes and transcriptomes of common wheat 7182 with moderate sensitivity to sheath blight and H83 with moderate resistance.

Results: The cytological observation showed that the growth of Rhizoctonia cerealis on the surface and its expansion inside the leaf sheath tissue were more rapid in the susceptible material. According to the transcriptome sequencing results, a total of 88685 genes were identified in both materials, including 20156 differentially expressed genes (DEGs) of which 12087 was upregulated genes and 8069 was downregulated genes. At 36 h post-inoculation, compared with the uninfected control, 11498 DEGs were identified in resistant materials, with 5064 downregulated genes and 6434 upregulated genes, and 13058 genes were detected in susceptible materials, with 6759 downregulated genes and 6299 upregulated genes. At 72 h post-inoculation, compared with the uninfected control, 6578 DEGs were detected in resistant materials, with 2991 downregulated genes and 3587 upregulated genes, and 7324 genes were detected in susceptible materials, with 4119 downregulated genes and 3205 upregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included biosynthesis of secondary metabolites, carbon metabolism, plant hormone signal transduction, and plant-pathogen interaction. In particular, phenylpropane biosynthesis pathway is specifically activated in resistant variety H83 after infection. Many DEGs also belonged to the MYB, AP2, NAC, and WRKY transcription factor families.

Conclusions: Thus, we suggest that the normal functioning of plant signaling pathways and differences in the expression of key genes and transcription factors in some important metabolic pathways may be important for defending wheat against sheath blight. These findings may facilitate further exploration of the sheath blight resistance mechanism in wheat and the cloning of related genes.

Keywords: Comparative transcriptome; Plant hormone; Plant–fungus interaction; Rhizoctonia cerealis; Sheath blight; Wheat (Triticum aestivum L.).

Fig. 1

Infection of hypha in inoculated leaf sheath in resistant susceptible material H83 and susceptible material 7182 at different time point. G-12h-G-120h: hypha growth on leaf sheath of susceptible material 7182 at different time points after inoculation; H-12h-H-120h: hypha growth on leaf sheath of susceptible material 7182 at different time points after inoculation; A-H: electron microscopic image of hyphae invading leaf sheath; Bar: (G-12h-H-120h): 200 μm; (A, C, D, E): 100 μm; B: 5 μm; F: 2 μm; G:5 μm; H:1 μm

Fig. 2

Images of sheath blight mycelium infection of leaf sheaths at different times after inoculation. G-12h-G-120h: hypha growth on leaf sheath of susceptible material 7182 at different time points after inoculation; H-12h-H-120h: hypha growth on leaf sheath of susceptible material 7182 at different time points after inoculation. Bar: 50μm

Fig. 3

Principal component analysis of samples (a). Distribution of expressed genes in each sample (b). The horizontal axis represents each sample and the vertical axis represents the fragments per kilobase of transcripts per million mapped reads (FPKMs) values for different samples

Fig. 4

Histogram (a) and Venn diagram (b) based on the DEGs in H83 and 7182 after Rhizoctonia cerealis infection at the different time points. The horizontal axis represents different samples, the the vertical axis indicates the number of DEGs. The blue column, brick red column and gray column represent the total DEGs, up-regulated DEGs and down-regulated DEGs, respectively. Each circle represents all differentially expressed genes expressed in one sample

Fig. 5

GO enrichment analysis of DEGs in resistant material H83 and susceptible material 7182 at different times after inoculation. The x-axis represents the GO term for the annotated DEG and the y-axis represents the number of DEGs annotated for each GO term. (a–b) GO enrichment analysis of DEGs in susceptible material 7182 at 36 and 72 h post-inoculation, respectively. (c–d) GO enrichment analysis of DEGs in resistant material H83 at 36 and 72 h post-inoculation, respectively

Fig. 6

KEGG enrichment analysis of DEGs in resistant material H83 and susceptible material 7182 at different times after inoculation. The x-axis represents the gene ratio. The y-axis represents the KEGG pathways enriched for DEGs. The bubble size indicates the number of DEGs. The color of the bubble indicates the significance of the pathway enriched for DEGs according to the adjusted P-value. (a–b) KEGG classifications of DEGs in susceptible material 7182 at 36 and 72 h post-inoculation, respectively. (c–d) KEGG classifications of DEGs in resistant material H83 at 36 and 72 h post-inoculation, respectively

Fig. 7

Analysis of specific differentially expressed transcription factors in both materials. Expression levels are shown for the MYB, AP2, WRKY, NAC and transcription factors in resistant material H83 and susceptible material 7182. FPKM values are represented by color gradient of low = navy blue to high = red brick

Fig. 8

Overview of gene expression and signal transduction in resistant material H83 at 36 h post-inoculation. Each box represents a DEG; Navy blue and red brick colors denote down- and up regulated DEG. The Figure 8 is drawn by me using drawing software (Adobe Illustrator CS5) according to my own experimental results on the basis Fig. 6 b in article of Zhang et al. (2020) [88]. JA: jasmonic acid; SA: salicylic acid (SA); JAZ: jasmonate ZIM-domain; NPR1: Nonexpressor of pathogenesis-related genes 1; CNGCs: cyclic nucleotide gated channels; CaM/CML: calmodulin/calmodulin-like proteins; CDPK: calcium-dependent protein kinase; NPR1: non-expresser of pathogenesis related [PR] 1; TFs: transcription factors; TGA: TGACG motif-binding factor; MAPK: Mitogen-activated protein kinase; COI1: CORONATINE INSENSITIVE1

Fig. 9

qRT-PCR identification of DEGs obtained from RNA sequencing results. The qRT-PCR values are the averages based on three replicates. Log2 (fold change) represents the logarithm of the gene expression level at 72 h relative to that at 0 h post-inoculation. The grid histogram represents the gene expression data in the susceptible material 7182 and the plain histogram represents the expression data in the resistant material H83