A Comparative Transcriptome Analysis, Conserved Regulatory Elements and Associated Transcription Factors Related to Accumulation of Fusariotoxins in Grain of Rye (Secale cereale L.) Hybrids

Abstract

Detoxification of fusariotoxin is a type V Fusarium head blight (FHB) resistance and is considered a component of type II resistance, which is related to the spread of infection within spikes. Understanding this type of resistance is vital for FHB resistance, but to date, nothing is known about candidate genes that confer this resistance in rye due to scarce genomic resources. In this study, we generated a transcriptomic resource. The molecular response was mined through a comprehensive transcriptomic analysis of two rye hybrids differing in the build-up of fusariotoxin contents in grain upon pathogen infection. Gene mining identified candidate genes and pathways contributing to the detoxification of fusariotoxins in rye. Moreover, we found cis regulatory elements in the promoters of identified genes and linked them to transcription factors. In the fusariotoxin analysis, we found that grain from the Nordic seed rye hybrid “Helltop” accumulated 4 times higher concentrations of deoxynivalenol (DON), 9 times higher nivalenol (NIV), and 28 times higher of zearalenone (ZEN) than that of the hybrid “DH372” after artificial inoculation under field conditions. In the transcriptome analysis, we identified 6675 and 5151 differentially expressed genes (DEGs) in DH372 and Helltop, respectively, compared to non-inoculated control plants. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DEGs were associated with glycolysis and the mechanistic target of rapamycin (mTOR) signaling pathway in Helltop, whereas carbon fixation in photosynthesis organisms were represented in DH372. The gene ontology (GO) enrichment and gene set enrichment analysis (GSEA) of DEGs lead to identification of the metabolic and biosynthetic processes of peptides and amides in DH372, whereas photosynthesis, negative regulation of catalytic activity, and protein-chromophore linkage were the significant pathways in Helltop. In the process of gene mining, we found four genes that were known to be involved in FHB resistance in wheat and that were differentially expressed after infection only in DH372 but not in Helltop. Based on our results, we assume that DH372 employed a specific response to pathogen infection that led to detoxification of fusariotoxin and prevented their accumulation in grain. Our results indicate that DH372 might resist the accumulation of fusariotoxin through activation of the glycolysis and drug metabolism via cytochrome P450. The identified genes in DH372 might be regulated by the WRKY family transcription factors as associated cis regulatory elements found in the in silico analysis. The results of this study will help rye breeders to develop strategies against type V FHB.

Comparative Transcriptome Analysis Reveals the Gene Expression and Regulatory Characteristics of Broad-Spectrum Immunity to Leaf Rust in a Wheat–Agropyron cristatum 2P Addition Line

“…KEGG enrichment analysis counted only genes that were significantly differentially expressed, while GSEA, from the perspective of the enrichment of gene sets, was not limited to the DEGs, so it was theoretically easier to identify some genes that had small changes in expression but played a role in biological functions [37]. GSEA has been widely used for gene functional analysis in plants [38]. In this study, both KEGG enrichment analysis and GSEA revealed the disease resistance pathways of II-9-3.…”

Linking Multi-Omics to Wheat Resistance Types to Fusarium Head Blight to Reveal the Underlying Mechanisms

“…FHB is caused primarily by Fusarium graminearum infection, leading to the accumulation of several mycotoxins in grain such as predominantly deoxynivalenol (DON), nivalenol (NIV), and zearalenone (ZEN) which make grain unsuitable for human consumption and livestock feed [112]. Low mycotoxin accumulation is Type III FHB resistance [4], which is also considered as a component of Type II resistance because it commonly reduces the spread of disease [113]. Boutigny et al [114] further proposed classification of Type III resistance into two types: resistance to trichothecene accumulation by metabolic transformation of the toxin and resistance via inhibition of trichothecene biosynthesis.…”

Wild Rosa Endophyte M7SB41-Mediated Host Plant’s Powdery Mildew Resistance

“…The objective of this study was to elucidate how M7SB41 enhanced host plants PM resistance. Comprehensive transcriptome analysis can provide an ideal platform to investigate the genome-wide differentiations underlying the differently physiological traits, as well as to uncover complex signaling pathways activated in response to pathogen infection [ 25 ]. Therefore, to elucidate the mechanisms involved in host plants PM resistance induced by M7SB41, the differentially expressed genes between E+ and E− plants were studied by transcriptomic techniques.…”