Quantitative trait loci conferring resistance to Fusarium head blight in barley respond differentially to Fusarium graminearum infection

Barley Resistance to Fusarium graminearum Infections: From Transcriptomics to Field with Food Safety Concerns

Global climate change and the urgency to transform food crops require substantial breeding efforts to meet the food security challenges. Barley, an important cereal, has remained a preferential host of phytotoxic diseases caused by the Fusarium graminearum that not only severely reduces the crop yield but also compromises its food quality due to the accumulation of mycotoxins. To develop resistance against Fusarium infections, a better understanding of the host-pathogen interaction is inevitable and could be tracked through molecular insights. Here, we focused precisely on the potential gene targets that are exclusive to this devastating pathosystem and could be harnessed for fast breeding of barley. We also discuss the eco-friendly applications of nanobio hybrid and the CRISPR technology for barley protection. This review covers the critical information gaps within the subject and may be useful for the sustainable improvement of barley from the perspective of food and environmental safety concerns.

Integrative Analysis of Genes Involved in the Global Response to Potato Wart Formation

Synchytrium endobioticum, the causal agent of potato wart disease, poses a major threat to commercial potato production. Understanding the roles of transcriptionally regulated genes following pathogen infection is necessary for understanding the system-level host response to pathogen. Although some understanding of defense mechanisms against S. endobioticum infection has been gained for incompatible interactions, the genes and signaling pathways involved in the compatible interaction remain unclear. Based on the collection of wart diseased tubers of a susceptible cultivar, we performed phenotypic and dual RNA-Seq analyses of wart lesions in seven stages of disease progression. We totally detected 5,052 differentially expressed genes (DEGs) by comparing the different stages of infection to uninfected controls. The tendency toward differential gene expression was active rather than suppressed under attack by the pathogen. The number of DEGs step-up along with the development of the disease and the first, third and seventh of the disease stages showed substantially increase of DEGs in comparison of the previous stage. The important functional groups identified via Gene ontology (GO) and KEGG enrichment were those responsible for plant-pathogen interaction, fatty acid elongation and phenylpropanoid biosynthesis. Gene coexpression networks, composed of 17 distinct gene modules that contained between 25 and 813 genes, revealed high interconnectivity of the induced response and led to the identification of a number of hub genes enriched at different stages of infection. These results provide a comprehensive perspective on the global response of potato to S. endobioticum infection and identify a potential transcriptional regulatory network underlying this susceptible response, which contribute to a better understanding of the potato-S. endobioticum pathosystem.

Genetic dissection of a pericentromeric region of barley chromosome 6H associated with Fusarium head blight resistance, grain protein content and agronomic traits

Fine mapping of barley 6H pericentromeric region identified FHB QTL with opposite effects, and high grain protein content was associated with increased FHB severity. Resistance to Fusarium head blight (FHB), kernel discoloration (KD), deoxynivalenol (DON) accumulation and grain protein content (GPC) are important traits for breeding malting barley varieties. Previous work mapped a Chevron-derived FHB QTL to the pericentromeric region of 6H, coinciding with QTL for KD resistance and GPC. The Chevron allele reduced FHB and KD, but unfavorably increased GPC. To determine whether the correlations are caused by linkage or pleiotropy, a fine mapping approach was used to dissect the QTL underlying these quality and disease traits. Two populations, referred to as Gen10 and Gen10/Lacey, derived from a recombinant near-isogenic line (rNIL) were developed. Recombinants were phenotyped for FHB, KD, DON, GPC and other agronomic traits. Three FHB, two DON and two KD QTLs were identified. One of the three FHB QTLs, one DON QTL and one KD QTL were coincident with the GPC QTL, which contains the Hv-NAM1 locus affecting grain protein accumulation. The Chevron allele at the GPC QTL increased GPC and FHB and decreased DON and KD. The other two FHB QTL and the other DON and KD QTL were identified in the regions flanking the Hv-NAM1 locus, and the Chevron alleles decreased FHB, DON and KD. Our results suggested that the QTL associated with FHB, KD, DON and GPC in the pericentromeric region of 6H was controlled by both pleiotropy and tightly linked loci. The rNILs identified in this study with low FHB severity and moderate GPC may be used for breeding malting barley cultivars.

Hyperspectral imaging and improved feature variable selection for automated determination of deoxynivalenol in various genetic lines of barley kernels for resistance screening

Fusarium head blight (FHB), a fungus disease of small grain cereal crops, results in reduced yields and diminished value of harvested grain due to the presence of deoxynivalenol (DON), a mycotoxin produced by the causal pathogen Fusarium graminearum. DON and other tricothecene mycotoxins pose serious health risks to both humans and livestock, especially swine. Due to these health concerns, barley used for malting, food or feed is routinely assayed for DON levels. Various methods are available for assaying DON levels in grain samples including enzyme-linked immunosorbent assay (ELISA) and gas chromatography-mass spectrometry (GC-MS). ELISA and GC-MS are very accurate; however, assaying grain samples by these techniques are laborious, expensive and destructive. In this study, we explored the feasibility of using hyperspectral imaging (382-1030 nm) to develop a rapid and non-destructive protocol for assaying DON in barley kernels. Samples of 888 and 116 from various genetic lines were selected for calibration and prediction. Full-wavelength locally weighted partial least squares regression (LWPLSR) achieved high accuracy with the coefficient of determination in prediction (R²_P) of 0.728 and root mean square error of prediction (RMSEP) of 3.802. Competitive adaptive reweighted sampling (CARS) was used to choose potential feature wavelengths, and these selected variables were further optimized using the iterative selection of successive projections algorithm (ISSPA). The CARS-ISSPA-LWPLSR model developed using 7 feature variables yielded R²_P of 0.680 and RMSEP of 4.213 in DON content prediction. Based on the 7 wavelengths selected by CARS-ISSPA, partial least square discriminant analysis (PLSDA) discriminated barley kernels having lower DON (less than1.25 mg/kg) levels from those with higher levels (including 1.25-3 mg/kg, 3-5 mg/kg, and 5-10 mg/kg), with Matthews correlation coefficient in cross-validation (M-R_CV) of as high as 0.931. The results demonstrate that hyperspectral imaging have potential for accelerating non-destructive DON assays of barley samples.

Transcriptomics of cereal-Fusarium graminearum interactions: what we have learned so far

The ascomycete fungal pathogen Fusarium graminearum causes the globally important Fusarium head blight (FHB) disease on cereal hosts, such as wheat and barley. In addition to reducing grain yield, infection by this pathogen causes major quality losses. In particular, the contamination of food and feed with the F. graminearum trichothecene toxin deoxynivalenol (DON) can have many adverse short- and long-term effects on human and animal health. During the last decade, the interaction between F. graminearum and both cereal and model hosts has been extensively studied through transcriptomic analyses. In this review, we present an overview of how such analyses have advanced our understanding of this economically important plant-microbe interaction. From a host point of view, the transcriptomes of FHB-resistant and FHB-susceptible cereal genotypes, including near-isogenic lines (NILs) that differ by the presence or absence of quantitative trait loci (QTLs), have been studied to understand the mechanisms of disease resistance afforded by such QTLs. Transcriptomic analyses employed to dissect host responses to DON have facilitated the identification of the genes involved in toxin detoxification and disease resistance. From the pathogen point of view, the transcriptome of F. graminearum during pathogenic vs. saprophytic growth, or when infecting different cereal hosts or different tissues of the same host, have been studied. In addition, comparative transcriptomic analyses of F. graminearum knock-out mutants with altered virulence have provided new insights into pathogenicity-related processes. The F. graminearum transcriptomic data generated over the years are now being exploited to build a systems level understanding of the biology of this pathogen, with an ultimate aim of developing effective and sustainable disease prevention strategies.

Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

BACKGROUND

Fusarium graminearum causes Fusarium head blight (FHB), a major disease problem worldwide. Resistance to FHB is controlled by quantitative trait loci (QTL) of which two are located on barley chromosomes 2H bin8 and 6H bin7. The mechanisms of resistance mediated by FHB QTL are poorly defined.

RESULTS

Near-isogenic lines (NILs) carrying Chevron-derived resistant alleles for the two QTL were developed and exhibited FHB resistance in field trials. To understand the molecular responses associated with resistance, transcriptomes of the NILs and recurrent parents (M69 and Lacey) were investigated with RNA sequencing (RNA-Seq) after F. graminearum or mock inoculation. A total of 2083 FHB-responsive transcripts were detected and provide a gene expression atlas for the barley-F. graminearum interaction. Comparative analysis of the 2Hb8 resistant (R) NIL and M69 revealed that the 2Hb8 R NIL exhibited an elevated defense response in the absence of fungal infection and responded quicker than M69 upon fungal infection. The 6Hb7 R NIL displayed a more rapid induction of a set of defense genes than Lacey during the early stage of fungal infection. Overlap of differentially accumulated genes were identified between the two R NILs, suggesting that certain responses may represent basal resistance to F. graminearum and/or general biotic stress response and were expressed by both resistant genotypes. Long noncoding RNAs (lncRNAs) have emerged as potential key regulators of transcription. A total of 12,366 lncRNAs were identified, of which 604 were FHB responsive.

CONCLUSIONS

The current transcriptomic analysis revealed differential responses conferred by two QTL during F. graminearum infection and identified genes and lncRNAs that were associated with FHB resistance.

Transcriptome dynamics of a susceptible wheat upon Fusarium head blight reveals that molecular responses to Fusarium graminearum infection fit over the grain development processes

In many plant/pathogen interactions, host susceptibility factors are key determinants of disease development promoting pathogen growth and spreading in plant tissues. In the Fusarium head blight (FHB) disease, the molecular basis of wheat susceptibility is still poorly understood while it could provide new insights into the understanding of the wheat/Fusarium graminearum (Fg) interaction and guide future breeding programs to produce cultivars with sustainable resistance. To identify the wheat grain candidate genes, a genome-wide gene expression profiling was performed in the French susceptible wheat cultivar, Recital. Gene-specific two-way ANOVA of about 40 K transcripts at five grain developmental stages identified 1309 differentially expressed genes. Out of these, 536 were impacted by the Fg effect alone. Most of these Fg-responsive genes belonged to biological and molecular functions related to biotic and abiotic stresses indicating the activation of common stress pathways during susceptibility response of wheat grain to FHB. This analysis revealed also 773 other genes displaying either specific Fg-responsive profiles along with grain development stages or synergistic adjustments with the grain development effect. These genes were involved in various molecular pathways including primary metabolism, cell death, and gene expression reprogramming. An increasingly complex host response was revealed, as was the impact of both Fg infection and grain ontogeny on the transcription of wheat genes. This analysis provides a wealth of candidate genes and pathways involved in susceptibility responses to FHB and depicts new clues to the understanding of the susceptibility determinism in plant/pathogen interactions.

Cytological and molecular characterization of quantitative trait locus qRfg1, which confers resistance to gibberella stalk rot in maize

Tremendous progress has been made recently in understanding plant response to Fusarium graminearum infection. Here, the cytological aspect and molecular mechanism of maize defense to F. graminearum infection were characterized using a pair of near-isogenic lines (NIL), the resistant and the susceptible NIL. F. graminearum primarily penetrated the maize root tip and no penetration structure was found. The fungal biomass within the root correlated well with root-disease severity. Following inoculation, R-NIL and S-NIL plants significantly differed in percentage of diseased primary roots. In R-NIL roots, a fraction of exodermal cells collapsed to form cavities, and hyphae were confined to the outer exodermal cells. However, most exodermal cells shrank and turned brown, and fungi colonized the entire S-NIL root. In the R-NIL roots, the exodermal cells exhibited plasmolysis and atropous hyphal growth whereas, in the exodermal cells of the S-NIL roots, severe cellular degradation and membrane-coated, lushly grown hyphae were found. Transcriptome sequencing revealed comprehensive transcription reprogramming, reinforcement of a complex defense network, to enhance the systemic and basal resistance. This study reports a detailed microscopic analysis of F. graminearum infection on maize root, and provides insights into the molecular mechanisms underlying maize resistance to the pathogen.

Assessment and introduction of quantitative resistance to Fusarium head blight in elite spring barley

Breeding for resistance is a key task to control Fusarium head blight (FHB), a devastating disease of small cereals leading to economic losses and grain contamination with mycotoxins harmful for humans and animals. In the present work, FHB resistance of the six-rowed spring barley 'Chevron' to FHB in Germany was compared with those of adapted German spring barley cultivars. Both under natural infection conditions and after spray inoculation with conidia of Fusarium culmorum, F. sporotrichioides, and F. avenaceum under field conditions, Chevron showed a high level of quantitative resistance to the infection and contamination of grain with diverse mycotoxins. This indicates that Chevron is not only a little susceptible to deoxynivalenol-producing Fusarium spp. but also to Fusarium spp. producing type A trichothecenes and enniatins. Monitoring the initial infection course of F. culmorum on barley lemma tissue by confocal laser-scanning microscopy provided evidence that FHB resistance of Chevron is partially mediated by a preformed penetration resistance, because direct penetration of floral tissue by F. culmorum was observed rarely on Chevron but was common on susceptible genotypes. Alternatively, F. culmorum penetrated Chevron lemma tissue via stomata, which was unusual for susceptible genotypes. We generated double-haploid barley populations segregating for the major FHB resistance quantitative trait loci (QTL) Qrgz-2H-8 of Chevron. Subsequently, we characterized these populations by spray inoculation with conidia of F. culmorum and F. sporotrichioides. This suggested that Qrgz-2H-8 was functional in the genetic background of European elite barley cultivars. However, the degree of achieved resistance was very low when compared with quantitative resistance of the QTL donor Chevron, and the introgression of Qrgz-2H-8 was not sufficient to mediate the cellular resistance phenotype of Chevron in the European backgrounds.

On the trail of a cereal killer: recent advances in Fusarium graminearum pathogenomics and host resistance

The ascomycete fungal pathogen Fusarium graminearum (sexual stage: Gibberella zeae) causes the devastating head blight or scab disease on wheat and barley, and cob or ear rot disease on maize. Fusarium graminearum infection causes significant crop and quality losses. In addition to roles as virulence factors during pathogenesis, trichothecene mycotoxins (e.g. deoxynivalenol) produced by this pathogen constitute a significant threat to human and animal health if consumed in respective food or feed products. In the last few years, significant progress has been made towards a better understanding of the processes involved in F. graminearum pathogenesis, toxin biosynthesis and host resistance mechanisms through the use of high-throughput genomic and phenomic technologies. In this article, we briefly review these new advances and also discuss how future research can contribute to the development of sustainable plant protection strategies against this important plant pathogen.