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

Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus

Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the "narrow" generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties: New species: Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology 104: 87-148. doi: 10.3114/sim.2022.104.02.

Morphological characterization, pathogenicity screening, and molecular identification of Fusarium spp. isolates causing post-flowering stalk rot in maize

Post flowering stalk rot (PFSR) of maize caused by the Fusarium species complex is a serious threat to maize production worldwide. The identification of Fusarium species causing PFSR based on morphology traditionally relies on a small set of phenomic characteristics with only minor morphological variations among distinct Fusarium species. Seventy-one isolates were collected from 40 sites in five agro-climatic zones of India to assess the diversity of Fusarium spp. associated with maize crops showing symptoms of PFSR in the field. To investigate the pathogenicity of Fusarium spp. causing PFSR sixty isolates were toothpick inoculated between the first and second node at 55 days after sowing during the tassel formation stage of the crop in Kharif (Rainy season), and Rabi (Winter season) season field trials. Ten most virulent Fusarium isolates, based on the highest observed disease index, were identified by homology and phylogenetic analyses of partial sequences of the translation elongation factor 1 α (Tef-1α). Based on morphological traits such as mycelial growth patterns and mycelial pigmentation, Fusarium isolates were divided into nine clusters. The isolates were judged to be virulent based on their ability to decrease seedling vigour in in-vivo situations and high disease severity in field experiments. Pathogenicity test during the Kharif season showed 12 isolates with virulent disease symptoms with a mean severity ranging between 50 to 67 percent disease index (PDI) whereas in Rabi season, only five isolates were considered virulent, and the mean severity ranged between 52 to 67 PDI. Based on pathological characterization and molecular identification, 10 strains of Fusarium species namely, Fusarium acutatum (2/10), Fusarium verticillioides (Syn. Gibberella fujikuroi var. moniliformis) (7/10), Fusarium andiyazi (2/10) recorded the highest diseases index. All these species are part of the Fusarium fujikuroi species complex (FFSC). The distribution of virulent isolates is specific to a geographical location with a hot humid climate. Increased knowledge regarding the variability of Fusarium spp. responsible for PFSR of maize occurring across wide geographical locations of India will enable more informed decisions to be made to support the management of the disease, including screening for resistance in maize-inbred lines.

Comparative transcriptome meta-analysis reveals a set of genes involved in the responses to multiple pathogens in maize

Maize production is constantly threatened by the presence of different fungal pathogens worldwide. Genetic resistance is the most favorable approach to reducing yield losses resulted from fungal diseases. The molecular mechanism underlying disease resistance in maize remains largely unknown. The objective of this study was to identify key genes/pathways that are consistently associated with multiple fungal pathogen infections in maize. Here, we conducted a meta-analysis of gene expression profiles from seven publicly available RNA-seq datasets of different fungal pathogen infections in maize. We identified 267 common differentially expressed genes (co-DEGs) in the four maize leaf infection experiments and 115 co-DEGs in all the seven experiments. Functional enrichment analysis showed that the co-DEGs were mainly involved in the biosynthesis of diterpenoid and phenylpropanoid. Further investigation revealed a set of genes associated with terpenoid phytoalexin and lignin biosynthesis, as well as potential pattern recognition receptors and nutrient transporter genes, which were consistently up-regulated after inoculation with different pathogens. In addition, we constructed a weighted gene co-expression network and identified several hub genes encoding transcription factors and protein kinases. Our results provide valuable insights into the pathways and genes influenced by different fungal pathogens, which might facilitate mining multiple disease resistance genes in maize.

Multi-Omics Analysis Reveals a Regulatory Network of ZmCCT During Maize Resistance to Gibberella Stalk Rot at the Early Stage

Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases in maize; however, the regulatory mechanism of resistance to GSR remains largely unknown. We performed a comparative multi-omics analysis to reveal the early-stage resistance of maize to GSR. We inoculated F. graminearum to the roots of susceptible (Y331) and resistant (Y331-ΔTE) near-isogenic lines containing GSR-resistant gene ZmCCT for multi-omics analysis. Transcriptome detected a rapid reaction that confers resistance at 1-3 hpi as pattern-triggered immunity (PTI) response to GSR. Many key properties were involved in GSR resistance, including genes in photoperiod and hormone pathways of salicylic acid and auxin. The activation of programmed cell death-related genes and a number of metabolic pathways at 6 hpi might be important to prevent further colonization. This is consistent with an integrative analysis of transcriptomics and proteomics that resistant-mediated gene expression reprogramming exhibited a dynamic pattern from 3 to 6 hpi. Further metabolomics analysis revealed that the amount of many chemical compounds was altered in pathways associated with the phenylpropanoid biosynthesis and the phenylalanine metabolism, which may play key roles to confer the GSR resistance. Taken together, we generated a valuable resource to interpret the defense mechanism during early GSR resistance.

GT Factor ZmGT-3b Is Associated With Regulation of Photosynthesis and Defense Response to Fusarium graminearum Infection in Maize Seedling

It is of critical importance for plants to correctly and efficiently allocate their resources between growth and defense to optimize fitness. Transcription factors (TFs) play crucial roles in the regulation of plant growth and defense response. Trihelix TFs display multifaceted functions in plant growth, development, and responses to various biotic and abiotic stresses. In our previous investigation of maize stalk rot disease resistance mechanism, we found a trihelix TF gene, ZmGT-3b, which is primed for its response to Fusarium graminearum challenge by implementing a rapid and significant reduction of its expression to suppress seedling growth and enhance disease resistance. The disease resistance to F. graminearum was consistently increased and drought tolerance was improved, while seedling growth was suppressed and photosynthesis activity was significantly reduced in the ZmGT-3b knockdown seedlings. Thus, the seedlings finally led to show a kind of growth-defense trade-off phenotype. Moreover, photosynthesis-related genes were specifically downregulated, especially ZmHY5, which encodes a conserved central regulator of seedling development and light responses; ZmGT-3b was confirmed to be a novel interacting partner of ZmHY5 in yeast and in planta. Constitutive defense responses were synchronically activated in the ZmGT-3b knockdown seedlings as many defense-related genes were significantly upregulated, and the contents of major cell wall components, such as lignin, were increased in the ZmGT-3b knockdown seedlings. These suggest that ZmGT-3b is involved in the coordination of the metabolism during growth-defense trade-off by optimizing the temporal and spatial expression of photosynthesis- and defense-related genes.

Integrated Gene Co-expression Analysis and Metabolites Profiling Highlight the Important Role of ZmHIR3 in Maize Resistance to Gibberella Stalk Rot

Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases causing significant yield loss of maize, and GSR resistance is a quantitative trait controlled by multiple genes. Although a few quantitative trait loci/resistance genes have been identified, the molecular mechanisms underlying GSR resistance remain largely unexplored. To identify potential resistance genes and to better understand the molecular mechanism of GSR resistance, a joint analysis using a comparative transcriptomic and metabolomic approaches was conducted using two inbred lines with contrasting GSR resistance, K09 (resistant) and A08 (susceptible), upon infection with F. graminearum. While a substantial number of differentially expressed genes associated with various defense-related signaling pathways were identified between two lines, multiple hub genes likely associated with GSR resistance were pinpointed using Weighted Gene Correlation Network Analysis and K-means clustering. Moreover, a core set of metabolites, including anthocyanins, associated with the hub genes was determined. Among the complex co-expression networks, ZmHIR3 showed strong correlation with multiple key genes, and genetic and histological studies showed that zmhir3 mutant is more susceptible to GSR, accompanied by enhanced cell death in the stem in response to infection with F. graminearum. Taken together, our study identified differentially expressed key genes and metabolites, as well as co-expression networks associated with distinct infection stages of F. graminearum. Moreover, ZmHIR3 likely plays a positive role in disease resistance to GSR, probably through the transcriptional regulation of key genes, functional metabolites, and the control of cell death.

First Report of Maize Stalk Rot Caused by Fusarium kyushuense in China

During 2017 to 2019, a field survey for maize stalk rot was conducted in 21 counties (districts) across the Guangxi province of China. This disease caused yield losses ranging from 20% to 30%. Maize plants with stalk rot were collected during the late milk stage and pieces of diseased pith tissue were cultured as previously described (Shan et al. 2017). Fungal colonies and mycelia with morphological characteristics of Fusarium species were subcultured onto fresh potato dextrose agar (PDA) and carnation leaf agar (CLA) plates. Based on morphological characteristics and molecular detection by amplification of Fusarium genus-specific primers (Duan et al. 2016), 39 Fusarium isolates were identified. Among them, five isolates from Du'an, Pingguo, Debao, and Daxin had abundant, pale orange to yellow aerial mycelium with deep red pigments when grown on PDA (Fig. 1A; 1B). The average growth rate was 8.0 to 12.0 mm per day at 25°C in the dark. The fungi produced two types of spores on CLA. Microconidia were ovoid to clavate, generally 0- to 3-septate, and 4.6 to 9.4 μm in length (n = 30) (Fig. 1D); Macroconidia were slightly curved with an acute apical cell, mostly 3- to 4- septate, and 19.4 to 38.2 μm in length (n = 30) (Fig. 1C). No chlamydospores were observed. These five isolates were initially identified as Fusarium kyushuense based on morphological features. PCR was performed to amplify three phylogenetic genes (TEF1-α, RPB1, and RPB2) (O'Donnell et al. 1998) and species specific primers kyuR1F/kyuR1R (5-TTTTCCTCACCAAGGAGCAGATCATG-3/5-TCCAATGGACTGGGCAGCCAAAACACC-3), kyuR2F/kyuR2R (5-CAGATATACATTTGCCTCGACAC-3/5-TACTTGAGCACGGAGCTTG-3) were used to confirm species identity. The obtained sequences were deposited in GenBank under the accession numbers MT997084, MT997080, MT997081 (TEF1-α); MT550012, MT997085, MT997086 (RPB1); MT550009, MT997089, and MT997090 (RPB2), respectively. Using BLAST, sequences of TEF1-α, RPB1, and RPB2 of the isolates were 99.33% (MH582297.1) to 100% (MG282364.1) similar to those of F. kyushuense strains (Supplementary Table 1). Based on phylogenetic analysis with maximum likelihood methods using tools of the website of CIPRES (http://www.phylo.org), isolates GX27, GX167, and GX204 clustered with F. kyushuense with 100% bootstrap support (Fig. 2). The pathogenicity of the three isolates was tested using young seedlings and adult plants as previously described with modification (Ye et al. 2013; Zhang et al. 2016). The primary roots of three-leaf-old seedlings were inoculated by immersing the roots into a 1 × 106 macroconidia solution, incubating for 6 h at 25°C, and transferring to normal growth conditions (26°C, 16 h light/22°C, 8 h dark). The second or third internode above the soil surface of flowering stage plants grown in a greenhouse was bored with a Bosch electric drill to make a hole (ca. 8 mm in diameter) and inoculated with 0.5 mL of mycelia plug then sealed with petrolatum. The inoculum was created by homogenizing five plates of flourish hyphal mats (approximately 125 mL) with kitchen blender and adjusting to a final volume of 200 mL with sterilized ddH2O. No symptoms were observed in the seedlings or adult plants that were mock-inoculated with PDA plugs. Three days post-inoculation (dpi), roots of the infected seedling turned dark-brown and shrunk and the leaves wilted (Fig. 1E). Typical stalk rot symptoms observed in the inoculated plants were premature wilting of entire plant and hollow and weak stalks, leading to lodging; the longitudinal section of the internodes exhibited obvious dark brown necrosis and reddish discoloration at 14 dpi and 30 dpi, respectively (Fig. 1F). Fusarium kyushuense was re-isolated from the inoculated stalk lesions but not from the control. This is the first record of stalk rot caused by F. kyushuense on maize plants in China. However, F. kyushuense is known to cause maize ear rot in China (Wang et al. 2014) and can produce type A and type B trichothecene mycotoxins in kernels (Aoki and O'Donnell 1998). The occurrence of maize stalk rot and ear rot caused by F. kyushuense should be monitored in China due to the potential risk for crop loss and mycotoxin contamination.

First Report of Fusarium thapsinum Causing Maize Stalk Rot in China

Maize (Zea mays L.) is the most widely grown crop in China, which was planted 41.28 million hectares in 2019 (http://data.stats.gov.cnw/easyquery.htm?cn=C01&zb=A0D0F&sj=2019). Several fungal diseases of maize are reported in which stalk rot has become one of the most destructive diseases in China. The average yield losses affected by the disease are estimated at 10% to 20% (Yu et al. 2016). From 2017 to 2019, a survey was conducted to determine the population diversity of Fusarium species associated with maize diseases in 18 cities across Henan province. Fusarium stalk rot of maize with disease incidence more than 25% was observed in two continuous maize fields at Xuchang city. The diseased stem tissues from junctions in health and disease were chopped into small pieces (3 × 8 mm), superficially disinfected (70% ethyl alcohol for 1 min), placed onto potato dextrose agar (PDA) amended with L-(+)-Lactic-acid (1 g/L), poured in petri plates and incubated at 25°C for 4 days. Mycelia showing morphological characteristic of Fusarium spp. were sub-cultured from single conidium. The pure fungal isolates produced fluffy colonies, white aerial mycelium with yellow pigment in agar. The radial mycelial growth was measured and calculated at an average growth rate 10.9 mm/day at 25°C (Fig. 1A; 1B). Macroconidia produced on carnation leaf agar (CLA) were relatively slender, slightly curved and thick-walled, mostly 3 to 5 marked septa, with a curved and tapering apical cell and poorly developed foot cell, 46.9 ± 5.6 µm × 4.9 ± 0.2 µm (Fig. 1C). Microconidia formed abundantly and were generally oval on CLA, 8.2 ± 0.5 µm × 3.4± 0.1 µm (Fig. 1D). No chlamydospores were observed. Morphological characteristics of the isolates matched the description of Fusarium thapsinum (Leslie and Summerell 2006). To further get the phylogenetic evidence, TEF1-α (translation elongation factor), RPB1 (the largest subunit of RNA polymerase II) and RPB2 (the second largest subunit of RNA polymerase II) were amplified with primer pairs EF1/EF2 (O'Donnell et al. 1998), thapR1F (5'-TTTTCCTCACAAAGGAGCAAATCATG-3')/thapR1R (5'-GTTCACCCAAGATATGGTCGAAAGCC-3'), and thapR2F (5'-ACTCTTTCACATTTGCGCCGAAC-3')/thapR2R (5'-CGGAGCTTTCGTCCAGTGTGAC-3'), and sequenced, respectively. The BLAST search of the sequences of EF1-α, RPB1 and RPB2 shared 99.87% to 100% identity with those of F. thapsinum strains deposited in the GenBank (Supplementary Table 1). Sequences from two isolates (XCCG-3-B-1 and XCCG-3-A-1) were deposited in GenBank (Accession No. MT550014, MT997082 for EF-1α; MT550011, MT997087 for RPB1 and MT550008, MT997091 for RPB2). The phylogenetic relationships based on analysis of the partial sequences showed the representive isolates clustered together with F. thapsinum at 96% bootstrap values (Fig. 2). Combined with the results of morphological characteristics and phylogenetic analysis, the strain designated as Fusarium thapsinum. To complete Koch's postulates, the pathogenicity of the isolates was tested using the silking-stage plants in a greenhouse based on previously described method with modification (Zhang et al. 2016). An 8 mm in diameter wound hole was created at the second or third internode of the plant above the soil surface and injected with 0.5 ml of mycelia plug. The inoculated stalk exhibited internal dark brown necrotic regions and the brown area elongated obviously around the insertion at 14 dpi (days post inoculation). At 30 dpi, the stalks turned soft, hollow and even lodging of the plants for those severe ones, which are similar to those observed on naturally infected maize plants in the field (Fig. 1F). When the roots of the three-leaf-stage seedlings were inoculated with 1×106 macroconidia solution (Ye et al. 2013), the root rot and leaf wilting symptoms were observed (Fig. 1E). While the control plants that were inoculated with only sterile water showed no disease symptoms. The pathogen was re-isolated from the inoculated tissues and the identity was confirmed by the morphological characters. Fusarium thapsinum had been described as causal agent of maize stalk rot in Pakistan (Tahir et al. 2018). To our knowledge, this is the first report of F. thapsinum associated with maize stalk rot in China. The discovery will strengthen the theoretical foundation of maize stalk rot disease management.

Genome-wide identification of the maize 2OGD superfamily genes and their response to Fusarium verticillioides and Fusarium graminearum

In maize, eat rot and stalk rot caused by Fusarium verticillioides and Fusarium graminearum lead to contamination of moldy grains to produce mycotoxins. Identification of resistance genes against these pathogens for maize breeding is an effective way for disease control. Several 2-oxoglutarate-dependent dioxygenase (2OGD) proteins have been found to confer resistance to different pathogens in diverse plant species. However, little is known about the 2OGD superfamily in maize. Here, we identified 103 putative 2OGD genes in maize from a genome-wide analysis, and divided them into three classes - DOXA, DOXB, and DOXC. We further comprehensively investigated their gene structure, chromosome distribution, phylogenetic tree, gene-function enrichment, and expression profiles among different tissues. The genes encoding three 2OGD proteins, ACO, F3H, and NCS involved in ethylene biosynthesis, flavonoids biosynthesis, and alkaloids biosynthesis pathways, respectively, were identified to be induced by F. verticillioides and F. graminearum. The promoters of the three genes contain the binding sites for the transcription factor ZmDOF and ZmHSF, which are also induced by the two pathogens. The results imply that the three 2OGDs and the two transcription factors might be involved in the resistance to the two pathogens. This study provided a comprehensive understanding of the 2OGD superfamily in maize and laid the foundation for the further functional analysis of their roles in maize resistance to eat rot and stalk rot.

Characterization and Molecular Mapping of Two Novel Genes Resistant to Pythium Stalk Rot in Maize

Pythium stalk rot caused by Pythium inflatum is becoming a more and more serious disease in maize, and it has caused severe yield loss in China in recent years. Deployment of resistant maize varieties is the most effective way to control this disease. Searching for the resistant maize germplasm and identifying the resistance genes are the vital processes in the breeding program. The maize inbred line X178 previously showed high resistance to Pythium stalk rot. Thus, this study aimed to reveal the gene(s) resistance to Pythium stalk rot in X178 by resistance inheritance analysis using the derived F₂ and F_2:3 genetic populations. The results showed that two independently inherited dominant genes, designated RpiX178-1 and RpiX178-2, carried by X178 are responsible for its resistance relative to the susceptible parent Ye107; they are located on regions of maize chromosome (chr.) 1 bin 1.09 and chr. 4 bin 4.08, respectively, and flanked by markers umc2047 and bnlg1671 as well as bnlg1444 and umc1313, respectively, by linkage analysis. Subsequently, RpiX178-1 was finely mapped between markers SSRZ8 and IDP2347, with genetic distances of 0.6 and 1.1 cM, respectively, and the physical distance of the target region was about 700 kb. RpiX178-2 was also further located between markers bnlg1444 and umc2041, with a genetic distance of 2.4 cM. Moreover, we confirmed that the two genes RpiX178-1 and RpiX178-2 were newly identified and different from those genes known on chrs. 1 and 4 according to results of allelism testing. Herein, we newly identified two genes resistant to P. inflatum, which provided important genetic information for resistance to Pythium stalk rot in maize.

The Auxin-Regulated Protein ZmAuxRP1 Coordinates the Balance between Root Growth and Stalk Rot Disease Resistance in Maize

To optimize fitness, plants must efficiently allocate their resources between growth and defense. Although phytohormone crosstalk has emerged as a major player in balancing growth and defense, the genetic basis by which plants manage this balance remains elusive. We previously identified a quantitative disease-resistance locus, qRfg2, in maize (Zea mays) that protects against the fungal disease Gibberella stalk rot. Here, through map-based cloning, we demonstrate that the causal gene at qRfg2 is ZmAuxRP1, which encodes a plastid stroma-localized auxin-regulated protein. ZmAuxRP1 responded quickly to pathogen challenge with a rapid yet transient reduction in expression that led to arrested root growth but enhanced resistance to Gibberella stalk rot and Fusarium ear rot. ZmAuxRP1 was shown to promote the biosynthesis of indole-3-acetic acid (IAA), while suppressing the formation of benzoxazinoid defense compounds. ZmAuxRP1 presumably acts as a resource regulator modulating indole-3-glycerol phosphate and/or indole flux at the branch point between the IAA and benzoxazinoid biosynthetic pathways. The concerted interplay between IAA and benzoxazinoids can regulate the growth-defense balance in a timely and efficient manner to optimize plant fitness.

Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots

The production and regulation of defensive specialized metabolites play a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance. We used comparative metabolomics to identify previously unknown antifungal metabolites in maize seedling roots, and investigated the genetic and physiological mechanisms underlying their natural variation using quantitative trait locus mapping and comparative transcriptomics approaches. Two maize metabolites, smilaside A (3,6-diferuloyl-3',6'-diacetylsucrose) and smiglaside C (3,6-diferuloyl-2',3',6'-triacetylsucrose), were identified that could contribute to maize resistance against Fusarium graminearum and other fungal pathogens. Elevated expression of an ethylene signaling gene, ETHYLENE INSENSITIVE 2 (ZmEIN2), co-segregated with a decreased smilaside A : smiglaside C ratio. Pharmacological and genetic manipulation of ethylene availability and sensitivity in vivo indicated that, whereas ethylene was required for the production of both metabolites, the smilaside A : smiglaside C ratio was negatively regulated by ethylene sensitivity. This ratio, rather than the absolute abundance of these two metabolites, was important for maize seedling root defense against F. graminearum. Ethylene signaling regulates the relative abundance of the two F. graminearum-resistance-related metabolites and affects resistance against F. graminearum in maize seedling roots.

Fusarium graminearum-induced shoot elongation and root reduction in maize seedlings correlate with later seedling blight severity

Fusarium graminearum seedling blight is a common disease of maize (Zea mays). Development of genetic resistance to seedling blight in maize germplasm requires efficient and accurate quantitative assessment of disease severity. Through artificial inoculation experiments under controlled growth conditions, we determined that host genotype, pathogen genotype, and infection dose influence the extent to which F. graminearum induces shoot elongation and inhibits root growth in maize seedlings. A comparison of 15 maize inbred lines showed independent variation of these two fungus-induced effects on seedling growth. In a broader survey with nine commercial maize hybrids and three field-collected fungal isolates, there was significant correlation between these seedling growth responses, as well as with later seedling blight severity. Analysis of variance suggested that this variation and the observed correlative relationships were primarily driven by differing pathogenicity of the three fungal isolates. Together, our results indicate that F. graminearum-induced shoot elongation and root reduction in maize seedlings have distinct underlying physiological mechanisms, and that early observations of seedling growth responses can serve as a proxy for investigating natural variation in host resistance and pathogen aggressiveness at later growth stages.

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.

The Apoplastic Secretome of Trichoderma virens During Interaction With Maize Roots Shows an Inhibition of Plant Defence and Scavenging Oxidative Stress Secreted Proteins

In Nature, almost every plant is colonized by fungi. Trichoderma virens is a biocontrol fungus which has the capacity to behave as an opportunistic plant endophyte. Even though many plants are colonized by this symbiont, the exact mechanisms by which Trichoderma masks its entrance into its plant host remain unknown, but likely involve the secretion of different families of proteins into the apoplast that may play crucial roles in the suppression of plant immune responses. In this study, we investigated T. virens colonization of maize roots under hydroponic conditions, evidencing inter- and intracellular colonization by the fungus and modifications in root morphology and coloration. Moreover, we show that upon host penetration, T. virens secretes into the apoplast an arsenal of proteins to facilitate inter- and intracellular colonization of maize root tissues. Using a gel-free shotgun proteomics approach, 95 and 43 secretory proteins were identified from maize and T. virens, respectively. A reduction in the maize secretome (36%) was induced by T. virens, including two major groups, glycosyl hydrolases and peroxidases. Furthermore, T. virens secreted proteins were mainly involved in cell wall hydrolysis, scavenging of reactive oxygen species and secondary metabolism, as well as putative effector-like proteins. Levels of peroxidase activity were reduced in the inoculated roots, suggesting a strategy used by T. virens to manipulate host immune responses. The results provide an insight into the crosstalk in the apoplast which is essential to maintain the T. virens-plant interaction.

A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize

A major resistance quantitative trait locus, qRfg1, significantly enhances maize resistance to Gibberella stalk rot, a devastating disease caused by Fusarium graminearum. However, the underlying molecular mechanism remains unknown. We adopted a map-based cloning approach to identify the resistance gene at qRfg1 and examined the dynamic epigenetic changes during qRfg1-mediated maize resistance to the disease. A CCT domain-containing gene, ZmCCT, is the causal gene at the qRfg1 locus and a polymorphic CACTA-like transposable element (TE1) c. 2.4 kb upstream of ZmCCT is the genetic determinant of allelic variation. The non-TE1 ZmCCT allele is in a poised state, with predictive bivalent chromatin enriched for both repressive (H3K27me3/H3K9me3) and active (H3K4me3) histone marks. Upon pathogen challenge, this non-TE1 ZmCCT allele was promptly induced by a rapid yet transient reduction in H3K27me3/H3K9me3 and a progressive decrease in H3K4me3, leading to disease resistance. However, TE1 insertion in ZmCCT caused selective depletion of H3K4me3 and enrichment of methylated GC to suppress the pathogen-induced ZmCCT expression, resulting in disease susceptibility. Moreover, ZmCCT-mediated resistance to Gibberella stalk rot is not affected by photoperiod sensitivity. This chromatin-based regulatory mechanism enables ZmCCT to be more precise and timely in defense against F. graminearum infection.

qRfg3, a novel quantitative resistance locus against Gibberella stalk rot in maize

A quantitative trait locus  qRfg3 imparts recessive resistance to maize Gibberella stalk rot. qRfg3 has been mapped into a 350-kb interval and could reduce the disease severity index by ~26.6%. Gibberella stalk rot, caused by the fungal pathogen Fusarium graminearum, severely affects maize yield and grain quality worldwide. To identify more resistance quantitative trait loci (QTLs) against this disease, we analyzed a recombinant inbred line (RIL) population derived from a cross between resistant H127R and susceptible C7-2 inbred lines. Within this population, maize resistance to Gibberella stalk rot had high broad-sense heritability. A major QTL, qRfg3, on chromosome 3 was consistently detected across three field trials, accounting for 10.7-19.4% of the total phenotypic variation. Using a progeny-based sequential fine-mapping strategy, we narrowed qRfg3 down to an interval of ~350 kb. We further demonstrated that qRfg3 is a recessive resistance locus to Gibberella stalk rot that reduced the disease severity index by ~26.6%. Both the gene location and recessive genetic mode distinguish qRfg3 from other stalk rot resistance loci. Hence, qRfg3 is valuable as a complement to existing resistance QTLs to improve maize resistance to Gibberella stalk rot.

Susceptibility of Maize to Stalk Rot Caused by Fusarium graminearum Deoxynivalenol and Zearalenone Mutants

Fusarium graminearum is a destructive pathogen of cereals that can cause stalk rot in maize. Stalk rot results in yield losses due to impaired grain filling, premature senescence, and lodging, which limits production and harvesting of ears. In addition, mycotoxins can make infected tissues unfit for silage. Our objectives were to evaluate the natural variation in stalk rot resistance among maize inbreds, to establish whether deoxynivalenol (DON)- and zearalenone (ZEA)-deficient strains are pathogenic on a panel of diverse inbreds, and to quantify the accumulation of DON in infected stalk tissue. Wild-type F. graminearum and mycotoxin mutants (DON and ZEA) were used to separately inoculate stalks of 9-week-old plants of 20 inbreds in the greenhouse. Plants were evaluated for lesion area at the inoculation point at 0, 2, 14, and 28 days postinoculation and tissues around lesions were sampled to determine the DON content. Regardless of their ability to produce DON or ZEA, all tested F. graminearum strains caused stalk rot; however, significant differences in disease levels were detected. Among the tested inbreds, Mp717 was resistant to all three F. graminearum strains while Mp317 and HP301 were only partially resistant. Accumulation of DON was significantly lower in infected stalks of the resistant and partially resistant inbreds than the susceptible inbreds. Analysis of the 20 inbreds using data from 17 simple-sequence repeats revealed population structure among the individuals; however, there was no association between genetic clustering and stalk rot resistance. These findings are an additional step toward breeding maize inbreds suitable for planting in fields infested with F. graminearum.

Transcriptome analysis of maize resistance to Fusarium graminearum

BACKGROUND

Gibberella stalk rot caused by Fusarium graminearum is one of the most destructive soil-borne diseases of maize (Zea mays L.). Chemical means of controlling Gibberella stalk rot are not very effective; development of highly resistant hybrids is the best choice for disease control. Hence, understanding of the molecular basis underlying maize resistance against Gibberella stalk rot would undoubtedly facilitate the resistance breeding for stalk rot.

RESULTS

Two quantitative trait loci (QTL), qRfg1 and qRfg2, conferring resistance to Gibberella stalk rot were detected in our previous study. Three near-isogenic lines (NILs) of maize with either qRfg1 (NIL1) or qRfg2 (NIL2), or neither (NIL3) were generated and subjected to RNA sequencing to study the transcriptional changes after F. graminearum inoculation at 0 (control), 6, and 18 h post-inoculation (hpi). In total, 536,184,652 clean reads were generated, and gene expression levels were calculated using FPKM (fragments per kilobase of exon model per million mapped reads). A total of 7252 differentially expressed genes (DEGs) were found in the three NILs after F. graminearum inoculation. As many as 2499 DEGs were detected between NIL1 and NIL3 at 0 hpi, of which 884 DEGs were more abundant in NIL1 and enriched in defense responses. After F. graminearum inoculation, 1070 and 751 genes were exclusively up- and downregulated, respectively, in NIL1 as compared to NIL3. The 1070 upregulated DEGs were enriched in growth/development, photosynthesis/biogenesis, and defense-related responses. Genes encoding putative auxin-induced proteins and GH3 family proteins in auxin signaling pathway were highly induced and lasted longer in NIL3. Genes involved in polar auxin transport (PAT) were more abundant in NIL3 as compared with NIL2.

CONCLUSIONS

The qRfg1 confers its resistance to Gibberella stalk rot through both constitutive and induced high expression of defense-related genes; while qRfg2 enhances maize resistance to the disease via relatively lower induction of auxin signaling and repression of PAT. The defense-related transcriptional changes underlying each QTL will undoubtedly facilitate our understanding of the resistance mechanism and resistance breeding for maize stalk rot.

Quantitative trait loci mapping for Gibberella ear rot resistance and associated agronomic traits using genotyping-by-sequencing in maize

Unique and co-localized chromosomal regions affecting Gibberella ear rot disease resistance and correlated agronomic traits were identified in maize. Dissecting the mechanisms underlying resistance to Gibberella ear rot (GER) disease in maize provides insight towards more informed breeding. To this goal, we evaluated 410 recombinant inbred lines (RIL) for GER resistance over three testing years using silk channel and kernel inoculation techniques. RILs were also evaluated for agronomic traits like days to silking, husk cover, and kernel drydown rate. The RILs showed significant genotypic differences for all traits with above average to high heritability estimates. Significant (P < 0.01) but weak genotypic correlations were observed between disease severity and agronomic traits, indicating the involvement of agronomic traits in disease resistance. Common QTLs were detected for GER resistance and kernel drydown rate, suggesting the existence of pleiotropic genes that could be exploited to improve both traits at the same time. The QTLs identified for silk and kernel resistance shared some common regions on chromosomes 1, 2, and 8 and also had some regions specific to each tissue on chromosomes 9 and 10. Thus, effective GER resistance breeding could be achieved by considering screening methods that allow exploitation of tissue-specific disease resistance mechanisms and include kernel drydown rate either in an index or as indirect selection criterion.

Transcriptome analysis highlights preformed defences and signalling pathways controlled by the prAe1 quantitative trait locus (QTL), conferring partial resistance to Aphanomyces euteiches in Medicago truncatula

To gain an insight into the molecular mechanisms of quantitative disease resistance in Medicago truncatula to the root-infecting oomycete Aphanomyces euteiches, we selected two near-isogenic lines (NILs), NR and NS, partially resistant and susceptible, respectively, differing in the allelic state of the quantitative resistance locus (QRL) prAe1 (partially resistant to A. euteiches 1). Complementary molecular and cytological phenotyping methods showed that prAe1 alone confers quantitative resistance to A. euteiches. Root and stem tissues were colonized in NS plants and 80% of NS plants died by 21 days post-inoculation (dpi). In contrast, A. euteiches mycelium was restricted to the root cortex and the spread of symptoms was arrested in aerial parts of NR plants. A transcriptome analysis performed at 0, 1 and 6 dpi identified 1198 differentially expressed genes (DEGs) between NR and NS lines. More than 87% of the DEGs were significantly more expressed in NR. The highest number of DEGs was found in control conditions, with 723 genes over-expressed in NR versus 85 in NS. Genes belonging to secondary metabolism, pathogenesis-related (PR) proteins and kinases were significantly enriched. The significant role of the flavonoid pathway in resistance was corroborated by the detection of larger amounts of flavonoids in NR roots and the inhibition of A. euteiches zoospore germination by 2'-O-methyl-isoliquiritigenin, a compound synthesized by enzymes specifically induced in NR. Our study revealed that prAe1-dependent resistance relies mainly on the constitutive expression of defence-related pathways and signalling elements, which can be re-amplified in later time points of the infection.

Identification and mapping of quantitative trait loci (QTL) conferring resistance to Fusarium graminearum from soybean PI 567301B

KEY MESSAGE

A major novel QTL was identified in a recombinant inbred line population derived from a cross of 'Wyandot' × PI 567301B for Fusarium graminearum, a seed and seedling pathogen of soybean. Fusarium graminearum is now recognized as a primary pathogen of soybean, causing root, seed rot and seedling damping-off in North America. In a preliminary screen, 'Wyandot' and PI 567301B were identified with medium and high levels of partial resistance to F. graminearum, respectively. The objective of this study was to characterise resistance towards F. graminearum using 184 recombinant inbred lines (RILs) derived from a cross of 'Wyandot' × PI 567301B. The parents and the RILs of the mapping population were evaluated for resistance towards F. graminearum using the rolled towel assay in a randomized incomplete block design. A genetic map was constructed from 2545 SNP markers and 2 SSR markers by composite interval mapping. One major and one minor QTL were identified on chromosomes 8 and 6, respectively, which explained 38.5 and 8.1 % of the phenotypic variance. The major QTL on chromosome 8 was mapped to a 300 kb size genomic region of the Williams 82 sequence. Annotation of this region indicates that there are 39 genes including the Rhg4 locus for soybean cyst nematode (SCN) resistance. Based on previous screens, PI 567301B is susceptible to SCN. Fine mapping of this locus will assist in cloning these candidate genes as well as identifying DNA markers flanking the QTL that can be used in marker-assisted breeding to develop cultivars with high levels of resistance to F. graminearum.