Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Fusarium graminearum Infection in Wheat

Abstract

RNA/DNA difference (RDD) is a post-transcriptional modification playing a crucial role in regulating diverse biological processes in eukaryotes. Although it has been extensively studied in plant chloroplast and mitochondria genomes, RDDs in plant nuclear genomes are not well studied at present. Here, we investigated the RDDs associated with fusarium head blight (FHB) through a novel method by comparing the RNA-seq data between Fusarium-infected and control samples of four wheat genotypes. A total of 187 high-confidence unique RDDs in 36 genes were identified, representing the first landscape of the FHB-responsive RDD in wheat. The majority (26) of these 36 RDD genes were correlated either positively or negatively with FHB levels. Effects of these RDDs on RNA and protein sequences have been identified, their editing frequency and the expression level of the corresponding genes provided, and the prediction of the effect on the minimum folding free energy of mRNA, miRNA binding, and colocation of RDDs with conserved domains presented. RDDs were predicted to induce modifications in the mRNA and protein structures of the corresponding genes. In two genes, TraesCS1B02G294300 and TraesCS3A02G263900, editing was predicted to enhance their affinity with tae-miR9661-5p and tae-miR9664-3p, respectively. To our knowledge, this study is the first report of the association between RDD and FHB in wheat; this will contribute to a better understanding of the molecular basis underlying FHB resistance, and potentially lead to novel strategies to improve wheat FHB resistance through epigenetic methods.

Multi-locus genome-wide association study of fusarium head blight in relation to days to anthesis and plant height in a spring wheat association panel

“…MORF family proteins are involved in RNA editing (Benne et al, 1986) in the organelles of flowering plants (Takenaka et al, 2012). The first study of RNA editing or RNA/DNA difference (RDDs) in wheat, in response to F. graminearum infection, was carried out by Yang et al (2022), using publicly available RNA-seq samples of four wheat genotypes, Nyubai, Wuhan 1, HC374, and Shaw. The sixth (QTN7A_200-266-273-287) pleiotropic FHB trait QTN, also on chromosome 7A, co-locates with an actin-fragmin kinase (AFK) catalytic domaincontaining protein.…”

Comparative transcriptomics identifies the key in planta-expressed genes of Fusarium graminearum during infection of wheat varieties

“…In recent years, transcriptomic analysis based on RNA sequencing has been widely used to dissect key genes and underlying mechanisms involved in host– F. graminearum interactions ( Kazan and Gardiner, 2018 ). Most studies have focused on comparing the expression of genes during the infection of a single plant host, including F. graminearum genes and plant host genes, or comparing the expression of host genes between different plant hosts ( Boedi et al, 2016 ; Chetouhi et al, 2016 ; Puri et al, 2016 ; Mentges et al, 2020 ; Yang et al, 2022 ; Yin et al, 2022 ). However, the mechanistic interplay between F. graminearum and different wheat varieties during FHB infection, especially for susceptible and resistant varieties, needs further analysis.…”