Quantitative Disease Resistance: Dissection and Adoption in Maize

The ZmCPK39-ZmDi19-ZmPR10 immune module regulates quantitative resistance to multiple foliar diseases in maize

Gray leaf spot, northern leaf blight and southern leaf blight are three of the most destructive foliar diseases affecting maize (Zea mays L.). Here we identified a gene, ZmCPK39, that encodes a calcium-dependent protein kinase and negatively regulates quantitative resistance to these three diseases. The ZmCPK39 allele in the resistant line displayed significantly lower pathogen-induced gene expression than that in the susceptible line. A marked decrease in ZmCPK39 abundance mitigated the phosphorylation and degradation of the transcription factor ZmDi19. This led to elevated expression of ZmPR10, a gene known to encode an antimicrobial protein, thereby enhancing maize resistance to foliar diseases. Moreover, the F1 hybrid with reduced ZmCPK39 expression favored disease resistance, thereby increasing yield. Hence, the discovery of the ZmCPK39-ZmDi19-ZmPR10 immune module provides insight into the mechanisms underlying broad-spectrum quantitative disease resistance and also offers a new avenue for the genetic control of maize foliar diseases.

Regulatory balance between ear rot resistance and grain yield and their breeding applications in maize and other crops

BACKGROUND

Fungi are prevalent pathogens that cause substantial yield losses of major crops. Ear rot (ER), which is primarily induced by Fusarium or Aspergillus species, poses a significant challenge to maize production worldwide. ER resistance is regulated by several small effect quantitative trait loci (QTLs). To date, only a few ER-related genes have been identified that impede molecular breeding efforts to breed ER-resistant maize varieties.

AIM OF REVIEW

Our aim here is to explore the research progress and mine genic resources related to ER resistance, and to propose a regulatory model elucidating the ER-resistant mechanism in maize as well as a trade-off model illustrating how crops balance fungal resistance and grain yield. Key Scientific Concepts of Review: This review presents a comprehensive bibliometric analysis of the research history and current trends in the genetic and molecular regulation underlying ER resistance in maize. Moreover, we analyzed and discovered the genic resources by identifying 162 environmentally stable loci (ESLs) from various independent forward genetics studies as well as 1391 conservatively differentially expressed genes (DEGs) that respond to Fusarium or Aspergillus infection through multi-omics data analysis. Additionally, this review discusses the syntenies found among maize ER, wheat Fusariumhead blight (FHB), and rice Bakanaedisease (RBD) resistance-related loci, along with the significant overlap between fungal resistance loci and reported yield-related loci, thus providing valuable insights into the regulatory mechanisms underlying the trade-offs between yield and defense in crops.

Comparative genomics of Fusarium species causing Fusarium ear rot of maize

Fusarium ear rot (FER), caused by the fungal pathogen Fusarium verticillioides, stands as one of the most economically burdensome and pervasive diseases affecting maize worldwide. Its impact on food security is particularly pronounced due to the production of fumonisins, toxic secondary metabolites that pose serious health risks, especially for livestock. FER disease severity is complex and polygenic, with few resistance (R) genes being identified for use in breeding resistant varieties. While FER is the subject of several breeding programs, only a few studies have investigated entire populations of F. verticillioides with corresponding virulence data to better understand and characterize the pathogenomics. Here, we sequenced and compared the genomes of 50 Fusarium isolates (43 F. verticillioides and 7 other Fusarium spp.) that were used to inoculate a diverse maize population. Our objectives were to elucidate the genome size and composition of F. verticillioides, explore the variable relationship between fumonisin production and visual disease severity, and shed light on the phylogenetic relationships among the isolates. Additionally, we conducted a comparative analysis of the nucleotide variants (SNPs) and the isolates' effectoromes to uncover potential genetic determinants of pathogenicity. Our findings revealed several promising leads, notably the association of certain gene groups, such as pectate lyase, with disease severity. These genes should be investigated further as putative alleles for breeding resistant maize varieties. We suggest that, beyond validation of the alleles identified in this study, researchers validate each phenotypic dataset on an individual basis, particularly if considering fumonisin concentrations and when using diverse populations. Our study underscores the importance of genomic analysis in tackling FER and offers insights that could inform the development of resilient maize cultivars. By leveraging advances in genomics and incorporating pathogen populations into breeding programs, resistance to FER can be advanced.

Natural variations of maize ZmLecRK1 determine its interaction with ZmBAK1 and resistance patterns to multiple pathogens

Maize (Zea mays) is one of the most important crops in the world, but its yield and quality are seriously affected by diverse diseases. Identifying broad-spectrum resistance genes is crucial for developing effective strategies to control the disease in maize. In a genome-wide study in maize, we identified a G-type lectin receptor kinase ZmLecRK1, as a new resistance protein against Pythium aphanidermatum, one of the causal pathogens of stalk rot in maize. Genetic analysis showed that the specific ZmLecRK1 allele can confer resistance to multiple pathogens in maize. The cell death and disease resistance phenotype mediated by the resistant variant of ZmLecRK1 requires the co-receptor ZmBAK1. A naturally occurring A404S variant in the extracellular domain of ZmLecRK1 determines the ZmLecRK1-ZmBAK1 interaction and the formation of ZmLecRK1-related protein complexes. Interestingly, the ZmLecRK1 susceptible variant was found to possess the amino acid S404 that is present in the ancestral variants of ZmLecRK1 and conserved among the majority of grass species, while the resistance variant of ZmLecRK1 with A404 is only present in a few maize inbred lines. Substitution of S by A at position 404 in ZmLecRK1-like proteins of sorghum and rice greatly enhances their ability to induce cell death. Further transcriptomic analysis reveals that ZmLecRK1 likely regulates gene expression related to the pathways in cell wall organization or biogenesis in response to pathogen infection. Taken together, these results suggest that the ZmLecRK1 resistance variant enhances its binding affinity to the co-receptor ZmBAK1, thereby enhancing the formation of active complexes for defense in maize. Our work highlights the biotechnological potential for generating disease-resistant crops by precisely modulating the activity of ZmLecRK1 and its homologs through targeted base editing.

A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize

Northern corn leaf blight (NCLB), caused by Setosphaeria turcica, is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an association mapping panel and linkage mapping with three doubled haploid (DH) and three F3 populations of tropical maize. These populations were phenotyped for NCLB resistance across six hotspot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1-9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 quantitative trait loci (QTLs) were identified, each explaining between 2.7% and 15.8% of the observed phenotypic variance. Collectively, the detected QTLs explained 34.28%, 51.37%, 41.12%, 12.46%, 12.11%, and 14.66% of the total phenotypic variance in DH populations 1, 2, and 3 and F3 populations 4, 5, and 6, respectively. GWAS, using 337,110 high-quality single nucleotide polymorphisms (SNPs), identified 15 marker-trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55, and 0.42 for within GWAS panel, DH pop1, DH pop2, and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major-effect and many minor-effect QTLs. We conclude that genomic regions consistently detected across mapping approaches and populations should be prioritized for improving NCLB resistance, while genome-wide prediction results can help incorporate both major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB.

Reconsidering the Lessons Learned from the 1970 Southern Corn Leaf Blight Epidemic

The southern corn leaf blight epidemic of 1970 caused estimated losses of about 16% for the U.S. corn crop, equivalent to about $8 billion in current terms. The epidemic was caused by the prevalence of Texas male sterile cytoplasm (cms-T), used to produce most of the hybrid corn seed planted that year, combined with the emergence of a novel race of the fungus Cochliobolus heterostrophus that was exquisitely virulent on cms-T corn. Remarkably, the epidemic lasted just a single year. This episode has often been portrayed in the literature and textbooks over the last 50 years as a catastrophic mistake perpetrated by corn breeders and seed companies of the time who did not understand or account for the dangers of crop genetic uniformity. In this perspective article, we aim to present an alternative interpretation of these events. First, we contend that, rather than being caused by a grievous error on the part of the corn breeding and seed industry, this epidemic was a particularly unfortunate, unusual, and unlucky consequence of a technological advancement intended to improve the efficiency of corn seed production for America's farmers. Second, we tell the story of the resolution of the epidemic as an example of timely, meticulously applied research in the public sector for the public good.

Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models

KEY MESSAGE

Integrating disease screening data and genomic data for host and pathogen populations into prediction models provides breeders and pathologists with a unified framework to develop disease resistance. Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective.

Integrated analysis of transcriptomics and defense-related phytohormones to discover hub genes conferring maize Gibberella ear rot caused by Fusarium Graminearum

BACKGROUND

Gibberella ear rot (GER) is one of the most devastating diseases in maize growing areas, which directly reduces grain yield and quality. However, the underlying defense response of maize to pathogens infection is largely unknown.

RESULTS

To gain a comprehensive understanding of the defense response in GER resistance, two contrasting inbred lines 'Nov-82' and 'H10' were used to explore transcriptomic profiles and defense-related phytohormonal alterations during Fusarium graminearum infection. Transcriptomic analysis revealed 4,417 and 4,313 differentially expressed genes (DEGs) from the Nov-82 and H10, respectively, and 647 common DEGs between the two lines. More DEGs were obviously enriched in phenylpropanoid biosynthesis, secondary metabolites biosynthesis, metabolic process and defense-related pathways. In addition, the concentration of the defense-related phytohormones, jasmonates (JAs) and salicylates (SAs), was greatly induced after the pathogen infection. The level of JAs in H10 was more higher than in Nov-82, whereas an opposite pattern for the SA between the both lines. Integrated analysis of the DEGs and the phytohormones revealed five vital modules based on co-expression network analysis according to their correlation. A total of 12 hub genes encoding fatty acid desaturase, subtilisin-like protease, ethylene-responsive transcription factor, 1-aminocyclopropane-1-carboxylate oxidase, and sugar transport protein were captured from the key modules, indicating that these genes might play unique roles in response to pathogen infection, CONCLUSIONS: Overall, our results indicate that large number DEGs related to plant disease resistance and different alteration of defensive phytohormones were activated during F. graminearum infection, providing new insight into the defense response against pathogen invasion, in addition to the identified hub genes that can be further investigated for enhancing maize GER resistance.

PlantPAD: a platform for large-scale image phenomics analysis of disease in plant science

Plant disease, a huge burden, can cause yield loss of up to 100% and thus reduce food security. Actually, smart diagnosing diseases with plant phenomics is crucial for recovering the most yield loss, which usually requires sufficient image information. Hence, phenomics is being pursued as an independent discipline to enable the development of high-throughput phenotyping for plant disease. However, we often face challenges in sharing large-scale image data due to incompatibilities in formats and descriptions provided by different communities, limiting multidisciplinary research exploration. To this end, we build a Plant Phenomics Analysis of Disease (PlantPAD) platform with large-scale information on disease. Our platform contains 421 314 images, 63 crops and 310 diseases. Compared to other databases, PlantPAD has extensive, well-annotated image data and in-depth disease information, and offers pre-trained deep-learning models for accurate plant disease diagnosis. PlantPAD supports various valuable applications across multiple disciplines, including intelligent disease diagnosis, disease education and efficient disease detection and control. Through three applications of PlantPAD, we show the easy-to-use and convenient functions. PlantPAD is mainly oriented towards biologists, computer scientists, plant pathologists, farm managers and pesticide scientists, which may easily explore multidisciplinary research to fight against plant diseases. PlantPAD is freely available at http://plantpad.samlab.cn.

Physiological Effects of Microbial Biocontrol Agents in the Maize Phyllosphere

In a world with constant population growth, and in the context of climate change, the need to supply the demand of safe crops has stimulated an interest in ecological products that can increase agricultural productivity. This implies the use of beneficial organisms and natural products to improve crop performance and control pests and diseases, replacing chemical compounds that can affect the environment and human health. Microbial biological control agents (MBCAs) interact with pathogens directly or by inducing a physiological state of resistance in the plant. This involves several mechanisms, like interference with phytohormone pathways and priming defensive compounds. In Argentina, one of the world's main maize exporters, yield is restricted by several limitations, including foliar diseases such as common rust and northern corn leaf blight (NCLB). Here, we discuss the impact of pathogen infection on important food crops and MBCA interactions with the plant's immune system, and its biochemical indicators such as phytohormones, reactive oxygen species, phenolic compounds and lytic enzymes, focused mainly on the maize-NCLB pathosystem. MBCA could be integrated into disease management as a mechanism to improve the plant's inducible defences against foliar diseases. However, there is still much to elucidate regarding plant responses when exposed to hemibiotrophic pathogens.

CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives

Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.

Kernel Bioassay Evaluation of Maize Ear Rot and Genome-Wide Association Analysis for Identifying Genetic Loci Associated with Resistance to Fusarium graminearum Infection

Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is one of the most destructive diseases in maize, which severely reduces yield and contaminates several potential mycotoxins in the grain. However, few efforts had been devoted to dissecting the genetic basis of maize GER resistance. In the present study, a genome-wide association study (GWAS) was conducted in a maize association panel consisting of 303 diverse inbred lines. The phenotypes of GER severity were evaluated using kernel bioassay across multiple time points in the laboratory. Then, three models, including the fixed and random model circulating probability unification model (FarmCPU), general linear model (GLM), and mixed linear model (MLM), were conducted simultaneously in GWAS to identify single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance. A total of four individual significant association SNPs with the phenotypic variation explained (PVE) ranging from 3.51 to 6.42% were obtained. Interestingly, the peak SNP (PUT-163a-71443302-3341) with the greatest PVE value, was co-localized in all models. Subsequently, 12 putative genes were captured from the peak SNP, and several of these genes were directly or indirectly involved in disease resistance. Overall, these findings contribute to understanding the complex plant-pathogen interactions in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the kernel bioassay that can be used for evaluating and selecting elite germplasm resources with GER resistance in maize.

Streptomyces as a promising biological control agents for plant pathogens

Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.

A transcription factor ZmGLK36 confers broad resistance to maize rough dwarf disease in cereal crops

Maize rough dwarf disease (MRDD), caused by maize rough dwarf virus (MRDV) or rice black-streaked dwarf virus (RBSDV), seriously threatens worldwide production of all major cereal crops, including maize, rice, wheat and barley. Here we report fine mapping and cloning of a previously reported major quantitative trait locus (QTL) (qMrdd2) for RBSDV resistance in maize. Subsequently, we show that qMrdd2 encodes a G2-like transcription factor named ZmGLK36 that promotes resistance to RBSDV by enhancing jasmonic acid (JA) biosynthesis and JA-mediated defence response. We identify a 26-bp indel located in the 5' UTR of ZmGLK36 that contributes to differential expression and resistance to RBSDV in maize inbred lines. Moreover, we show that ZmDBF2, an AP2/EREBP family transcription factor, directly binds to the 26-bp indel and represses ZmGLK36 expression. We further demonstrate that ZmGLK36 plays a conserved role in conferring resistance to RBSDV in rice and wheat using transgenic or marker-assisted breeding approaches. Our results provide insights into the molecular mechanisms of RBSDV resistance and effective strategies to breed RBSDV-resistant cereal crops.

Genome-Wide Association Study Discovers Novel Germplasm Resources and Genetic Loci with Resistance to Gibberella Ear Rot Caused by Fusarium graminearum

Gibberella ear rot (GER) in maize caused by Fusarium graminearum is one of the most devastating maize diseases reducing grain yield and quality worldwide. The genetic bases of maize GER resistance remain largely unknown. Using artificial inoculation across multiple environments, the GER severity of an association panel consisting of 316 diverse inbred lines was observed with wide phenotypic variation. In the association panel, a genome-wide association study using a general linear model identified 69 single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance at the threshold of 2.04 × 10-5, and the average phenotypic variation explained (PVE) of these SNPs was 5.09%. We also conducted a genome-wide association study analysis using a mixed linear model at a threshold of 1.0 × 10-4, and 16 significantly associated SNPs with an average PVE of 4.73% were detected. A combined general linear model and mixed linear model method obtained 10 co-localized significantly associated SNPs linked to GER resistance, including the most significant SNP (PZE-105079915) with the greatest PVE value, 9.07%, at bin 5.05 following 10 candidate genes. These findings are significant for the exploration of the complicated genetic variations in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the elite germplasm resources that can be used for breeding GER resistance in maize.

A Combination of QTL Mapping and GradedPool-Seq to Dissect Genetic Complexity for Gibberella Ear Rot Resistance in Maize Using an IBM Syn10 DH Population

Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is one of the most devastating maize diseases that reduces grain yield and quality worldwide. Utilization of host genetic resistance has become one of the most suitable strategies to control GER. In this study, a set of 246 diverse inbred lines derived from the intermated B 73 × Mo 17 doubled haploid population (IBM Syn10 DH) were used to detect quantitative trait loci (QTL) associated with resistance to GER. Meanwhile, a GradedPool-Seq (GPS) approach was performed to identify genomic variations involved in GER resistance. Using artificial inoculation across multiple environments, GER severity of the population was observed with wide phenotypic variation. Based on the linkage mapping, a total of 14 resistant QTLs were detected, accounting for 5.11 to 14.87% of the phenotypic variation, respectively. In GPS analysis, five significant single nucleotide polymorphisms (SNPs) associated with GER resistance were identified. Combining QTL mapping and GPS analysis, a peak-value SNP on chromosome 4 from GPS was overlapped with the QTL qGER4.2, suggesting that the colocalized region could be the most possible target location conferring resistance to GER. Subsequently, seven candidate genes were identified within the peak SNP, linking them to GER resistance. These findings are useful for exploring the complicated genetic variations in maize GER resistance. The genomic regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the combined strategy that can be used for quantitative traits in plant species.

Peptidome and Transcriptome Analysis of Plant Peptides Involved in Bipolaris maydis Infection of Maize

Southern corn leaf blight (SCLB) caused by Bipolaris maydis threatens maize growth and yield worldwide. In this study, TMT-labeled comparative peptidomic analysis was established between infected and uninfected maize leaf samples using liquid-chromatography-coupled tandem mass spectrometry. The results were further compared and integrated with transcriptome data under the same experimental conditions. Plant peptidomic analysis identified 455 and 502 differentially expressed peptides (DEPs) in infected maize leaves on day 1 and day 5, respectively. A total of 262 common DEPs were identified in both cases. Bioinformatic analysis indicated that the precursor proteins of DEPs are associated with many pathways generated by SCLB-induced pathological changes. The expression profiles of plant peptides and genes in maize plants were considerably altered after B. maydis infection. These findings provide new insights into the molecular mechanisms of SCLB pathogenesis and offer a basis for the development of maize genotypes with SCLB resistance.

Negative effects of soil warming, and adaptive cultivation strategies of maize: A review

Temperature is a key factor in regulating and controlling several ecological processes. As there is a feedback relationship between many biogeochemical processes and climate change, their response to temperature changes is particularly important. Previously, a large volume of literature has extensively explored the impact of rising air temperature on shoot growth and maize yield, from enzymatic responses within the leaf to grain yield. As the global temperature continues to increase and the frequency, duration, and/or intensity of heat wave events increases, the soil temperature of the tilth is likely to rise sharply. As one of the most widely planted food crops in the world, maize may be subjected to additional soil temperature pressure. However, as a nutrient organ in direct contact with soil, the root plays a key role in adapting the whole plant to excessive soil temperature. Little research has been done on the effect of the soil microenvironment induced by higher soil temperature on maize root growth and root to shoot communication regulation. Therefore, this review summarizes (1) the effects of excessive soil temperature on the soil microenvironment, including soil respiration, microbial community composition, carbon mineralization, and enzyme activity; (2) the negative response of absorption of water and nutrients by roots and maize root-shoot growth to excessive soil temperature; and (3) potential cultivation strategies to improve maize yield, including improving tillage methods, adding biochar amendments, applying organic fertilizers, optimizing irrigation, and farmland mulching.

Fungal CFEM effectors negatively regulate a maize wall-associated kinase by interacting with its alternatively spliced variant to dampen resistance

The fungus Fusarium graminearum causes a devastating disease Gibberella stalk rot of maize. Our knowledge of molecular interactions between F. graminearum effectors and maize immunity factors is lacking. Here, we show that a group of cysteine-rich common in fungal extracellular membrane (CFEM) domain proteins of F. graminearum are required for full virulence in maize stalk infection and that they interact with two secreted maize proteins, ZmLRR5 and ZmWAK17ET. ZmWAK17ET is an alternative splicing isoform of a wall-associated kinase ZmWAK17. Both ZmLRR5 and ZmWAK17ET interact with the extracellular domain of ZmWAK17. Transgenic maize overexpressing ZmWAK17 shows increased resistance to F. graminearum, while ZmWAK17 mutants exhibit enhanced susceptibility to F. graminearum. Transient expression of ZmWAK17 in Nicotiana benthamiana triggers hypersensitive cell death, whereas co-expression of CFEMs with ZmWAK17ET or ZmLRR5 suppresses the ZmWAK17-triggered cell death. Our results show that ZmWAK17 mediates stalk rot resistance and that F. graminearum delivers apoplastic CFEMs to compromise ZmWAK17-mediated resistance.

CRISPR-Cas technology opens a new era for the creation of novel maize germplasms

Maize (Zea mays) is one of the most important food crops in the world with the greatest global production, and contributes to satiating the demands for human food, animal feed, and biofuels. With population growth and deteriorating environment, efficient and innovative breeding strategies to develop maize varieties with high yield and stress resistance are urgently needed to augment global food security and sustainable agriculture. CRISPR-Cas-mediated genome-editing technology (clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated)) has emerged as an effective and powerful tool for plant science and crop improvement, and is likely to accelerate crop breeding in ways dissimilar to crossbreeding and transgenic technologies. In this review, we summarize the current applications and prospects of CRISPR-Cas technology in maize gene-function studies and the generation of new germplasm for increased yield, specialty corns, plant architecture, stress response, haploid induction, and male sterility. Optimization of gene editing and genetic transformation systems for maize is also briefly reviewed. Lastly, the challenges and new opportunities that arise with the use of the CRISPR-Cas technology for maize genetic improvement are discussed.

SNP-based bulk segregant analysis revealed disease resistance QTLs associated with northern corn leaf blight in maize

Maize (Zea mays L.) is the most important food security crop worldwide. Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, severely reduces production causing millions of dollars in losses worldwide. Therefore, this study aimed to identify significant QTLs associated with NCLB by utilizing next-generation sequencing-based bulked-segregant analysis (BSA). Parental lines GML71 (resistant) and Gui A10341 (susceptible) were used to develop segregating population F₂. Two bulks with 30 plants each were further selected from the segregating population for sequencing along with the parental lines. High throughput sequencing data was used for BSA. We identified 10 QTLs on Chr 1, Chr 2, Chr 3, and Chr 5 with 265 non-synonymous SNPs. Moreover, based on annotation information, we identified 27 candidate genes in the QTL regions. The candidate genes associated with disease resistance include AATP1, At4g24790, STICHEL-like 2, BI O 3-BIO1, ZAR1, SECA2, ABCG25, LECRK54, MKK7, MKK9, RLK902, and DEAD-box ATP-dependent RNA helicase. The annotation information suggested their involvement in disease resistance-related pathways, including protein phosphorylation, cytoplasmic vesicle, protein serine/threonine kinase activity, and ATP binding pathways. Our study provides a substantial addition to the available information regarding QTLs associated with NCLB, and further functional verification of identified candidate genes can broaden the scope of understanding the NCLB resistance mechanism in maize.

Metagenomic identification of novel viruses of maize and teosinte in North America

Background

Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America.

Results

Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize.

Conclusions

Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.

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.

High-resolution mapping reveals a Ht3-like locus against northern corn leaf blight

Northern corn leaf blight (NCLB), caused by the fungal pathogen Exserohilum turcicum, poses a grave threat to maize production worldwide. The resistance gene in A619Ht3, discovered decades ago, is an important genetic resource for NCLB control. By using a pair of near-isogenic lines (NILs) A619Ht3 and A619, together with the resistant and susceptible bulks derived from the cross of A619Ht3 and L3162 lines, we initially detected a Ht3-like (Ht3L) locus in bin 8.06 that was closely associated with NCLB resistance. We then performed five rounds of fine-mapping, which ultimately delimited the Ht3L locus to a 577-kb interval flanked by SNP markers KA002081 and KA002084. Plants homozygous for the Ht3L/Ht3L genotype exhibited an average reduction in diseased leaf area (DLA) by 16.5% compared to plants lacking Ht3L locus. The Ht3L locus showed extensive variation in genomic architecture among different maize lines and did not appear to contain any genes encoding canonical cell wall-associated kinases against NCLB. Moreover, the Ht3L locus was located ∼2.7 Mb away from the known Htn1 locus. We speculate that the Ht3L locus may contain a bona fide Ht3 gene or a novel NCLB resistance gene closely linked to Ht3. In practice, the Ht3L locus is a valuable resource for improving maize resistance to NCLB.

Assembly, Annotation, and Comparative Whole Genome Sequence of Fusarium verticillioides Isolated from Stored Maize Grains

Fusarium verticillioides is a plant pathogenic fungus affecting a wide range of crops worldwide due to its toxigenic properties. F. verticillioides BIONCL4 strain was isolated from stored maize grain samples in India, and produces high amount of fumonisin B1 (FB1). We report a comparative genomic analysis of F. verticillioides, covering the basic genome information, secretome, and proteins involved in host-pathogen interactions and mycotoxin biosynthesis. Whole-genome sequencing (WGS) was performed using the Illumina platform with an assembly size of 42.91 Mb, GC content of 48.24%, and 98.50% coverage with the reference genome (GCA000149555). It encodes 15,053 proteins, including 2058 secretory proteins, 676 classical secretory proteins, and 569 virulence and pathogenicity-related proteins. There were also 1447 genes linked to carbohydrate active enzymes (CaZymes) and 167 genes related to mycotoxin production. Furthermore, F. verticillioides genome comparison revealed information about the species' evolutionary history. The overall study helps in disease prevention and management of mycotoxins to ensure food safety.

Molecular Genetics of Anthracnose Resistance in Maize

Maize (Zea mays), also called corn, is one of the top three staple food crops worldwide and is also utilized as feed (e.g., feed grain and silage) and a source of biofuel (e.g., bioethanol). Maize production is hampered by a myriad of factors, including although not limited to fungal diseases, which reduce grain yield and downgrade kernel quality. One such disease is anthracnose leaf blight and stalk rot (ALB and ASR) caused by the hemibiotrophic fungal pathogen Colletotrichum graminicola. The pathogen deploys a biphasic infection strategy to colonize susceptible maize genotypes, comprising latent (symptomless) biotrophic and destructive (symptomatic) necrotrophic phases. However, the resistant maize genotypes restrict the C. graminicola infection and in planta fungal proliferation during the biotrophic phase of the infection. Some studies on the inheritance of ASR resistance in the populations derived from biparental resistant and susceptible genotypes reveal that anthracnose is likely a gene-for-gene disease in which the resistant maize genotypes and C. graminicola recognize each other by their matching pairs of nucleotide-binding leucine-rich repeat resistance (NLR) proteins (whose coding genes are localized in disease QTL) and effectors (1–2 effectors/NLR) during the biotrophic phase of infection. The Z. mays genome encodes approximately 144 NLRs, two of which, RCg1 and RCg1b, located on chromosome 4, were cloned and functionally validated for their role in ASR resistance. Here, we discuss the genetic architecture of anthracnose resistance in the resistant maize genotypes, i.e., disease QTL and underlying resistance genes. In addition, this review also highlights the disease cycle of C. graminicola and molecular factors (e.g., virulence/pathogenicity factors such as effectors and secondary metabolites) that contribute to the pathogen’s virulence on maize. A detailed understanding of molecular genetics underlying the maize—C. graminicola interaction will help devise effective management strategies against ALB and ASR.

Back to the wild: mining maize (Zea mays L.) disease resistance using advanced breeding tools

Cultivated modern maize (Zea mays L.) originated through the continuous process of domestication from its wild progenitors. Today, maize is considered as the most important cereal crop which is extensively cultivated in all parts of the world. Maize shows remarkable genotypic and phenotypic diversity which makes it an ideal model species for crop genetic research. However, intensive breeding and artificial selection of desired agronomic traits greatly narrow down the genetic bases of maize. This reduction in genetic diversity among cultivated maize led to increase the chance of more attack of biotic stress as climate changes hampering the maize grain production globally. Maize germplasm requires to integrate both durable multiple-diseases and multiple insect-pathogen resistance through tapping the unexplored resources of maize landraces. Revisiting the landraces seed banks will provide effective opportunities to transfer the resistant genes into the modern cultivars. Here, we describe the maize domestication process and discuss the unique genes from wild progenitors which potentially can be utilized for disease resistant in maize. We also focus on the genetics and disease resistance mechanism of various genes against maize biotic stresses and then considered the different molecular breeding tools for gene transfer and advanced high resolution mapping for gene pyramiding in maize lines. At last, we provide an insight for targeting identified key genes through CRISPR/Cas9 genome editing system to enhance the maize resilience towards biotic stress.

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.

Identification and First Report of Fusarium andiyazi Causing Sheath Rot of Zizania latifolia in China

Zizania latifolia is a perennial plant native to East Asia. The swollen culm of Z. latifolia is a popular vegetable and traditional herbal medicine consumed in China and some other Asian countries. From 2019 to 2021, a sheath rot disease was found in Zhejiang Province of China. Symptoms mainly occurred in the leaf sheath showing as brown necrotic lesions surrounded by yellow halos. The pathogen fungal isolates were isolated from the affected sheaths. Ten representative isolates were selected for morphological and molecular identification by phylogenetic analyses of the translation elongation factor 1-α (TEF1) and the RNA polymerase II subunit beta (RPB2) gene regions. Based on the combined datasets, the fungal isolates were identified as Fusarium andiyazi. Koch’s postulates were confirmed by pathogenicity test, re-isolation and re-identification of the fungal isolates. To the best of our knowledge, this is the first report of sheath rot caused by F. andiyazi in Z. latifolia in China.

The potential roles of different metacaspases in maize defense response

Metacaspases (MCs), a class of cysteine-dependent proteases, act as important regulators in plant defense response. In maize genome, there are 11 ZmMCs which have been categorized into two types (type I and II) based on their structural differences. In this study, we investigated the different transcript patterns of 11 ZmMCs in maize defense response mediated by the nucleotide-binding, leucine-rich-repeat protein Rp1-D21. We further predicted that many cis-elements responsive to salicylic acid (SA), methyl jasmonate (MeJA), abscisic acid (ABA) and auxin were identified in the promoter regions of ZmMCs, and several different transcription factors were predicted to bind to their promoters. We analyzed the localization of ZmMCs with previously identified quantitative trait loci (QTLs) in maize disease resistance, and found that all other ZmMCs, except for ZmMC6-8, are co-located with at least one QTL associated with disease resistance to southern leaf blight, northern leaf blight, gray leaf spot or Fusarium ear rot. Based on previous RNA-seq analysis, different ZmMCs display different transcript levels in response to Cochliobolous heterostrophus and Fusarium verticillioides. All the results imply that the members of ZmMCs might have differential functions to different maize diseases. This study lays the basis for further investigating the roles of ZmMCs in maize disease resistance.

Genetic dissection of maize disease resistance and its applications in molecular breeding

Disease resistance is essential for reliable maize production. In a long-term tug-of-war between maize and its pathogenic microbes, naturally occurring resistance genes gradually accumulate and play a key role in protecting maize from various destructive diseases. Recently, significant progress has been made in deciphering the genetic basis of disease resistance in maize. Enhancing disease resistance can now be explored at the molecular level, from marker-assisted selection to genomic selection, transgenesis technique, and genome editing. In view of the continuing accumulation of cloned resistance genes and in-depth understanding of their resistance mechanisms, coupled with rapid progress of biotechnology, it is expected that the large-scale commercial application of molecular breeding of resistant maize varieties will soon become a reality.

High-density mapping for gray leaf spot resistance using two related tropical maize recombinant inbred line populations

Gray leaf spot (GLS) caused by Cercospora zeae-maydis or Cercospora zeina is one of the devastating maize foliar diseases worldwide. Identification of GLS-resistant quantitative trait loci (QTL)/genes plays an urgent role in improving GLS resistance in maize breeding practice. Two groups of recombinant inbred line (RIL) populations derived from CML373 × Ye107 and Chang7-2 × Ye107 were generated and subjected to genotyping-by-sequencing (GBS). A total of 1,929,222,287 reads in CML373 × Ye107 (RIL-YCML) and 2,585,728,312 reads in Chang7-2 × Ye107 (RIL-YChang), with an average of 10,961,490 (RIL-YCML) and 13,609,096 (RIL-YChang) reads per individual, were got, which was roughly equal to 0.70-fold and 0.87-fold coverage of the maize B73 RefGen_V4 genome for each F₇ individual, respectively. 6418 and 5139 SNP markers were extracted to construct two high-density genetic maps. Comparative analysis using these physically mapped marker loci demonstrated a satisfactory colinear relationship with the reference genome. 11 GLS-resistant QTL have been detected. The individual QTL accounted for 1.53-24.00% of the phenotypic variance explained (PVE). The new consensus QTL (qYCM-DS3-3/qYCM-LT3-1/qYCM-LT3-2) with the largest effect was located in chromosome bin 3.05, with an interval of 2.7 Mb, representing 13.08 to 24.00% of the PVE. Further gene annotation indicated that there were four candidate genes (GRMZM2G032384, GRMZM2G041415, GRMZM2G041544, and GRMZM2G035992) for qYCM-LT3-1, which may be related to GLS resistance. Combining RIL populations and GBS-based high-density genetic maps, a new larger effect QTL was delimited to a narrow genomic interval, which will provide a new resistance source for maize breeding programs.

Genetic dissection of Striga hermonthica (Del.) Benth. resistance via genome-wide association and genomic prediction in tropical maize germplasm

KEY MESSAGE

Genome-wide association revealed that resistance to Striga hermonthica is influenced by multiple genomic regions with moderate effects. It is possible to increase genetic gains from selection for Striga resistance using genomic prediction. Striga hermonthica (Del.) Benth., commonly known as the purple witchweed or giant witchweed, is a serious problem for maize-dependent smallholder farmers in sub-Saharan Africa. Breeding for Striga resistance in maize is complicated due to limited genetic variation, complexity of resistance and challenges with phenotyping. This study was conducted to (i) evaluate a set of diverse tropical maize lines for their responses to Striga under artificial infestation in three environments in Kenya; (ii) detect quantitative trait loci associated with Striga resistance through genome-wide association study (GWAS); and (iii) evaluate the effectiveness of genomic prediction (GP) of Striga-related traits. An association mapping panel of 380 inbred lines was evaluated in three environments under artificial Striga infestation in replicated trials and genotyped with 278,810 single-nucleotide polymorphism (SNP) markers. Genotypic and genotype x environment variations were significant for measured traits associated with Striga resistance. Heritability estimates were moderate (0.42) to high (0.92) for measured traits. GWAS revealed 57 SNPs significantly associated with Striga resistance indicator traits and grain yield (GY) under artificial Striga infestation with low to moderate effect. A set of 32 candidate genes physically near the significant SNPs with roles in plant defense against biotic stresses were identified. GP with different cross-validations revealed that prediction of performance of lines in new environments is better than prediction of performance of new lines for all traits. Predictions across environments revealed high accuracy for all the traits, while inclusion of GWAS-detected SNPs led to slight increase in the accuracy. The item-based collaborative filtering approach that incorporates related traits evaluated in different environments to predict GY and Striga-related traits outperformed GP for Striga resistance indicator traits. The results demonstrated the polygenic nature of resistance to S. hermonthica, and that implementation of GP in Striga resistance breeding could potentially aid in increasing genetic gain for this important trait.

Symptoms and pathogens diversity of Corn Fusarium sheath rot in Sichuan Province, China

To elucidate the symptoms and pathogens diversity of corn Fusarium sheath rot (CFSR), diseased samples were collected from 21 county-level regions in 12 prefecture-level districts of Sichuan Province from 2015 to 2018 in the present study. In the field, two symptom types appeared including small black spots with a linear distribution and wet blotches with a tawny or brown color. One hundred thirty-seven Fusarium isolates were identified based on morphological characteristics and phylogenetic analysis (EF1-α), and Koch's postulates were also assessed. The results identified the isolates as 8 species in the Fusarium genus, including F. verticillioides, F. proliferatum, F. fujikuroi, F. asiaticum, F. equiseti, F. meridionale, F. graminearum and F. oxysporum, with isolation frequencies of 30.00, 22.67, 15.33, 7.33, 6.00, 5.33, 3.33 and 1.33%, respectively. Fusarium verticillioides and F. proliferatum were the dominant and subdominant species, respectively. Two or more Fusarium species such as F. verticillioides and F. proliferatum were simultaneously identified at a mixed infection rate of 14.67% in the present study. The pathogenicity test results showed that F. proliferatum and F. fujikuroi exhibited the highest virulence, with average disease indices of 30.28 ± 2.87 and 28.06 ± 1.96, followed by F. equiseti and F. verticillioides, with disease indices of 21.48 ± 2.14 and 16.21 ± 1.84, respectively. Fusarium asiaticum, F. graminearum and F. meridonale showed lower virulence, with disease indices of 13.80 ± 2.07, 11.57 ± 2.40 and 13.89 ± 2.49, respectively. Finally, F. orysporum presented the lowest virulence in CFSR, with a disease index of 10.14 ± 1.20. To the best of our knowledge, this is the first report of F. fujikuroi, F. meridionale and F. asiaticum as CFSR pathogens in China.

Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight

Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB.

Characterization of black spot resistance in diploid roses with QTL detection, meta-analysis and candidate-gene identification

Two environmentally stable QTLs linked to black spot disease resistance in the Rosa wichurana genetic background were detected, in different connected populations, on linkage groups 3 and 5. Co-localization between R-genes and defense response genes was revealed via meta-analysis. The widespread rose black spot disease (BSD) caused by the hemibiotrophic fungus Diplocarpon rosae Wolf. is efficiently controlled with fungicides. However, in the actual context of reducing agrochemical use, the demand for rose bushes with higher levels of resistance has increased. Qualitative resistance conferred by major genes (Rdr genes) has been widely studied but quantitative resistance to BSD requires further investigation. In this study, segregating populations connected through the BSD resistant Rosa wichurana male parent were phenotyped for disease resistance over several years and locations. A pseudo-testcross approach was used, resulting in six parental maps across three populations. A total of 45 individual QTLs with significant effect on BSD resistance were mapped on the male maps (on linkage groups (LG) B3, B4, B5 and B6), and 12 on the female maps (on LG A1, A2, A3, A4 and A5). Two major regions linked to BSD resistance were identified on LG B3 and B5 of the male maps and were integrated into a consensus map built from all three of the male maps. A meta-analysis was used to narrow down the confidence intervals of individual QTLs from three populations by generating meta-QTLs. Two 'hot spots' or meta-QTLs were found per LG, enabling reduction of the confidence interval to 10.42 cM for B3 and 11.47 cM for B5. An expert annotation of NBS-LRR encoding genes of the genome assembly of Hibrand et al. was performed and used to explore potential co-localization with R-genes. Co-localization with defense response genes was also investigated.

Identification of Loci That Confer Resistance to Bacterial and Fungal Diseases of Maize

Crops are hosts to numerous plant pathogenic microorganisms. Maize has several major disease issues; thus, breeding multiple disease resistant (MDR) varieties is critical. While the genetic basis of resistance to multiple fungal pathogens has been studied in maize, less is known about the relationship between fungal and bacterial resistance. In this study, we evaluated a disease resistance introgression line (DRIL) population for the foliar disease Goss’s bacterial wilt and blight (GW) and conducted quantitative trait locus (QTL) mapping. We identified a total of ten QTL across multiple environments. We then combined our GW data with data on four additional foliar diseases (northern corn leaf blight, southern corn leaf blight, gray leaf spot, and bacterial leaf streak) and conducted multivariate analysis to identify regions conferring resistance to multiple diseases. We identified 20 chromosomal bins with putative multiple disease effects. We examined the five chromosomal regions (bins 1.05, 3.04, 4.06, 8.03, and 9.02) with the strongest statistical support. By examining how each haplotype effected each disease, we identified several regions associated with increased resistance to multiple diseases and three regions associated with opposite effects for bacterial and fungal diseases. In summary, we identified several promising candidate regions for multiple disease resistance in maize and specific DRILs to expedite interrogation.

Isolation and identification of bioactive substance 1-hydroxyphenazine from Pseudomonas aeruginosa and its antimicrobial activity

A strain named as Pseudomonas aeruginosa 2016NX1, which could produce phenazine and cereusitin, was isolated from the root of Millettia specisoa. Phenazines were extracted, isolated and purified by chloroform, thin-layer chromatography, column chromatography and high-performance liquid chromatography. Then the purified materials were identified by analysis of nuclear magnetic resonance. The major yellow component is 1-hydroxyphenazine and the minor blue component is cereusitin A. The tests of antimicrobial activity of yellow component showed that the growth of several common plant pathogenic fungi and bacteria (such as Cochliobolus miyabeanus, Diaporthe citri, Salmonella sp., Klebsiella oxytoca) could be strongly inhibited. This study suggested that Pseudomonas aeruginosa strain 2016NX1 had a significant potential for biological control of phytopathogenic fungi. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study, one bioactive substance from Pseudomonas aeruginosa 2016NX1 was identified and its antimicrobial activity was verified. This study demonstrated that one bioactive substance from P. aeruginosa can strongly inhibit the growth of plant pathogenic fungi and bacteria. This study suggested that P. aeruginosa strain 2016NX1 has a significant potential for biological control of phytopathogenic fungi.

Exploiting Broad-Spectrum Disease Resistance in Crops: From Molecular Dissection to Breeding

Plant diseases reduce crop yields and threaten global food security, making the selection of disease-resistant cultivars a major goal of crop breeding. Broad-spectrum resistance (BSR) is a desirable trait because it confers resistance against more than one pathogen species or against the majority of races or strains of the same pathogen. Many BSR genes have been cloned in plants and have been found to encode pattern recognition receptors, nucleotide-binding and leucine-rich repeat receptors, and defense-signaling and pathogenesis-related proteins. In addition, the BSR genes that underlie quantitative trait loci, loss of susceptibility and nonhost resistance have been characterized. Here, we comprehensively review the advances made in the identification and characterization of BSR genes in various species and examine their application in crop breeding. We also discuss the challenges and their solutions for the use of BSR genes in the breeding of disease-resistant crops.

Grain Yields and Nitrogen Use Efficiencies in Different Types of Stay-Green Maize in Response to Nitrogen Fertilizer

The stay-green leaf phenotype is typically associated with increased yields and improved stress resistance in maize breeding, due to higher nitrogen (N) nutrient levels that prolong greenness. The application of N fertilizer can regulate the N status of plants, and furthermore, impact the photosynthetic rates of leaves at the productive stage; however, N deficiencies and N excesses will reduce maize yields. Consequently, it is necessary to develop N fertilizer management strategies for different types of stay-green maize. For this study, the senescent cultivar Lianchuang 808 (LC808), moderate-stay-green cultivar Zhengdan 958 (ZD958), and over stay-green cultivar Denghai 685 (DH685) were selected as experimental models. Our results revealed that yields of ZD958 were slightly higher than DH685 and notably improved over than LC808. Compared with a non-stay-green cultivar LC808, ZD958 and DH685 still maintained higher chlorophyll contents and cell activities following the silking stage, while efficiently slowing the senescence rate. The supply of N fertilizer significantly prolonged leaf greenness and delayed senescence for ZD958 and DH685; however, the effect was not obvious for LC808. The stem remobilization efficiency of N was higher in the moderate-stay-green cultivar ZD958, in contrast to LC808, while the transfer of leaf N was lower than LC808, which guaranteed high leaf N levels, and that sufficient N was transferred to grains in ZD958. To obtain the highest yields, the optimal N fertilizer rates were 228.1 kg hm⁻² for LC0808, 180 kg hm⁻² for ZD958, and 203.8 kg hm⁻² for DH685. In future, the selection of stay-green type crops might serve as an important agricultural strategy to reduce the quantity of N fertilizer and increase N efficiency.

Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-spectrum disease resistance

Plant genotype strongly affects disease resistance, and also influences the composition of the leaf microbiome. However, these processes have not been studied and linked in the microevolutionary context of breeding for improved disease resistance. We hypothesised that broad-spectrum disease resistance alleles also affect colonisation by nonpathogenic symbionts. Quantitative trait loci (QTL) conferring resistance to multiple fungal pathogens were introgressed into a disease-susceptible maize inbred line. Bacterial and fungal leaf microbiomes of the resulting near-isogenic lines were compared with the microbiome of the disease-susceptible parent line at two time points in multiple fields. Introgression of QTL from disease-resistant lines strongly shifted the relative abundance of diverse fungal and bacterial taxa in both 3-wk-old and 7-wk-old plants. Nevertheless, the effects on overall community structure and diversity were minor and varied among fields and years. Contrary to our expectations, host genotype effects were not any stronger in fields with high disease pressure than in uninfected fields, and microbiome succession over time was similar in heavily infected and uninfected plants. These results show that introgressed QTL can greatly improve broad-spectrum disease resistance while having only limited and inconsistent pleiotropic effects on the leaf microbiome in maize.

A helitron-induced RabGDIα variant causes quantitative recessive resistance to maize rough dwarf disease

Maize rough dwarf disease (MRDD), caused by various species of the genus Fijivirus, threatens maize production worldwide. We previously identified a quantitative locus qMrdd1 conferring recessive resistance to one causal species, rice black-streaked dwarf virus (RBSDV). Here, we show that Rab GDP dissociation inhibitor alpha (RabGDIα) is the host susceptibility factor for RBSDV. The viral P7-1 protein binds tightly to the exon-10 and C-terminal regions of RabGDIα to recruit it for viral infection. Insertion of a helitron transposon into RabGDIα intron 10 creates alternative splicing to replace the wild-type exon 10 with a helitron-derived exon 10. The resultant splicing variant RabGDIα-hel has difficulty being recruited by P7-1, thus leading to quantitative recessive resistance to MRDD. All naturally occurring resistance alleles may have arisen from a recent single helitron insertion event. These resistance alleles are valuable to improve maize resistance to MRDD and potentially to engineer RBSDV resistance in other crops.

Maize rough dwarf disease threatens its production. Here, the authors show that a helitron transposon insertion in the Rab GDP dissociation inhibitor alpha leads to recessive viral resistance by affecting its interaction with viral P7-1 protein and that all naturally occurring alleles come from a single mutation event after domestication.

The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement

After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.

Next-generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.)

Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease affecting over 350 plant species. A few peanut cultivars were found to possess stable and durable bacterial wilt resistance (BWR). Genomics-assisted breeding can accelerate the process of developing resistant cultivars by using diagnostic markers. Here, we deployed sequencing-based trait mapping approach, QTL-seq, to discover genomic regions, candidate genes and diagnostic markers for BWR in a recombination inbred line population (195 progenies) of peanut. The QTL-seq analysis identified one candidate genomic region on chromosome B02 significantly associated with BWR. Mapping of newly developed single nucleotide polymorphism (SNP) markers narrowed down the region to 2.07 Mb and confirmed its major effects and stable expressions across three environments. This candidate genomic region had 49 nonsynonymous SNPs affecting 19 putative candidate genes including seven putative resistance genes (R-genes). Two diagnostic markers were successfully validated in diverse breeding lines and cultivars and could be deployed in genomics-assisted breeding of varieties with enhanced BWR.

Dissecting the Regulatory Network of Leaf Premature Senescence in Maize (Zea mays L.) Using Transcriptome Analysis of ZmELS5 Mutant

Leaf premature senescence largely determines maize (Zea mays L.) grain yield and quality. A natural recessive premature-senescence mutant was selected from the breeding population, and near-isogenic lines were constructed using Jing24 as the recurrent parent. In the near-isogenic lines, the dominant homozygous material was wild-type (WT), and the recessive material of early leaf senescence was the premature-senescence-type ZmELS5. To identify major genes and regulatory mechanisms involved in leaf senescence, a transcriptome analysis of the ZmELS5 and WT near-isogenic lines (NILs) was performed. A total of 8796 differentially expressed transcripts were identified between ZmELS5 and WT, including 3811 up-regulated and 4985 down-regulated transcripts. By combining gene ontology, Kyoto Encyclopedia of Genes and Genomes, gene set, and transcription factor enrichment analyses, key differentially expressed genes were screened. The senescence regulatory network was predicted based on these key differentially expressed genes, which indicated that the senescence process is mainly regulated by bHLH, WRKY, and AP2/EREBP family transcription factors, leading to the accumulations of jasmonic acid and ethylene. This causes stress responses and reductions in the chlorophyll a/b-binding protein activity level. Then, decreased ATP synthase activity leads to increased photosystem II photodamage, ultimately leading to leaf senescence.

Quantitative Phenotyping of Northern Leaf Blight in UAV Images Using Deep Learning

Plant disease poses a serious threat to global food security. Accurate, high-throughput methods of quantifying disease are needed by breeders to better develop resistant plant varieties and by researchers to better understand the mechanisms of plant resistance and pathogen virulence. Northern leaf blight (NLB) is a serious disease affecting maize and is responsible for significant yield losses. A Mask R-CNN model was trained to segment NLB disease lesions in unmanned aerial vehicle (UAV) images. The trained model was able to accurately detect and segment individual lesions in a hold-out test set. The mean intersect over union (IOU) between the ground truth and predicted lesions was 0.73, with an average precision of 0.96 at an IOU threshold of 0.50. Over a range of IOU thresholds (0.50 to 0.95), the average precision was 0.61. This work demonstrates the potential for combining UAV technology with a deep learning-based approach for instance segmentation to provide accurate, high-throughput quantitative measures of plant disease.

Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots

Recently, long noncoding RNAs (lncRNAs) have emerged as vital regulators of many biological processes in animals and plants. However, to our knowledge no investigations on plant lncRNAs which respond to arbuscular mycorrhizal (AM) fungi have been reported thus far. In this study, maize roots colonized with AM fungus were analyzed by strand-specific RNA-Seq to identify AM fungi-responsive lncRNAs and construct an associated regulatory network. A total of 1837 differentially expressed protein coding genes (DEGs) were identified from maize roots with Rhizophagus irregularis inoculation. Many AM fungi-responsive genes were homologs to MtPt4, STR, STR2, MtFatM, and enriched pathways such as fatty acid biosynthesis, response to phosphate starvation, and nitrogen metabolism are consistent with previous studies. In total, 5941 lncRNAs were identified, of which more than 3000 were new. Of those, 63 lncRNAs were differentially expressed. The putative target genes of differentially expressed lncRNAs (DELs) were mainly related to phosphate ion transmembrane transport, cellular response to potassium ion starvation, and lipid catabolic processes. Regulatory network analysis showed that DELs might be involved in the regulation of bidirectional nutrient exchange between plant and AM fungi as mimicry of microRNA targets. The results of this study can broaden our knowledge on the interaction between plant and AM fungi.