Relating significance and relations of differentially expressed genes in response to Aspergillus flavus infection in maize

Degradation of aflatoxin B1 in corn by water-assisted microwave irradiation and its kinetic

Aflatoxin B1 (AFB1) is a highly toxic, carcinogenic, teratogenic, and mutagenic mycotoxin commonly found in corn. In this work, water-assisted microwave irradiation (WMI1) was used to degrade AFB1 in corn, during which the influencing factors and kinetics of AFB1 degradation were also studied. The results showed that the degree of corn crushing, the heating rate of WMI, the temperature of WMI, the solid-liquid ratio, the initial content of AFB1 and the microwave power were all important factors affecting the degradation of AFB1. With the increase of WMI temperature, AFB1 content in corn, microwave power and the decrease of solid-liquid ratio, the degradation rate of AFB1 in corn by WMI rose continuously. Its maximum degradation rate was more than 90.6%. Meanwhile, the degradation kinetics of AFB1 in corn revealed that the degradation process of WMI followed a pseudo-first-order kinetic equation. It was demonstrated that water molecules not only acted as solvents for AFB1 but also actively participated in its degradation process within corn samples during WMI treatment. Consequently, the results indicated that WMI was an effective method for degrading AFB1 in corn.

Effects of Aspergillus flavus infection on multi-scale structures and physicochemical properties of maize starch during storage

This study systematically analyzed the effect of Aspergillus flavus infection on the maize starch multi-scale structure, physicochemical properties, processing characteristics, and synthesis regulation. A. flavus infection led to a decrease in the content of starch, an increase in the content of reactive oxygen species (ROS) and malondialdehyde (MDA), a significant decrease in the activities of peroxidase (POD) and superoxide dismutase (SOD). In addition, A. flavus infection had a significant destructive effect on the double helix structure, relative crystallinity and lamellar structure of starch, resulting in the reduction of starch viscosity, affecting the viscoelastic properties of starch, and complicating the gel formation process. However, the eugenol treatment group significantly inhibited the growth of A. flavus during maize storage, protecting the multi-scale structure and processing characteristics of maize starch from being damaged. Transcriptome analysis showed that genes involved in carbohydrate synthesis in maize were significantly downregulated and genes involved in energy synthesis were significantly upregulated, indicating that maize converted its energy storage into energy synthesis to fight the invasion of A. flavus. These results of this study enriched the mechanism of quality deterioration during maize storage, and provide theoretical and technical support for the prevention of A. flavus infection during maize storage.

The Inhibitory Effect of Pseudomonas stutzeri YM6 on Aspergillus flavus Growth and Aflatoxins Production by the Production of Volatile Dimethyl Trisulfide

Aspergillus flavus and the produced aflatoxins cause great hazards to food security and human health across all countries. The control of A. flavus and aflatoxins in grains during storage is of great significance to humans. In the current study, bacteria strain YM6 isolated from sea sediment was demonstrated effective in controlling A. flavus by the production of anti-fungal volatiles. According to morphological characteristics and phylogenetic analysis, strain YM6 was identified as Pseudomonas stutzeri. YM6 can produce abundant volatile compounds which could inhibit mycelial growth and conidial germination of A. flavus. Moreover, it greatly prevented fungal infection and aflatoxin production on maize and peanuts during storage. The inhibition rate was 100%. Scanning electron microscopy further supported that the volatiles could destroy the cell structure of A. flavus and prevent conidia germination on the grain surface. Gas chromatography/mass spectrometry revealed that dimethyl trisulfide (DMTS) with a relative abundance of 13% is the most abundant fraction in the volatiles from strain YM6. The minimal inhibitory concentration of DMTS to A. flavus conidia is 200 µL/L (compound volume/airspace volume). Thus, we concluded that Pseudomonas stutzeri YM6 and the produced DMTS showed great inhibition to A. flavus, which could be considered as effective biocontrol agents in further application.

Non-thermal plasma induces changes in aflatoxin production, devitalization, and surface chemistry of Aspergillus parasiticus

Non-thermal plasma (NTP) represents the fourth state of matter composed of neutral molecules, atoms, ions, radicals, and electrons. It has been used by various industries for several decades, but only recently NTPs have emerged in fields such as medicine, agriculture, and the food industry. In this work, we studied the effect of NTP exposure on aflatoxin production, conidial germination and mycelial vitality, morphological and surface changes of conidia and mycelium. When compared with colonies grown from untreated conidia, the colonies from NTP-treated conidia produced significantly higher levels of aflatoxins much earlier during development than colonies from untreated conidia. However, at the end of cultivation, both types of cultures yielded similar aflatoxin concentrations. The increase in the accumulation of aflatoxins was supported by high transcription levels of aflatoxin biosynthetic genes, which indicated a possibility that NTP treatment of conidia was having a longer-lasting effect on colony development and aflatoxins accumulation. NTP generated in the air at atmospheric pressure effectively devitalized Aspergillus parasiticus in conidia and hyphae within a few minutes of treatment. To describe devitalization kinetics, we applied Weibull and Hill models on sets of data collected at different exposure times during NTP treatment. The damage caused by NTP to hyphal cell wall structures was displayed by raptures visualized by scanning electron microscopy. Fourier transform infrared spectroscopy demonstrated that changes in cell envelope correlated with shifts in characteristic chemical bonds indicating dehydration, oxidation of lipids, proteins, and polysaccharides. Key points • Non-thermal plasma increases aflatoxin production shortly after treatment. • Non-thermal plasma rapidly devitalizes Aspergillus parasiticus. • Non-thermal plasma disrupts the cell surface and oxidizes biological components.

Aspergillus flavus Exploits Maize Kernels Using an "Orphan" Secondary Metabolite Cluster

Aspergillus flavus is a saprophytic cosmopolitan fungus, capable of infecting crops both pre- and post-harvest and exploiting different secondary metabolites, including aflatoxins. Aflatoxins are known carcinogens to animals and humans, but display no clear effect in host plants such as maize. In a previous study, we mined the genome of A. flavus to identify secondary metabolite clusters putatively involving the pathogenesis process in maize. We now focus on cluster 32, encoding for fungal effectors such as salicylate hydroxylase (SalOH), and necrosis- and ethylene-inducing proteins (npp1 domain protein) whose expression is triggered upon kernel contact. In order to understand the role of this genetic cluster in maize kernel infection, mutants of A. flavus, impaired or enhanced in specific functions (e.g., cluster 32 overexpression), were studied for their ability to cause disease. Within this frame, we conducted histological and histochemical experiments to verify the expression of specific genes within the cluster (e.g., SalOH, npp1), the production of salicylate, and the presence of its dehydroxylated form. Results suggest that the initial phase of fungal infection (2 days) of the living tissues of maize kernels (e.g., aleuron) coincides with a significant increase of fungal effectors such as SalOH and Npp1 that appear to be instrumental in eluding host defences and colonising the starch-enriched tissues, and therefore suggest a role of cluster 32 to the onset of infection.

Use of Dual RNA-seq for Systems Biology Analysis of Zea mays and Aspergillus flavus Interaction

The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore, the authors undertook a systems biology approach involving dual RNA-seq to determine the simultaneous response from the host and the pathogen. What was dramatically highlighted in the analysis is the uniformity in the development patterns of gene expression of the host and the pathogen during infection. This led to the development of a "stage of infection index" that was subsequently used to categorize the samples before down-stream system biology analysis. Additionally, we were able to ascertain that key maize genes in pathways such as the jasmonate, ethylene and ROS pathways, were up-regulated in the study. The stage of infection index used for the transcriptomic analysis revealed that A. flavus produces a relatively limited number of transcripts during the early stages (0 to 12 h) of infection. At later stages, in A. flavus, transcripts and pathways involved in endosomal transport, aflatoxin production, and carbohydrate metabolism were up-regulated. Multiple WRKY genes targeting the activation of the resistance pathways (i.e., jasmonate, phenylpropanoid, and ethylene) were detected using causal inference analysis. This analysis also revealed, for the first time, the activation of Z. mays resistance genes influencing the expression of specific A. flavus genes. Our results show that A. flavus seems to be reacting to a hostile environment resulting from the activation of resistance pathways in Z. mays. This study revealed the dynamic nature of the interaction between the two organisms.

Staphylococcus saprophyticus L-38 produces volatile 3,3-dimethyl-1,2-epoxybutane with strong inhibitory activity against Aspergillus flavus germination and aflatoxin production

Controlling proliferation and aflatoxin production by Aspergillus flavus is a pressing challenge for global food safety and security. Marine bacterium Staphylococcus saprophyticus strain L-38 showed excellent antifungal activity toward A. flavus in vitro and in vivo. In sealed, non-contact confrontation assays, L-38 completely inhibited conidial germination and mycelial growth of A. flavus through the production of volatile organic compounds (VOCs). Gas chromatography-mass spectrometry identified 3,3-dimethyl-1,2-epoxybutane (3-DE) as the most abundant VOC (32.61% of total peak area, 78% matching). Exposure of A. flavus cultures to synthetic 3-DE similarly demonstrated strong inhibition of growth. Moreover, culture of L-38 in a sealed chamber with maize or peanuts artificially inoculated with A. flavus, at high water activity, resulted in significant inhibition of A. flavus germination and aflatoxin biosynthesis. Scanning electron microscopy of these samples revealed severe damage to conidial cells and hyphae compared to samples not exposed to L-38. L-38 also showed broad and effective antifungal activity toward eight other phytopathogenic fungi including Aspergillus niger, Fusarium verticillioides, Fusarium graminearum, Sclerotinia sclerotiorum, Rhizoctonia solani, Alternaria alternata, Monilinia fructicola, and Botrytis cinerea. This work introduces S. saprophyticus L-38 as a potential biocontrol agent and demonstrates the efficacy of the volatile 3-DE in the control of A. flavus and other destructive plant pathogens for post-harvest food safety.

Inhibitory Effect of Volatiles Emitted From Alcaligenes faecalis N1-4 on Aspergillus flavus and Aflatoxins in Storage

Controlling aflatoxigenic Aspergillus flavus and aflatoxins (AFs) in grains and food during storage is a great challenge to humans worldwide. Alcaligenes faecalis N1-4 isolated from tea rhizosphere soil can produce abundant antifungal volatiles, and greatly inhibited the growth of A. flavus in un-contacted face-to-face dual culture testing. Gas chromatography tandem mass spectrometry revealed that dimethyl disulfide (DMDS) and methyl isovalerate (MI) were two abundant compounds in the volatile profiles of N1-4. DMDS was found to have the highest relative abundance (69.90%, to the total peak area) in N1-4, which prevented the conidia germination and mycelial growth of A. flavus at 50 and 100 μL/L, respectively. The effective concentration for MI against A. flavus is 200 μL/L. Additionally, Real-time quantitative PCR analysis proved that the expression of 12 important genes in aflatoxin biosynthesis pathway was reduced by these volatiles, and eight genes were down regulated by 4.39 to 32.25-folds compared to control treatment with significant differences. And the A. flavus infection and AFs contamination in groundnut, maize, rice and soybean of high water activity were completely inhibited by volatiles from N1-4 in storage. Scanning electron microscope further proved that A. flavus conidia inoculated on peanuts surface were severely damaged by volatiles from N1-4. Furthermore, strain N1-4 showed broad and antifungal activity to other six important plant pathogens including Fusarium graminearum, F. equiseti, Alternaria alternata, Botrytis cinerea, Aspergillus niger, and Colletotrichum graminicola. Thus, A. faecalis N1-4 and volatile DMDS and MI may have potential to be used as biocontrol agents to control A. flavus and AFs during storage.

Changes in maize transcriptome in response to maize Iranian mosaic virus infection

Background

Maize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated.

Methodology/Principal findings

Complementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR.

Conclusion/Significance

Approximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.

Aflatoxins: biosynthesis, prevention and eradication

Filamentous fungi belonging to Aspergilli genera produce many compounds through various biosynthetic pathways. These compounds include a spectrum of products with beneficial medical properties (lovastatin) as well as those that are toxic and/or carcinogenic which are called mycotoxins. Aspergillus flavus, one of the most abundant soil-borne fungi, is a saprobe that is able growing on many organic nutrient sources, such as peanuts, corn and cotton seed. In many countries, food contamination by A. flavus is a huge problem, mainly due to the production of the most toxic and carcinogenic compounds known as aflatoxins. In this paper, we briefly cover current progress in aflatoxin biosynthesis and regulation, pre- and postharvest preventive measures, and decontamination procedures.

Expression Profiling Coupled with In-silico Mapping Identifies Candidate Genes for Reducing Aflatoxin Accumulation in Maize

Aflatoxin, produced by Aspergillus flavus, is hazardous to health of humans and livestock. The lack of information about large effect QTL for resistance to aflatoxin accumulation is a major obstacle to employ marker-assisted selection for maize improvement. The understanding of resistance mechanisms of the host plant and the associated genes is necessary for improving resistance to A. flavus infection. A suppression subtraction hybridization (SSH) cDNA library was made using the developing kernels of Mp715 (resistant inbred) and B73 (susceptible inbred) and 480 randomly selected cDNA clones were sequenced to identify differentially expressed genes (DEGs) in response to A. flavus infection and map these clones onto the corn genome by in-silico mapping. A total of 267 unigenes were identified and majority of genes were related to metabolism, stress response, and disease resistance. Based on the reverse northern hybridization experiment, 26 DEGs were selected for semi-quantitative RT-PCR analysis in seven inbreds with variable resistance to aflatoxin accumulation at two time points after A. flavus inoculation. Most of these genes were highly expressed in resistant inbreds. Quantitative RT-PCR analysis validated upregulation of PR-4, DEAD-box RNA helicase, and leucine rich repeat family protein in resistant inbreds. Fifty-six unigenes, which were placed on linkage map through in-silico mapping, overlapped the QTL regions for resistance to aflatoxin accumulation identified in a mapping population derived from the cross between B73 and Mp715. Since majority of these mapped genes were related to disease resistance, stress response, and metabolism, these should be ideal candidates to investigate host pathogen interaction and to reduce aflatoxin accumulation in maize.

Comparative Histological and Transcriptional Analysis of Maize Kernels Infected with Aspergillus flavus and Fusarium verticillioides

Aspergillus flavus and Fusarium verticillioides infect maize kernels and contaminate them with the mycotoxins aflatoxin, and fumonisin, respectively. Genetic resistance in maize to these fungi and to mycotoxin contamination has been difficult to achieve due to lack of identified resistance genes. The objective of this study was to identify new candidate resistance genes by characterizing their temporal expression in response to infection and comparing expression of these genes with genes known to be associated with plant defense. Fungal colonization and transcriptional changes in kernels inoculated with each fungus were monitored at 4, 12, 24, 48, and 72 h post inoculation (hpi). Maize kernels responded by differential gene expression to each fungus within 4 hpi, before the fungi could be observed visually, but more genes were differentially expressed between 48 and 72 hpi, when fungal colonization was more extensive. Two-way hierarchal clustering analysis grouped the temporal expression profiles of the 5,863 differentially expressed maize genes over all time points into 12 clusters. Many clusters were enriched for genes previously associated with defense responses to either A. flavus or F. verticillioides. Also within these expression clusters were genes that lacked either annotation or assignment to functional categories. This study provided a comprehensive analysis of gene expression of each A. flavus and F. verticillioides during infection of maize kernels, it identified genes expressed early and late in the infection process, and it provided a grouping of genes of unknown function with similarly expressed defense related genes that could inform selection of new genes as targets in breeding strategies.

Molecular dissection of pathway components unravel atisine biosynthesis in a non-toxic Aconitum species, A. heterophyllum Wall

Aconitum heterophyllum is an important component for various herbal drug formulations due to the occurrence of non-toxic aconites including marker compound, atisine. Despite huge pharmacological potential, the reprogramming of aconites production is limited due to lack of understanding on their biosynthesis. To address this problem, we have proposed here the complete atisine biosynthetic pathway for the first time connecting glycolysis, MVA/MEP, serine biosynthesis and diterpene biosynthetic pathways. The transcript profiling revealed phosphorylated pathway as a major contributor towards serine production in addition to repertoire of genes in glycolysis (G6PI, PFK, ALD and ENO), serine biosynthesis (PGDH and PSAT) and diterpene biosynthesis (KO and KH) sharing a similar pattern of expression (2-4-folds) in roots compared to shoots vis-à-vis atisine content (0-0.37 %). Quantification of steviol and comparative analysis of shortlisted genes between roots of high (0.37 %) vs low (0.14 %) atisine content accessions further confirmed the route of atisine biosynthesis. The results showed 6-fold increase in steviol content and 3-62-fold up-regulation of all the selected genes in roots of high content accession ascertaining their association towards atisine production. Moreover, significant positive correlations were observed between selected genes suggesting their co-expression and crucial role in atisine biosynthesis. This study, thus, offers unprecedented opportunities to explore the selected candidate genes for enhanced production of atisine in cultivated plant cells.

Comparative transcript profiling of resistant and susceptible peanut post-harvest seeds in response to aflatoxin production by Aspergillus flavus

BACKGROUND

Aflatoxin contamination caused by Aspergillus flavus in peanut (Arachis hypogaea) including in pre- and post-harvest stages seriously affects industry development and human health. Even though resistance to aflatoxin production in post-harvest peanut has been identified, its molecular mechanism has been poorly understood. To understand the mechanism of peanut response to aflatoxin production by A. flavus, RNA-seq was used for global transcriptome profiling of post-harvest seed of resistant (Zhonghua 6) and susceptible (Zhonghua 12) peanut genotypes under the fungus infection and aflatoxin production stress.

RESULT

A total of 128.72 Gb of high-quality bases were generated and assembled into 128, 725 unigenes (average length 765 bp). About 62, 352 unigenes (48.43%) were annotated in the NCBI non-redundant protein sequences, NCBI non-redundant nucleotide sequences, Swiss-Prot, KEGG Ortholog, Protein family, Gene Ontology, or eukaryotic Ortholog Groups database and more than 93% of the unigenes were expressed in the samples. Among obtained 30, 143 differentially expressed unigenes (DEGs), 842 potential defense-related genes, including nucleotide binding site-leucine-rich repeat proteins, polygalacturonase inhibitor proteins, leucine-rich repeat receptor-like kinases, mitogen-activated protein kinase, transcription factors, ADP-ribosylation factors, pathogenesis-related proteins and crucial factors of other defense-related pathways, might contribute to peanut response to aflatoxin production. Notably, DEGs involved in phenylpropanoid-derived compounds biosynthetic pathway were induced to higher levels in the resistant genotype than in the susceptible one. Flavonoid, stilbenoid and phenylpropanoid biosynthesis pathways were enriched only in the resistant genotype.

CONCLUSIONS

This study provided the first comprehensive analysis of transcriptome of post-harvest peanut seeds in response to aflatoxin production, and would contribute to better understanding of molecular interaction between peanut and A. flavus. The data generated in this study would be a valuable resource for genetic and genomic studies on crops resistance to aflatoxin contamination.

Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis

Background

Cereal cyst nematode Heterodera avenae, an important soil-borne pathogen in wheat, causes numerous annual yield losses worldwide, and use of resistant cultivars is the best strategy for control. However, target genes are not readily available for breeding resistant cultivars. Therefore, comparative transcriptomic analyses were performed to identify more applicable resistance genes for cultivar breeding.

Methods

The developing nematodes within roots were stained with acid fuchsin solution. Transcriptome assemblies and redundancy filteration were obtained by Trinity, TGI Clustering Tool and BLASTN, respectively. Gene Ontology annotation was yielded by Blast2GO program, and metabolic pathways of transcripts were analyzed by Path_finder. The ROS levels were determined by luminol-chemiluminescence assay. The transcriptional gene expression profiles were obtained by quantitative RT-PCR.

Results

The RNA-sequencing was performed using an incompatible wheat cultivar VP1620 and a compatible control cultivar WEN19 infected with H. avenae at 24 h, 3 d and 8 d. Infection assays showed that VP1620 failed to block penetration of H. avenae but disturbed the transition of developmental stages, leading to a significant reduction in cyst formation. Two types of expression profiles were established to predict candidate resistance genes after developing a novel strategy to generate clean RNA-seq data by removing the transcripts of H. avenae within the raw data before assembly. Using the uncoordinated expression profiles with transcript abundance as a standard, 424 candidate resistance genes were identified, including 302 overlapping genes and 122 VP1620-specific genes. Genes with similar expression patterns were further classified according to the scales of changed transcript abundances, and 182 genes were rescued as supplementary candidate resistance genes. Functional characterizations revealed that diverse defense-related pathways were responsible for wheat resistance against H. avenae. Moreover, phospholipase was involved in many defense-related pathways and localized in the connection position. Furthermore, strong bursts of reactive oxygen species (ROS) within VP1620 roots infected with H. avenae were induced at 24 h and 3 d, and eight ROS-producing genes were significantly upregulated, including three class III peroxidase and five lipoxygenase genes.

Conclusions

Large-scale identification of wheat resistance genes were processed by comparative transcriptomic analysis. Functional characterization showed that phospholipases associated with ROS production played vital roles in early defense responses to H. avenae via involvement in diverse defense-related pathways as a hub switch. This study is the first to investigate the early defense responses of wheat against H. avenae, not only provides applicable candidate resistance genes for breeding novel wheat cultivars, but also enables a better understanding of the defense mechanisms of wheat against H. avenae.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2037-8) contains supplementary material, which is available to authorized users.

The Shewanella algae strain YM8 produces volatiles with strong inhibition activity against Aspergillus pathogens and aflatoxins

Aflatoxigenic Aspergillus fungi and associated aflatoxins are ubiquitous in the production and storage of food/feed commodities. Controlling these microbes is a challenge. In this study, the Shewanella algae strain YM8 was found to produce volatiles that have strong antifungal activity against Aspergillus pathogens. Gas chromatography-mass spectrometry profiling revealed 15 volatile organic compounds (VOCs) emitted from YM8, of which dimethyl trisulfide was the most abundant. We obtained authentic reference standards for six of the VOCs; these all significantly reduced mycelial growth and conidial germination in Aspergillus; dimethyl trisulfide and 2,4-bis(1,1-dimethylethyl)-phenol showed the strongest inhibitory activity. YM8 completely inhibited Aspergillus growth and aflatoxin biosynthesis in maize and peanut samples stored at different water activity levels, and scanning electron microscopy revealed severely damaged conidia and a complete lack of mycelium development and conidiogenesis. YM8 also completely inhibited the growth of eight other agronomically important species of phytopathogenic fungi: A. parasiticus, A. niger, Alternaria alternate, Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Monilinia fructicola, and Sclerotinia sclerotiorum. This study demonstrates the susceptibility of Aspergillus and other fungi to VOCs from marine bacteria and indicates a new strategy for effectively controlling these pathogens and the associated mycotoxin production during storage and possibly in the field.

Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides

Background

Maize, a crop of global significance, is vulnerable to a variety of biotic stresses resulting in economic losses. Fusarium verticillioides (teleomorph Gibberella moniliformis) is one of the key fungal pathogens of maize, causing ear rots and stalk rots. To better understand the genetic mechanisms involved in maize defense as well as F. verticillioides virulence, a systematic investigation of the host-pathogen interaction is needed. The aim of this study was to computationally identify potential maize subnetwork modules associated with its defense response against F. verticillioides.

Results

We obtained time-course RNA-seq data from B73 maize inoculated with wild type F. verticillioides and a loss-of-virulence mutant, and subsequently established a computational pipeline for network-based comparative analysis.

Specifically, we first analyzed the RNA-seq data by a cointegration-correlation-expression approach, where maize genes were jointly analyzed with known F. verticillioides virulence genes to find candidate maize genes likely associated with the defense mechanism. We predicted maize co-expression networks around the selected maize candidate genes based on partial correlation, and subsequently searched for subnetwork modules that were differentially activated when inoculated with two different fungal strains. Based on our analysis pipeline, we identified four potential maize defense subnetwork modules. Two were directly associated with maize defense response and were associated with significant GO terms such as GO:0009817 (defense response to fungus) and GO:0009620 (response to fungus). The other two predicted modules were indirectly involved in the defense response, where the most significant GO terms associated with these modules were GO:0046914 (transition metal ion binding) and GO:0046686 (response to cadmium ion).

Conclusion

Through our RNA-seq data analysis, we have shown that a network-based approach can enhance our understanding of the complicated host-pathogen interactions between maize and F. verticillioides by interpreting the transcriptome data in a system-oriented manner. We expect that the proposed analytic pipeline can also be adapted for investigating potential functional modules associated with host defense response in diverse plant-pathogen interactions.

Aflatoxin Resistance in Maize: What Have We Learned Lately?

Aflatoxin contamination of maize grain is a huge economic and health problem, causing death and increased disease burden in much of the developing world and income loss in the developed world. Despite the gravity of the problem, deployable solutions are still being sought. In the past 15 years, much progress has been made in creating resistant maize inbred lines; mapping of genetic factors associated with resistance; and identifying possible resistance mechanisms. This review highlights this progress, most of which has occurred since the last time a review was published on this topic. Many of the needs highlighted in the last reviews have been addressed, and several solutions, taken together, can now greatly reduce the aflatoxin problem in maize grain. Continued research will soon lead to further solutions, which promise to further reduce and even eliminate the problem completely.

Toward elucidation of genetic and functional genetic mechanisms in corn host resistance to Aspergillus flavus infection and aflatoxin contamination

Aflatoxins are carcinogenic mycotoxins produced by some species in the Aspergillus genus, such as A. flavus and A. parasiticus. Contamination of aflatoxins in corn profusely happens at pre-harvest stage when heat and drought field conditions favor A. flavus colonization. Commercial corn hybrids are generally susceptible to A. flavus infection. An ideal strategy for preventing aflatoxin contamination is through the enhancement of corn host resistance to Aspergillus infection and aflatoxin production. Constant efforts have been made by corn breeders to develop resistant corn genotypes. Significantly low levels of aflatoxin accumulation have been determined in certain resistant corn inbred lines. A number of reports of quantitative trait loci have provided compelling evidence supporting the quantitative trait genetic basis of corn host resistance to aflatoxin accumulation. Important findings have also been obtained from the investigation on candidate resistance genes through transcriptomics approach. Elucidation of molecular mechanisms will provide in-depth understanding of the host-pathogen interactions and hence facilitate the breeding of corn with resistance to A. flavus infection and aflatoxin accumulation.