Time-course expression QTL-atlas of the global transcriptional response of wheat to Fusarium graminearum

Molecular mechanisms underpinning quantitative resistance to Phytophthora sojae in Glycine max using a systems genomics approach

Expression of quantitative disease resistance in many host-pathogen systems is controlled by genes at multiple loci, each contributing a small effect to the overall response. We used a systems genomics approach to study the molecular underpinnings of quantitative disease resistance in the soybean-Phytophthora sojae pathosystem, incorporating expression quantitative trait loci (eQTL) mapping and gene co-expression network analysis to identify the genes putatively regulating transcriptional changes in response to inoculation. These findings were compared to previously mapped phenotypic (phQTL) to identify the molecular mechanisms contributing to the expression of this resistance. A subset of 93 recombinant inbred lines (RILs) from a Conrad × Sloan population were inoculated with P. sojae isolate 1.S.1.1 using the tray-test method; RNA was extracted, sequenced, and the normalized read counts were genetically mapped from tissue collected at the inoculation site 24 h after inoculation from both mock and inoculated samples. In total, more than 100,000 eQTLs were mapped. There was a switch from predominantly cis-eQTLs in the mock treatment to an almost entirely nonoverlapping set of predominantly trans-eQTLs in the inoculated treatment, where greater than 100-fold more eQTLs were mapped relative to mock, indicating vast transcriptional reprogramming due to P. sojae infection occurred. The eQTLs were organized into 36 hotspots, with the four largest hotspots from the inoculated treatment corresponding to more than 70% of the eQTLs, each enriched for genes within plant-pathogen interaction pathways. Genetic regulation of trans-eQTLs in response to the pathogen was predicted to occur through transcription factors and signaling molecules involved in plant-pathogen interactions, plant hormone signal transduction, and MAPK pathways. Network analysis identified three co-expression modules that were correlated with susceptibility to P. sojae and associated with three eQTL hotspots. Among the eQTLs co-localized with phQTLs, two cis-eQTLs with putative functions in the regulation of root architecture or jasmonic acid, as well as the putative master regulators of an eQTL hotspot nearby a phQTL, represent candidates potentially underpinning the molecular control of these phQTLs for resistance.

Two major quantitative trait loci control wheat dwarf virus resistance in four related winter wheat populations

KEY MESSAGE

Qwdv.ifa-6A on chromosomes 6AL and Qwdv.ifa-1B on chromosome 1B are highly effective against wheat dwarf virus and act additively when combined. Wheat dwarf virus (WDV) is among the most damaging viral pathogens. Its prevalence has increased substantially in recent years, and it is predicted to increase even further due to global warming. There are limited options to control the virus. Growing resistant cultivars would safeguard crops, but most current wheat cultivars are highly susceptible. Thus, the aim of this study was to dissect the genetic architecture of WDV resistance in resistant germplasm and to identify quantitative trait loci (QTL) to support resistance breeding. QTL mapping was conducted using four related populations comprising 168, 105, 99 and 130 recombinant inbred lines. Populations were evaluated under field conditions for three years. Natural infestation was provoked by early autumn sowing. WDV symptom severity was visually assessed at two time points in spring. QTL analysis revealed two highly significant QTL with the major QTL Qwdv.ifa-6A mapping to the long arm of chromosome 6A between markers Tdurum_contig75700_411 (601,412,152 bp) and AX-95197581 (605,868,853 bp). Qwdv.ifa-6A descends from the Dutch experimental line SVP-72017 and was of high effect in all populations, explaining up to 73.9% of the phenotypic variance. The second QTL, Qwdv.ifa-1B, mapped to chromosome 1B and is putatively associated with the 1RS.1BL translocation, which was contributed by the CIMMYT line CM-82036. Qwdv.ifa-1B explained up to 15.8% of the phenotypic variance. Qwdv.ifa-6A and Qwdv.ifa-1B are among the first identified highly effective resistance QTL and represent valuable resources for improving WDV resistance in wheat.

Fusarium head blight resistance in European winter wheat: insights from genome-wide transcriptome analysis

Background

Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially the extent of extruded anthers, are strongly associated with FHB resistance.

Results

To characterize the genetic basis of FHB resistance, we generated and analyzed phenotypic and gene expression data on the response to Fusarium graminearum (Fg) infection in 96 European winter wheat genotypes, including several lines containing introgressions from the highly resistant Asian cultivar Sumai3. The 96 lines represented a broad range in FHB resistance and were assigned to sub-groups based on their phenotypic FHB severity score. Comparative analyses were conducted to connect sub-group-specific expression profiles in response to Fg infection with FHB resistance level. Collectively, over 12,300 wheat genes were Fusarium responsive. The core set of genes induced in response to Fg was common across different resistance groups, indicating that the activation of basal defense response mechanisms was largely independent of the resistance level of the wheat line. Fg-induced genes tended to have higher expression levels in more susceptible genotypes. Compared to the more susceptible non-Sumai3 lines, the Sumai3-derivatives demonstrated higher constitutive expression of genes associated with cell wall and plant-type secondary cell wall biogenesis and higher constitutive and Fg-induced expression of genes involved in terpene metabolism. Gene expression analysis of the FHB QTL Qfhs.ifa-5A identified a constitutively expressed gene encoding a stress response NST1-like protein (TraesCS5A01G211300LC) as a candidate gene for FHB resistance. NST1 genes are key regulators of secondary cell wall biosynthesis in anther endothecium cells. Whether the stress response NST1-like gene affects anther extrusion, thereby affecting FHB resistance, needs further investigation.

Conclusion

Induced and preexisting cell wall components and terpene metabolites contribute to resistance and limit fungal colonization early on. In contrast, excessive gene expression directs plant defense response towards programmed cell death which favors necrotrophic growth of the Fg pathogen and could thus lead to increased fungal colonization.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07800-1.

Merging Genomics and Transcriptomics for Predicting Fusarium Head Blight Resistance in Wheat

Genomic selection with genome-wide distributed molecular markers has evolved into a well-implemented tool in many breeding programs during the last decade. The resistance against Fusarium head blight (FHB) in wheat is probably one of the most thoroughly studied systems within this framework. Aside from the genome, other biological strata like the transcriptome have likewise shown some potential in predictive breeding strategies but have not yet been investigated for the FHB-wheat pathosystem. The aims of this study were thus to compare the potential of genomic with transcriptomic prediction, and to assess the merit of blending incomplete transcriptomic with complete genomic data by the single-step method. A substantial advantage of gene expression data over molecular markers has been observed for the prediction of FHB resistance in the studied diversity panel of breeding lines and released cultivars. An increase in prediction ability was likewise found for the single-step predictions, although this can mostly be attributed to an increased accuracy among the RNA-sequenced genotypes. The usage of transcriptomics can thus be seen as a complement to already established predictive breeding pipelines with pedigree and genomic data, particularly when more cost-efficient multiplexing techniques for RNA-sequencing will become more accessible in the future.

Fighting Fusarium Pathogens in the Era of Climate Change: A Conceptual Approach

Fusarium head blight (FHB) caused by Fusarium pathogens is one of the most devastating fungal diseases of small grain cereals worldwide, substantially reducing yield quality and food safety. Its severity is increasing due to the climate change caused by weather fluctuations. Intensive research on FHB control methods has been initiated more than a decade ago. Since then, the environment has been rapidly changing at regional to global scales due to increasing anthropogenic emissions enhanced fertilizer application and substantial changes in land use. It is known that environmental factors affect both the pathogen virulence as well as plant resistance mechanisms. Changes in CO2 concentration, temperature, and water availability can have positive, neutral, or negative effects on pathogen spread depending on the environmental optima of the pathosystem. Hence, there is a need for studies of plant-pathogen interactions in current and future environmental context. Long-term monitoring data are needed in order to understand the complex nature of plants and its microbiome interactions. We suggest an holobiotic approach, integrating plant phyllosphere microbiome research on the ecological background. This will enable the development of efficient strategies based on ecological know-how to fight Fusarium pathogens and maintain sustainable agricultural systems.

Characterization of QTL and eQTL controlling early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan 1 x Nyubai doubled haploid wheat population

BACKGROUND

Fusarium head blight (FHB) is a major disease of cereal crops, caused by the fungal pathogen Fusarium graminearum and related species. Breeding wheat for FHB resistance contributes to increase yields and grain quality and to reduce the use of fungicides. The identification of genes and markers for FHB resistance in different wheat genotypes has nevertheless proven challenging.

RESULTS

In this study, early infection by F. graminearum was analyzed in a doubled haploid population derived from the cross of the moderately resistant wheat genotypes Wuhan 1 and Nyubai. Three quantitative trait loci (QTL) were identified: 1AL was associated with lower deoxynivalenol content, and 4BS and 5A were associated with reduced F. graminearum infection at 2 days post inoculation. Early resistance alleles were inherited from Wuhan 1 for QTL 1AL and 4BS and inherited from Nyubai for the 5A QTL. Cis and trans expression QTL (eQTL) were identified using RNA-seq data from infected head samples. Hotspots for trans eQTL were identified in the vicinity of the 1AL and 4BS QTL peaks. Among differentially expressed genes with cis eQTL within the QTL support intervals, nine genes had higher expression associated with FHB early resistance, and four genes had higher expression associated with FHB early susceptibility.

CONCLUSIONS

Our analysis of genotype and gene expression data of wheat infected by F. graminearum identified three QTL associated with FHB early resistance, and linked genes with eQTL and differential expression patterns to those QTL. These findings may have applications in breeding wheat for early resistance to FHB.

Genetic factors affecting Fusarium head blight resistance improvement from introgression of exotic Sumai 3 alleles (including Fhb1, Fhb2, and Fhb5) in hard red spring wheat

BACKGROUND

Fusarium head blight resistance genes, Fhb1 (for Type-II resistance), Fhb2 (Type-II), and Fhb5 (Type-I plus some Type-II), which originate from Sumai 3, are among the most important that confer resistance in hexaploid wheat. Near-isogenic lines (NILs), in the CDC Alsask (susceptible; n = 32) and CDC Go (moderately susceptible; n = 38) backgrounds, carrying these genes in all possible combinations were developed using flanking microsatellite markers and evaluated for their response to FHB and deoxynivalenol (DON) accumulation in eight environments. NILs were haplotyped with wheat 90 K iSelect assay to elucidate the genomic composition and confirm alleles' presence. Other than evaluating the effects of three major genes in common genetic background, the study elucidated the epistatic gene interactions as they influence FHB measurements; identified loci other than Fhb1, Fhb2, and Fhb5, in both recurrent and donor parents and examined annotated proteins in gene intervals.

RESULTS

Genotyping using 81,857 single nucleotide polymorphism (SNP) markers revealed polymorphism on all chromosomes and that the NILs carried < 3% of alleles from the resistant donor. Significant improvement in field resistance (Type-I + Type-II) resulted only among the CDC Alsask NILs, not the CDC Go NILs. The phenotypic response of NILs carrying combinations of Sumai 3 derived genes suggested non-additive responses and Fhb5 was as good as Fhb1 in conferring field resistance in both populations. In addition to Fhb1, Fhb2, and Fhb5, four to five resistance improving alleles in both populations were identified and three of five in CDC Go were contributed by the susceptible parent. The introgressed chromosome regions carried genes encoding disease resistance proteins, protein kinases, nucleotide-binding and leucine rich repeats' domains. Complex epistatic gene-gene interactions among marker loci (including Fhb1, Fhb2, Fhb5) explained > 20% of the phenotypic variation in FHB measurements.

CONCLUSIONS

Immediate Sumai 3 derivatives carry a number of resistance improving minor effect alleles, other than Fhb1, Fhb2, Fhb5. Results verified that marker-assisted selection is possible for the introgression of exotic FHB resistance genes, however, the genetic background of the recipient line and epistatic interactions can have a strong influence on expression and penetrance of any given gene.

Identification, Molecular Cloning, and Functional Characterization of a Wheat UDP-Glucosyltransferase Involved in Resistance to Fusarium Head Blight and to Mycotoxin Accumulation

Plant uridine diphosphate (UDP)-glucosyltransferases (UGT) catalyze the glucosylation of xenobiotic, endogenous substrates and phytotoxic agents produced by pathogens such as mycotoxins. The Bradi5g03300 UGT-encoding gene from the model plant Brachypodium distachyon was previously shown to confer tolerance to the mycotoxin deoxynivalenol (DON) through glucosylation into DON 3-O-glucose (D3G). This gene was shown to be involved in early establishment of quantitative resistance to Fusarium Head Blight, a major disease of small-grain cereals. In the present work, using a translational biology approach, we identified and characterized a wheat candidate gene, Traes_2BS_14CA35D5D, orthologous to Bradi5g03300 on the short arm of chromosome 2B of bread wheat (Triticum aestivum L.). We showed that this UGT-encoding gene was highly inducible upon infection by a DON-producing Fusarium graminearum strain while not induced upon infection by a strain unable to produce DON. Transformation of this wheat UGT-encoding gene into B. distachyon revealed its ability to confer FHB resistance and root tolerance to DON as well as to potentially conjugate DON into D3G in planta and its impact on total DON reduction. In conclusion, we provide a UGT-encoding candidate gene to include in selection process for FHB resistance.

A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL

This study demonstrates how identification of genes underpinning disease-resistance QTL based on differential expression and SNPs can be improved by performing transcriptomic analysis on multiple near isogenic lines. Transcriptomic analysis has been widely used to understand the genetic basis of a trait of interest by comparing genotypes with contrasting phenotypes. However, these approaches identify such large sets of differentially expressed genes that it proves difficult to isolate which genes underpin the phenotype of interest. This study tests whether using multiple near isogenic lines (NILs) can improve the resolution of RNA-seq-based approaches to identify genes underpinning disease-resistance QTL. A set of NILs for a major effect Fusarium crown rot-resistance QTL in barley on the 4HL chromosome arm were analysed under Fusarium crown rot using RNA-seq. Differential gene expression and single nucleotide polymorphism detection analyses reduced the number of putative candidates from thousands within individual NIL pairs to only one hundred and two genes, which were differentially expressed or contained SNPs in common across NIL pairs and occurred on 4HL. Our findings support the value of performing RNA-seq analysis using multiple NILs to remove genetic background effects. The enrichment analyses indicated conserved differences in the response to infection between resistant and sensitive isolines suggesting that sensitive isolines are impaired in systemic defence response to Fusarium pseudograminearum.

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.

Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus

Brassica napus (B. napus, AACC), is an economically important allotetraploid crop species that resulted from hybridization between two diploid species, Brassica rapa (AA) and Brassica olereacea (CC). We have created one new synthetic B. napus genotype Da-Ae (AACC) and one introgression line Da-Ol-1 (AACC), which were used to generate an F₂ mapping population. Plants in this F₂ mapping population varied in fatty acid content, flowering time, and growth-related traits. Using quantitative trait locus (QTL) mapping, we aimed to determine if Da-Ae and Da-Ol-1 provided novel genetic variation beyond what has already been found in B. napus. Making use of the genotyping information generated from RNA-seq data of these two lines and their F₂ mapping population of 166 plants, we constructed a genetic map consisting of 2,021 single nucleotide polymorphism markers that spans 2,929 cM across 19 linkage groups. Besides the known major QTL identified, our high resolution genetic map facilitated the identification of several new QTL contributing to the different fatty acid levels, flowering time, and growth-related trait values. These new QTL probably represent novel genetic variation that existed in our new synthetic B. napus strain. By conducting genome-wide expression variation analysis in our F₂ mapping population, genetic regions that potentially regulate many genes across the genome were revealed. A FLOWERING LOCUS C gene homolog, which was identified as a candidate regulating flowering time and multiple growth-related traits, was found underlying one of these regions. Integrated QTL and expression QTL analyses also helped us identified candidate causative genes associated with various biological traits through expression level change and/or possible protein function modification.

Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen

Powdery mildew pathogens colonize over 9500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery of fungal effectors to the plant and exchange of nutrients from host to pathogen. We used expression Quantitative Trait Locus (eQTL) analysis to dissect the temporal control of immunity-associated gene expression in a doubled haploid barley population challenged with Bgh. Two highly significant regions possessing trans eQTL were identified near the telomeric ends of chromosomes (Chr) 2HL and 1HS. Within these regions reside diverse resistance loci derived from barley landrace H. laevigatum (MlLa) and H. vulgare cv. Algerian (Mla1), which associate with the altered expression of 961 and 3296 genes during fungal penetration of the host and haustorial development, respectively. Regulatory control of transcript levels for 299 of the 961 genes is reprioritized from MlLa on 2HL to Mla1 on 1HS as infection progresses, with 292 of the 299 alternating the allele responsible for higher expression, including Adaptin Protein-2 subunit μ AP2M and Vesicle Associated Membrane Protein VAMP72 subfamily members VAMP721/722. AP2M mediates effector-triggered immunity (ETI) via endocytosis of plasma membrane receptor components. VAMP721/722 and SNAP33 form a Soluble N-ethylmaleimide-sensitive factor Attachment Protein REceptor (SNARE) complex with SYP121 (PEN1), which is engaged in pathogen associated molecular pattern (PAMP)-triggered immunity via exocytosis. We postulate that genes regulated by alternate chromosomal positions are repurposed as part of a conserved immune complex to respond to different pathogen attack scenarios.