Commercial hybrids and mutant genotypes reveal complex protective roles for inducible terpenoid defenses in maize

Structurally diverse specialized metabolites of maize and their extensive biological functions

Maize originated in southern Mexico and various hybrid varieties have been bred during domestication. All maize tissues are rich in specialized plant metabolites (SPMs), which allow the plants to resist the stresses of herbivores and pathogens or environmental factors. To date, a total of 95 terpenoids, 91 phenolics, 31 alkaloids, and 6 other types of compounds have been identified from maize. Certain volatile sesquiterpenes released by maize plants attract the natural enemies of maize herbivores and provide an indirect defensive function. Kauralexins and dolabralexins are the most abundant diterpenoids in maize and are known to regulate and stabilize the maize rhizosphere microbial community. Benzoxazinoids and benzoxazolinones are the main alkaloids in maize and are found in maize plants at the highest concentrations at the seedling stage. These two kinds of alkaloids directly resist herbivory and pathogenic infection. Phenolics enhance the cross-links between maize cell walls. Meanwhile, SPMs also regulate plant-plant relationships. In conclusion, SPMs in maize show a large diversity of chemical structures and broad-spectrum biological activities. We use these to provide ideas and information to enable the improvement of maize resistances through breeding and to promote the rapid development of the maize industry.

Genome-wide association study and molecular marker development for susceptibility to Gibberella ear rot in maize

KEY MESSAGES

Sixty-nine quantitative trait nucleotides conferring maize resistance to Gibberella ear rot were detected, including eighteen novel loci. Four candidate genes were predicted, and four kompetitive allele-specific PCR markers were developed. Maize Gibberella ear rot (GER), caused by Fusarium graminearum, is one of the most devastating diseases in maize-growing regions worldwide. Enhancing maize cultivar resistance to this disease requires a comprehensive understanding of the genetic basis of resistance to GER. In this study, 334 maize inbred lines were phenotyped for GER resistance in five environments and genotyped using the Affymetrix CGMB56K SNP Array, and a genome-wide association study of resistance to GER was performed using a 3V multi-locus random-SNP-effect mixed linear model. A total of 69 quantitative trait nucleotides (QTNs) conferring resistance to GER were detected, and all of them explained individually less than 10% of the phenotypic variation, suggesting that resistance to GER is controlled by multiple minor-effect genetic loci. A total of 348 genes located around the 200-kb genomic region of these 69 QTNs were identified, and four of them (Zm00001d029648, Zm00001d031449, Zm00001d006397, and Zm00001d053145) were considered candidate genes conferring susceptibility to GER based on gene expression patterns. Moreover, four kompetitive allele-specific PCR markers were developed based on the non-synonymous variation of these four candidate genes and validated in two genetic populations. This study provides useful genetic resources for improving resistance to GER in maize.

Understanding the chemical language mediating maize immunity and environmental adaptation

Diverse networks of specialized metabolites promote plant fitness by mediating beneficial and antagonistic environmental interactions. In maize (Zea mays), constitutive and dynamically formed cocktails of terpenoids, benzoxazinoids, oxylipins, and phenylpropanoids contribute to plant defense and ecological adaptation. Recent research has highlighted the multifunctional nature of many specialized metabolites, serving not only as elaborate chemical defenses that safeguard against biotic and abiotic stress but also as regulators in adaptive developmental processes and microbiome interactions. Great strides have also been made in identifying the modular pathway networks that drive maize chemical diversity. Translating this knowledge into strategies for enhancing stress resilience traits has the potential to address climate-driven yield losses in one of the world's major food, feed, and bioenergy crops.

Hordedane diterpenoid phytoalexins restrict Fusarium graminearum infection but enhance Bipolaris sorokiniana colonization of barley roots

Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense responses. These include the induction of a cocktail of defense metabolites that typically restrict pathogen virulence. Here, we investigate the interaction between barley roots and the fungal pathogens Bipolaris sorokiniana (Bs) and Fusarium graminearum (Fg) at the metabolite level. We identify hordedanes, a previously undescribed set of labdane-related diterpenoids with antimicrobial properties, as critical players in these interactions. Infection of barley roots by Bs and Fg elicits hordedane synthesis from a 600-kb gene cluster. Heterologous reconstruction of the biosynthesis pathway in yeast and Nicotiana benthamiana produced several hordedanes, including one of the most functionally decorated products 19-β-hydroxy-hordetrienoic acid (19-OH-HTA). Barley mutants in the diterpene synthase genes of this cluster are unable to produce hordedanes but, unexpectedly, show reduced Bs colonization. By contrast, colonization by Fusarium graminearum, another fungal pathogen of barley and wheat, is 4-fold higher in the mutants completely lacking hordedanes. Accordingly, 19-OH-HTA enhances both germination and growth of Bs, whereas it inhibits other pathogenic fungi, including Fg. Analysis of microscopy and transcriptomics data suggest that hordedanes delay the necrotrophic phase of Bs. Taken together, these results show that adapted pathogens such as Bs can subvert plant metabolic defenses to facilitate root colonization.

Heterologous Biosynthesis of Kauralexin A1 in Saccharomyces cerevisiae through Metabolic and Enzyme Engineering

Kauralexin A1 (KA1) is a key intermediate of the kauralexin A series metabolites of maize phytoalexins. However, their application is severely limited by their low abundance in maize. In this study, an efficient biosynthetic pathway was constructed to produce KA1 in Saccharomyces cerevisiae. Also, metabolic and enzyme engineering strategies were applied to construct the high-titer strains, such as chassis modification, screening synthases, the colocalization of enzymes, and multiple genomic integrations. First, the KA1 precursor ent-kaurene was synthesized using the efficient diterpene synthase GfCPS/KS from Fusarium fujikuroi, and optimized to reach 244.36 mg/L in shake flasks, which displayed a 200-fold increase compared to the initial strain. Then, the KA1 was produced under the catalysis of ZmCYP71Z18 from Zea mays and SmCPR1 from Salvia miltiorrhiza, and the titer was further improved by integrating the fusion protein into the genome. Finally, an ent-kaurene titer of 763.23 mg/L and a KA1 titer of 42.22 mg/L were achieved through a single-stage fed-batch fermentation in a 5 L bioreactor. This is the first report of the heterologous biosynthesis of maize diterpene phytoalexins in S. cerevisiae, which lays a foundation for further pathway reconstruction and biosynthesis of the kauralexin A series maize phytoalexins.

The impact of climate change on maize chemical defenses

Climate change is increasingly affecting agriculture, both at the levels of crops themselves, and by altering the distribution and damage caused by insect or microbial pests. As global food security depends on the reliable production of major crops such as maize (Zea mays), it is vital that appropriate steps are taken to mitigate these negative impacts. To do this a clear understanding of what the impacts are and how they occur is needed. This review focuses on the impact of climate change on the production and effectiveness of maize chemical defenses, including volatile organic compounds, terpenoid phytoalexins, benzoxazinoids, phenolics, and flavonoids. Drought, flooding, heat stress, and elevated concentrations of atmospheric carbon dioxide, all impact the production of maize chemical defenses, in a compound and tissue-specific manner. Furthermore, changes in stomatal conductance and altered soil conditions caused by climate change can impact environmental dispersal and effectiveness certain chemicals. This can alter both defensive barrier formation and multitrophic interactions. The production of defense chemicals is controlled by stress signaling networks. The use of similar networks to co-ordinate the response to abiotic and biotic stress can lead to complex integration of these networks in response to the combinatorial stresses that are likely to occur in a changing climate. The impact of multiple stressors on maize chemical defenses can therefore be different from the sum of the responses to individual stressors and challenging to predict. Much work remains to effectively leverage these protective chemicals in climate-resilient maize.

A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize

Two major groups of specialized metabolites in maize (Zea mays), termed kauralexins and dolabralexins, serve as known or predicted diterpenoid defenses against pathogens, herbivores, and other environmental stressors. To consider the physiological roles of the recently discovered dolabralexin pathway, we examined dolabralexin structural diversity, tissue-specificity, and stress-elicited production in a defined biosynthetic pathway mutant. Metabolomics analyses support a larger number of dolabralexin pathway products than previously known. We identified dolabradienol as a previously undetected pathway metabolite and characterized its enzymatic production. Transcript and metabolite profiling showed that dolabralexin biosynthesis and accumulation predominantly occur in primary roots and show quantitative variation across genetically diverse inbred lines. Generation and analysis of CRISPR-Cas9-derived loss-of-function Kaurene Synthase-Like 4 (Zmksl4) mutants demonstrated dolabralexin production deficiency, thus supporting ZmKSL4 as the diterpene synthase responsible for the conversion of geranylgeranyl pyrophosphate precursors into dolabradiene and downstream pathway products. Zmksl4 mutants further display altered root-to-shoot ratios and root architecture in response to water deficit. Collectively, these results demonstrate dolabralexin biosynthesis via ZmKSL4 as a committed pathway node biochemically separating kauralexin and dolabralexin metabolism, and suggest an interactive role of maize dolabralexins in plant vigor during abiotic stress.

Maize Terpene Synthase 8 (ZmTPS8) Contributes to a Complex Blend of Fungal-Elicited Antibiotics

In maize (Zea mays), fungal-elicited immune responses include the accumulation of terpene synthase (TPS) and cytochrome P450 monooxygenases (CYP) enzymes resulting in complex antibiotic arrays of sesquiterpenoids and diterpenoids, including α/β-selinene derivatives, zealexins, kauralexins and dolabralexins. To uncover additional antibiotic families, we conducted metabolic profiling of elicited stem tissues in mapping populations, which included B73 × M162W recombinant inbred lines and the Goodman diversity panel. Five candidate sesquiterpenoids associated with a chromosome 1 locus spanning the location of ZmTPS27 and ZmTPS8. Heterologous enzyme co-expression studies of ZmTPS27 in Nicotiana benthamiana resulted in geraniol production while ZmTPS8 yielded α-copaene, δ-cadinene and sesquiterpene alcohols consistent with epi-cubebol, cubebol, copan-3-ol and copaborneol matching the association mapping efforts. ZmTPS8 is an established multiproduct α-copaene synthase; however, ZmTPS8-derived sesquiterpene alcohols are rarely encountered in maize tissues. A genome wide association study further linked an unknown sesquiterpene acid to ZmTPS8 and combined ZmTPS8-ZmCYP71Z19 heterologous enzyme co-expression studies yielded the same product. To consider defensive roles for ZmTPS8, in vitro bioassays with cubebol demonstrated significant antifungal activity against both Fusarium graminearum and Aspergillus parasiticus. As a genetically variable biochemical trait, ZmTPS8 contributes to the cocktail of terpenoid antibiotics present following complex interactions between wounding and fungal elicitation.

By-Products of Zea mays L.: A Promising Source of Medicinal Properties with Phytochemistry and Pharmacological Activities: A Comprehensive Review

Zea mays (Z. mays) is one of the main cereal crops in the world, and it's by-products have exhibited medicinal properties to explore. This article intends to review the chemical compositions and pharmacological activities of by-products of Z. mays (corn silks, roots, bract, stems, bran, and leaves) which support the therapeutic potential in the treatment of different diseases, with emphasis on the natural occurring compounds and detailed pharmacological developments. Based on this review, 231 natural compounds are presented. Among them, flavonoids, terpenes, phenylpropanoids, and alkaloids are the most frequently reported. The by-products of Z. mays possess diuretic effects, hepatoprotective, anti-diabetic, antioxidant, neuroprotective, anti-inflammatory, anti-cancer, plant protection activity, and other activities. This article reviewed the phytochemistry and pharmacological activities of Z. mays for comprehensive quality control and the safety and effectiveness to enhance future application.

Inoculation with carbofuran-degrading rhizobacteria promotes maize growth through production of IAA and regulation of the release of plant-specialized metabolites

Toxic residues of the insecticide carbofuran in farmland is an urgent problem, and high concentrations of carbofuran have been found in the rhizoshperic soil of maize treated with seed coating agents 120-180 days after planting. Using an enrichment co-culture method, we identify a bacterial strain obtained from these carbofuran-contaminated rhizosphere soils as Leclercia adecarboxylata MCH-1. This strain exhibited a significant ability to degrade both carbofuran and 3-keto carbofuran, with total degradation of 55.6 ± 4.6% and 75.7 ± 3.4%, respectively, 24 h following start of co-culture. Further activity screening revealed that the inoculation of maize roots with L. adecarboxylata MCH-1 promoted maize seedling growth. Quantitative analysis demonstrated that this bacterial strain had the ability to synthesize the phytohormone IAA. Simultaneously, the concentration of IAA in the rhizospheric soil increased following inoculation of maize roots with L. adecarboxylata MCH-1. Moreover, the concentrations of plant specialized metabolites, including phenolics, terpenoids, and alkaloids, decreased in maize seedlings and were elevated in the rhizospheric soil after maize roots had been inoculated with the MCH-1 strain. Interestingly, the growth of the strain MCH-1 was improved by co-culture with root exudates obtained from the rhizospheric soil, specifically 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, and zealexin A₁ (ZA₁). Taken together, our results suggest that the carbofuran-degrading rhizobacterium L. adecarboxylata MCH-1 is able to interact with maize plants through the regulation of maize root exudates. Moreover, inoculation with L. adecarboxylata MCH-1 promotes maize growth through the production of IAA and regulation of the release of plant specialized metabolites. Our results provide a new model organism for the remediation of farmland soils from pollution with carbofuran residues.

Comparative Analysis of Multiple GWAS Results Identifies Metabolic Pathways Associated with Resistance to A. flavus Infection and Aflatoxin Accumulation in Maize

Aflatoxins are carcinogenic secondary metabolites produced by several species of Aspergillus, including Aspergillus flavus, an important ear rot pathogen in maize. Most commercial corn hybrids are susceptible to infection by A. flavus, and aflatoxin contaminated grain causes economic damage to farmers. The creation of inbred lines resistant to Aspergillus fungal infection or the accumulation of aflatoxins would be aided by knowing the pertinent alleles and metabolites associated with resistance in corn lines. Multiple Quantitative Trait Loci (QTL) and association mapping studies have uncovered several dozen potential genes, but each with a small effect on resistance. Metabolic pathway analysis, using the Pathway Association Study Tool (PAST), was performed on aflatoxin accumulation resistance using data from four Genome-wide Association Studies (GWAS). The present research compares the outputs of these pathway analyses and seeks common metabolic mechanisms underlying each. Genes, pathways, metabolites, and mechanisms highlighted here can contribute to improving phenotypic selection of resistant lines via measurement of more specific and highly heritable resistance-related traits and genetic gain via marker assisted or genomic selection with multiple SNPs linked to resistance-related pathways.

Dedicated farnesyl diphosphate synthases circumvent isoprenoid-derived growth-defense tradeoffs in Zea mays

Zea mays (maize) makes phytoalexins such as sesquiterpenoid zealexins, to combat invading pathogens. Zealexins are produced from farnesyl diphosphate in microgram per gram fresh weight quantities. As farnesyl diphosphate is also a precursor for many compounds essential for plant growth, the question arises as to how Z. mays produces high levels of zealexins without negatively affecting vital plant systems. To examine if specific pools of farnesyl diphosphate are made for zealexin synthesis we made CRISPR/Cas9 knockouts of each of the three farnesyl diphosphate synthases (FPS) in Z. mays and examined the resultant impacts on different farnesyl diphosphate-derived metabolites. We found that FPS3 (GRMZM2G098569) produced most of the farnesyl diphosphate for zealexins, while FPS1 (GRMZM2G168681) made most of the farnesyl diphosphate for the vital respiratory co-factor ubiquinone. Indeed, fps1 mutants had strong developmental phenotypes such as reduced stature and development of chlorosis. The replication and evolution of the fps gene family in Z. mays enabled it to produce dedicated FPSs for developmentally related ubiquinone production (FPS1) or defense-related zealexin production (FPS3). This partitioning of farnesyl diphosphate production between growth and defense could contribute to the ability of Z. mays to produce high levels of phytoalexins without negatively impacting its growth.

Physiological and Molecular Characteristics of Southern Leaf Blight Resistance in Sweet Corn Inbred Lines

Southern corn leaf blight is one of the most widespread foliar diseases in maize-producing areas worldwide and can seriously reduce the yield and quality of sweet corn. However, the molecular mechanisms underlying the disease in sweet corn have not been widely reported. In this study, two sweet corn inbred lines, resistant K13 (RK13) and susceptible K39 (SK39), were used to explore the disease resistance mechanism of southern leaf blight. We observed morphological characteristics and assessed the changes in protective enzymatic activity in sweet corn leaves after inoculation of C. heterostrophus. RNA-seq was performed to elucidate the transcriptional dynamics and reveal the key pathways involved in southern leaf blight resistance without pathogens (Mock) and at 1 and 3 days post inoculation (1 and 3 dpi). Differentially expressed genes (DEGs) were identified in the SK39 group (including three pairwise combinations: SK39−0d_vs_SK39−1d, SK39−1d_vs_SK39−3d and SK39−1d_vs_SK39−3d), the RK13 group (including three pairwise combinations: RK13−0d_vs_RK13−1d, RK13−1d_vs_RK13−3d and RK13−1d_vs_RK13−3d), and the SK39_vs_RK13 group (including three pairwise combinations: SK39−0d_vs_RK13−0d, SK39−1d_vs_RK13−1d, and SK39−3d_vs_RK13−3d). In our study, 9455 DEGs from the RK13 group, 9626 from the SK39 group, and 9051 DEGs from the SK39_vs_RK13 group were obtained. Furthermore, 2775, 163, and 185 DEGs were co-expressed at SK39_vs_RK13, RK13, and SK39, respectively. A functional analysis of the DEGs revealed that five pathways—i.e., photosynthesis, plant hormone signal transduction, MAPK signaling pathway, phenylpropanoid biosynthesis, and biosynthesis of secondary metabolites—and transcription factor families play crucial roles in disease resistance. The results from the present study enabled the identification of the JA and SA signaling pathways, which are potentially involved in the response to southern leaf blight in maize. Our findings also highlight the significance of ZIM transcription factors and pathogenesis-related (PR) genes during pathogen infection. This study preliminarily explored the molecular mechanisms of the interaction between sweet corn and C. heterostrophus and provides a reference for identifying southern leaf blight resistance genes in the future.

Maize Anthracnose Stalk Rot in the Genomic Era

Anthracnose stalk rot (ASR) of maize results in millions of dollars in losses annually in the United States. ASR, together with anthracnose leaf blight and anthracnose top dieback, is caused by the fungus Colletotrichum graminicola. Current ASR management recommendations emphasize host resistance and reduction of plant stressors (e.g., drought, heat, low fertility, or soil acidity). Stress reduction may be more difficult to achieve in the future due to more high-intensity production protocols and climate change. Moreover, cultural and chemical management practices may conflict with other important goals, including environmental sustainability and maximization of yield potential. Thus, future ASR management may rely more heavily on host resistance, for which there are relatively few highly effective sources. The last comprehensive review of C. graminicola and maize anthracnose was written over two decades ago. The genomic age has brought important new insights into mechanisms governing the host-pathogen interaction from the application of molecular and cytological technologies. This review provides a summary of our current model of maize anthracnose etiology, including how increased knowledge of molecular and cellular events could contribute to better ASR management. Improved understanding of C. graminicola taxonomy has confirmed that the fungus is specific to Zea mays, and that it colonizes living maize tissues via a critical biotrophic phase. Successful biotrophic establishment relies on an array of secreted protein effectors and secondary metabolites produced at different stages of infection and dispersed to multiple locations. These molecules could provide therapeutic targets for the next generation of transgenic or gene-edited ASR-resistant hybrids.

Into a dilemma of plants: the antagonism between chemical defenses and growth

Chemical defenses are imperative for plant survival, but their production is often associated with growth restrictions. Here we review the most recent theories to explain this complex dilemma of plants. Plants are a nutritional source for a myriad of pests and pathogens that depend on green tissues to complete their life cycle. Rather than remaining passive victims, plants utilize an arsenal of chemical defenses to fend off biotic attack. While the deployment of such barriers is imperative for survival, the production of these chemical defenses is typically associated with negative impacts on plant growth. Here we discuss the most recent theories which explain this highly dynamic growth versus defense dilemma. Firstly, we discuss the hypothesis that the antagonism between the accumulation of chemical defenses and growth is rooted in the evolutionary history of plants and may be a consequence of terrestrialization. Then, we revise the different paradigms available to explain the growth versus chemical defense antagonism, including recent findings that update these into more comprehensive and plausible theories. Finally, we highlight state-of-the-art strategies that are now allowing the activation of growth and the concomitant production of chemical barriers in plants. Growth versus chemical defense antagonism imposes large ecological and economic costs, including increased crop susceptibility to pests and pathogens. In a world where these plant enemies are the main problem to increase food production, we believe that this review will summarize valuable information for future studies aiming to breed highly defensive plants without the typical accompanying penalties to growth.

Shielding the oil reserves: the scutellum as a source of chemical defenses

The cereal scutellum is a hub for diverse specialized defense metabolism and pathway discovery.

A maize leucine-rich repeat receptor-like protein kinase mediates responses to fungal attack

A maize receptor kinase controls defense response to fungal pathogens by regulating jasmonic acid and antimicrobial phytoalexin production. Plants use a range of pattern recognition receptors to detect and respond to biotic threats. Some of these receptors contain leucine-rich repeat (LRR) domains that recognize microbial proteins or peptides. Maize (Zea mays) has 226 LRR-receptor like kinases, making it challenging to identify those important for pathogen recognition. In this study, co-expression analysis with genes for jasmonic acid and phytoalexin biosynthesis was used to identify a fungal induced-receptor like protein kinase (FI-RLPK) likely involved in the response to fungal pathogens. Loss-of-function mutants in fi-rlpk displayed enhanced susceptibility to the necrotrophic fungal pathogen Cochliobolus heterostrophus and reduced accumulation of jasmonic acid and the anti-microbial phytoalexins -kauralexins and zealexins- in infected tissues. In contrast, fi-rlpk mutants displayed increased resistance to stem inoculation with the hemibiotrophic fungal pathogen Fusarium graminearum. These data indicate that FI-RLPK is important for fungal recognition and activation of defenses, and that F. graminearum may be able to exploit FI-RLPK function to increase its virulence.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).

Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience

Roots remain an understudied site of complex and important biological interactions mediating plant productivity. In grain and bioenergy crops, grass root specialized metabolites (GRSM) are central to key interactions, yet our basic knowledge of the chemical language remains fragmentary. Continued improvements in plant genome assembly and metabolomics are enabling large-scale advances in the discovery of specialized metabolic pathways as a means of regulating root-biotic interactions. Metabolomics, transcript coexpression analyses, forward genetic studies, gene synthesis and heterologous expression assays drive efficient pathway discoveries. Functional genetic variants identified through genome wide analyses, targeted CRISPR/Cas9 approaches, and both native and non-native overexpression studies critically inform novel strategies for bioengineering metabolic pathways to improve plant traits.

Commonly and Specifically Activated Defense Responses in Maize Disease Lesion Mimic Mutants Revealed by Integrated Transcriptomics and Metabolomics Analysis

Disease lesion mimic (Les/les) mutants display disease-like spontaneous lesions in the absence of pathogen infection, implying the constitutive activation of defense responses. However, the genetic and biochemical bases underlying the activated defense responses in those mutants remain largely unknown. Here, we performed integrated transcriptomics and metabolomics analysis on three typical maize Les mutants Les4, Les10, and Les17 with large, medium, and small lesion size, respectively, thereby dissecting the activated defense responses at the transcriptional and metabolomic level. A total of 1,714, 4,887, and 1,625 differentially expressed genes (DEGs) were identified in Les4, Les10, and Les17, respectively. Among them, 570, 3,299, and 447 specific differentially expressed genes (SGs) were identified, implying a specific function of each LES gene. In addition, 480 common differentially expressed genes (CGs) and 42 common differentially accumulated metabolites (CMs) were identified in all Les mutants, suggesting the robust activation of shared signaling pathways. Intriguingly, substantial analysis of the CGs indicated that genes involved in the programmed cell death, defense responses, and phenylpropanoid and terpenoid biosynthesis were most commonly activated. Genes involved in photosynthetic biosynthesis, however, were generally repressed. Consistently, the dominant CMs identified were phenylpropanoids and flavonoids. In particular, lignin, the phenylpropanoid-based polymer, was significantly increased in all three mutants. These data collectively imply that transcriptional activation of defense-related gene expression; increase of phenylpropanoid, lignin, flavonoid, and terpenoid biosynthesis; and inhibition of photosynthesis are generalnatures associated with the lesion formation and constitutively activated defense responses in those mutants. Further studies on the identified SGs and CGs will shed new light on the function of each LES gene as well as the regulatory network of defense responses in maize.

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize

BACKGROUND

The fungus Aspergillus flavus (A. flavus) is a serious threat to maize (Zea mays) production worldwide. It causes considerable yield and economic losses, and poses a health risk to humans and livestock due to the high toxicity of aflatoxin. However, key genes and regulatory networks conferring maize resistance to A. flavus are not clear, especially at the early stage of infection. Here, we performed a comprehensive transcriptome analysis of two maize inbred lines with contrasting resistance to A. flavus infection.

RESULTS

The pairwise comparisons between mock and infected kernels in each line during the first 6 h post inoculation (hpi) showed that maize resistance to A. flavus infection was specific to the genotype and infection stage, and defense pathways were strengthened in the resistant line. Further comparison of the two maize lines revealed that the infection-induced up-regulated differentially expressed genes (DEGs) in the resistant line might underlie the enhanced resistance. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) identified 7 modules that were significantly associated with different infection stages, and 110 hub genes of these modules. These key regulators mainly participate in the biosynthesis of fatty acid and antibiotics. In addition, 90 candidate genes for maize resistance to A. flavus infection and/or aflatoxin contamination obtained in previous studies were confirmed to be differentially expressed between the resistant and susceptible lines within the first 6 hpi.

CONCLUSION

This work unveiled more A. flavus resistance genes and provided a detailed regulatory network of early-stage resistance to A. flavus in maize.

Analysis of the transcriptomic, metabolomic, and gene regulatory responses to Puccinia sorghi in maize

Common rust, caused by Puccinia sorghi, is a widespread and destructive disease of maize. The Rp1-D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1-D-mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2-infected leaves from the near-isogenic lines H95 and H95:Rp1-D, which differed for the presence of Rp1-D. We observed up-regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up-regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1-D and H95 with an additional H95:Rp1-D-specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1-D-mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance-specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance-specific responses to P. sorghi.

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays)

Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges, including interactions with soil-dwelling microbial communities. However, the role of specialized metabolites in modulating plant-microbiome interactions often remains elusive. In this study, we report that maize (Zea mays) diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 (anther ear 2), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. The Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other large-scale metabolome alterations. Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.

Metabolomics by UHPLC-HRMS reveals the impact of heat stress on pathogen-elicited immunity in maize

INTRODUCTION

Studies investigating crop resistance to abiotic and biotic stress have largely focused on plant responses to singular forms of stress and individual biochemical pathways that only partially represent stress responses. Thus, combined abiotic and biotic stress treatments and the global assessment of their elicited metabolic expression remains largely unexplored. In this study, we employed targeted and untargeted metabolomics to investigate the molecular responses of maize (Zea mays) to abiotic, biotic, and combinatorial stress.

OBJECTIVE

We compared the inducible metabolomes of heat-stressed (abiotic) and C. heterostrophus-infected (biotic) maize and examined the effects of heat stress on the ability of maize to defend itself against C. heterostrophus.

METHODS

Ultra-high-performance liquid chromatography-high-resolution mass spectrometry was performed on plants grown under control conditions (28 °C), heat stress (38 °C), Cochliobolus heterostrophus infection, or combinatorial stress [heat (38 °C) + C. heterostrophus infection].

RESULTS

Multivariate analyses revealed differential metabolite expression between heat stress, C. heterostrophus infection, and their respective controls. In combinatorial experiments, treatment with heat stress prior to fungal inoculation negatively impacted maize disease resistance against C. heterostrophus, and distinct metabolome separation between combinatorial stressed plants and the non-heat-stressed infected controls was observed. Targeted analysis revealed inducible primary and secondary metabolite responses to abiotic/biotic stress, and combinatorial experiments indicated that deficiency in the hydroxycinnamic acid, p-coumaric acid, may contribute to the heat-induced susceptibility of maize to C. heterostrophus.

CONCLUSION

These findings demonstrate that abiotic stress can predispose crops to more severe disease symptoms, underlining the increasing need to investigate defense chemistry in plants under combinatorial stress.

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information

The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a breadth of plant biology inquiries. Data and code are available at GitHub: https://github.com/eporetsky/MutRank.

Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection

Maize (Zea mays L.) is a staple crop providing food security to millions of people in sub Saharan Africa. Fusarium verticillioides, an important fungal pathogen, infects maize causing ‘Fusarium Ear Rot’ disease, which decreases maize kernel yield and the quality of the crop harvested. Currently, no African maize line is completely resistant to infection by F. verticillioides. This study investigated an African maize line, Zea mays CML144, infected with F. verticillioides. Analysis of morphological characteristics showed significant differences between mock-infected and infected plants. RNA-sequencing (RNA-seq) was conducted on plants 14 days post-inoculation to identify differentially expressed genes (DEGs) involved in F. verticillioides infection. Analysis of RNA-seq data revealed DEGs that were both significantly up- and down-regulated in the infected samples compared to the mock-infected control. The maize TPS1 and cytochrome P450 genes were up-regulated, suggesting that kauralexins were involved in the CML144 defense response. This was substantiated by kauralexin analyses, which showed that kauralexins, belonging to class A and B, accumulated in infected maize tissue. Gene ontology terms relating to response to stimulus, chemical stimulus and carbohydrate metabolic processes were enriched, and the genes belonging to these GO-terms were down-regulated. Quantitative real-time PCR was performed on selected DEGs and measurement of phytoalexin accumulation validated the RNA-seq data and GO-analysis results. A comparison of DEGs from this study to DEGs found in F. verticillioides (ITEM 1744) infected susceptible (CO354) and resistant (CO441) maize genotypes in a previous study, matched 18 DEGs with 17 up-regulated and one down-regulated, respectively. This is the first transcriptomic study on the African maize line, CML144, in response to F. verticillioides infection.

Genomics of Maize Resistance to Fusarium Ear Rot and Fumonisin Contamination

Food contamination with mycotoxins is a worldwide concern, because these toxins produced by several fungal species have detrimental effects on animal and/or human health. In maize, fumonisins are among the toxins with the highest threatening potential because they are mainly produced by Fusarium verticillioides, which is distributed worldwide. Plant breeding has emerged as an effective and environmentally safe method to reduce fumonisin levels in maize kernels, but although phenotypic selection has proved effective for improving resistance to fumonisin contamination, further resources should be mobilized to meet farmers' needs. Selection based on molecular markers linked to quantitative trait loci (QTL) for resistance to fumonisin contamination or/and genotype values obtained using prediction models with markers distributed across the whole genome could speed up breeding progress. Therefore, in the current paper, previously identified genomic regions, genes, and/or pathways implicated in resistance to fumonisin accumulation will be reviewed. Studies done until now have provide many markers to be used by breeders, but to get further insight on plant mechanisms to defend against fungal infection and to limit fumonisin contamination, the genes behind those QTLs should be identified.

Specialized diterpenoid metabolism in monocot crops: Biosynthesis and chemical diversity

Among the myriad specialized metabolites that plants employ to mediate interactions with their environment, diterpenoids form a chemically diverse group with vital biological functions. A few broadly abundant diterpenoids serve as core pathway intermediates in plant general metabolism. The majority of plant diterpenoids, however, function in specialized metabolism as often species-specific chemical defenses against herbivores and microbial diseases, in below-ground allelopathic interactions, as well as abiotic stress responses. Dynamic networks of anti-microbial diterpenoids were first demonstrated in rice (Oryza sativa) over four decades ago, and more recently, unique diterpenoid blends with demonstrated antibiotic bioactivities were also discovered in maize (Zea mays). Enabled by advances in -omics and biochemical approaches, species-specific diterpenoid-diversifying enzymes have been identified in these and other Poaceous species, including wheat (Triticum aestivum) and switchgrass (Panicum virgatum), and are discussed in this article with an emphasis on the critical diterpene synthase and cytochrome P450 monooxygenase families and their products. The continued investigation of the biosynthesis, diversity, and function of terpenoid-mediated crop defenses provides foundational knowledge to enable the development of strategies for improving crop resistance traits in the face of impeding pest, pathogen, and climate pressures impacting global agricultural production.

Multiple genes recruited from hormone pathways partition maize diterpenoid defences

Duplication and divergence of primary pathway genes underlie the evolution of plant specialized metabolism; however, mechanisms partitioning parallel hormone and defence pathways are often speculative. For example, the primary pathway intermediate ent-kaurene is essential for gibberellin biosynthesis and is also a proposed precursor for maize antibiotics. By integrating transcriptional coregulation patterns, genome-wide association studies, combinatorial enzyme assays, proteomics and targeted mutant analyses, we show that maize kauralexin biosynthesis proceeds via the positional isomer ent-isokaurene formed by a diterpene synthase pair recruited from gibberellin metabolism. The oxygenation and subsequent desaturation of ent-isokaurene by three promiscuous cytochrome P450s and a new steroid 5α reductase indirectly yields predominant ent-kaurene-associated antibiotics required for Fusarium stalk rot resistance. The divergence and differential expression of pathway branches derived from multiple duplicated hormone-metabolic genes minimizes dysregulation of primary metabolism via the circuitous biosynthesis of ent-kaurene-related antibiotics without the production of growth hormone precursors during defence.

Biosynthesis and function of terpenoid defense compounds in maize (Zea mays)

Maize produces an array of herbivore-induced terpene volatiles that attract parasitoids to infested plants and a suite of pathogen-induced non-volatile terpenoids with antimicrobial activity to defend against pests. Plants rely on complex blends of constitutive and dynamically produced specialized metabolites to mediate beneficial ecological interactions and protect against biotic attack. One such class of metabolites are terpenoids, a large and structurally diverse class of molecules shown to play significant defensive and developmental roles in numerous plant species. Despite this, terpenoids have only recently been recognized as significant contributors to pest resistance in maize (Zea mays), a globally important agricultural crop. The current review details recent advances in our understanding of biochemical structures, pathways and functional roles of maize terpenoids. Dependent upon the lines examined, maize can harbor more than 30 terpene synthases, underlying the inherent diversity of maize terpene defense systems. Part of this defensive arsenal is the inducible production of volatile bouquets that include monoterpenes, homoterpenes and sesquiterpenes, which often function in indirect defense by enabling the attraction of parasitoids and predators. More recently discovered are a subset of sesquiterpene and diterpene hydrocarbon olefins modified by cytochrome P450s to produce non-volatile end-products such kauralexins, zealexins, dolabralexins and β-costic acid. These non-volatile terpenoid phytoalexins often provide effective defense against both microbial and insect pests via direct antimicrobial and anti-feedant activity. The diversity and promiscuity of maize terpene synthases, coupled with a variety of secondary modifications, results in elaborate defensive layers whose identities, regulation and precise functions are continuing to be elucidated.

Interactions Among Plants, Insects, and Microbes: Elucidation of Inter-Organismal Chemical Communications in Agricultural Ecology

The last 2 decades have witnessed a sustained increase in the study of plant-emitted volatiles and their role in plant-insect, plant-microbe, and plant-plant interactions. While each of these binary systems involves complex chemical and biochemical processes between two organisms, the progression of increasing complexity of a ternary system (i.e., plant-insect-microbe), and the study of a ternary system requires nontrivial planning. This planning can include an experimental design that factors in potential overarching ecological interactions regarding the binary or ternary system, correctly identifying and understanding unexpected observations that may occur during the experiment and thorough interpretation of the resultant data. This challenge of planning, performing, and interpreting a plant's defensive response to multiple biotic stressors will be even greater when abiotic stressors (i.e., temperature or water) are factored into the system. To fully understand the system, we need to not only continue to investigate and understand the volatile profiles but also include and understand the biochemistry of the plant's response to these stressors. In this review, we provide examples and discuss interaction considerations with respect to how readers and future authors of the Journal of Agricultural and Food Chemistry can contribute their expertise toward the extraction and interpretation of chemical information exchanged between agricultural commodities and their associated pests. This holistic, multidisciplinary, and thoughtful approach to interactions of plants, insects, and microbes, and the resultant response of the plants can lead to a better understanding of agricultural ecology, in turn leading to practical and viable solutions to agricultural problems.

Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize

Terpenoids are a major component of maize (Zea mays) chemical defenses that mediate responses to herbivores, pathogens, and other environmental challenges. Here, we describe the biosynthesis and elicited production of a class of maize diterpenoids, named dolabralexins. Dolabralexin biosynthesis involves the sequential activity of two diterpene synthases, ENT-COPALYL DIPHOSPHATE SYNTHASE (ZmAN2) and KAURENE SYNTHASE-LIKE4 (ZmKSL4). Together, ZmAN2 and ZmKSL4 form the diterpene hydrocarbon dolabradiene. In addition, we biochemically characterized a cytochrome P450 monooxygenase, ZmCYP71Z16, which catalyzes the oxygenation of dolabradiene to yield the epoxides 15,16-epoxydolabrene (epoxydolabrene) and 3β-hydroxy-15,16-epoxydolabrene (epoxydolabranol). The absence of dolabradiene and epoxydolabranol in Zman2 mutants under elicited conditions confirmed the in vivo biosynthetic requirement of ZmAN2. Combined mass spectrometry and NMR experiments demonstrated that much of the epoxydolabranol is further converted into 3β,15,16-trihydroxydolabrene (trihydroxydolabrene). Metabolite profiling of field-grown maize root tissues indicated that dolabralexin biosynthesis is widespread across common maize cultivars, with trihydroxydolabrene as the predominant diterpenoid. Oxidative stress induced dolabralexin accumulation and transcript expression of ZmAN2 and ZmKSL4 in root tissues, and metabolite and transcript accumulation were up-regulated in response to elicitation with the fungal pathogens Fusarium verticillioides and Fusarium graminearum Consistently, epoxydolabranol significantly inhibited the growth of both pathogens in vitro at 10 µg mL-1, while trihydroxydolabrene-mediated inhibition was specific to Fverticillioides These findings suggest that dolabralexins have defense-related roles in maize stress interactions and expand the known chemical space of diterpenoid defenses as genetic targets for understanding and ultimately improving maize resilience.

Functional Characterization of Two Class II Diterpene Synthases Indicates Additional Specialized Diterpenoid Pathways in Maize (Zea mays)

As a major staple food, maize (Zea mays) is critical to food security. Shifting environmental pressures increasingly hamper crop defense capacities, causing expanded harvest loss. Specialized labdane-type diterpenoids are key components of maize chemical defense and ecological adaptation. Labdane diterpenoid biosynthesis most commonly requires the pairwise activity of class II and class I diterpene synthases (diTPSs) that convert the central precursor geranylgeranyl diphosphate into distinct diterpenoid scaffolds. Two maize class II diTPSs, ANTHER EAR 1 and 2 (ZmAN1/2), have been previously identified as catalytically redundant ent-copalyl diphosphate (CPP) synthases. ZmAN1 is essential for gibberellin phytohormone biosynthesis, whereas ZmAN2 is stress-inducible and governs the formation of defensive kauralexin and dolabralexin diterpenoids. Here, we report the biochemical characterization of the two remaining class II diTPSs present in the maize genome, COPALYL DIPHOSPHATE SYNTHASE 3 (ZmCPS3) and COPALYL DIPHOSPHATE SYNTHASE 4 (ZmCPS4). Functional analysis via microbial co-expression assays identified ZmCPS3 as a (+)-CPP synthase, with functionally conserved orthologs occurring in wheat (Triticum aestivum) and numerous dicot species. ZmCPS4 formed the unusual prenyl diphosphate, 8,13-CPP (labda-8,13-dien-15-yl diphosphate), as verified by mass spectrometry and nuclear magnetic resonance. As a minor product, ZmCPS4 also produced labda-13-en-8-ol diphosphate (LPP). Root gene expression profiles did not indicate an inducible role of ZmCPS3 in maize stress responses. By contrast, ZmCPS4 showed a pattern of inducible gene expression in roots exposed to oxidative stress, supporting a possible role in abiotic stress responses. Identification of the catalytic activities of ZmCPS3 and ZmCPS4 clarifies the first committed reactions controlling the diversity of defensive diterpenoids in maize, and suggests the existence of additional yet undiscovered diterpenoid pathways.