Search

Southern leaf blight (SLB) is a foliar disease caused by the fungus Cochliobolus heterostrophus infecting maize plants in humid, warm weather conditions. SLB causes production losses to corn producers in different regions of the world such as Latin America, Europe, India, and Africa. In this paper, we demonstrate a non-destructive method to quantify the signs of fungal infection in SLB-infected corn plants using a deep UV (DUV) fluorescence spectrometer, with a 248.6 nm excitation wavelength, to acquire the emission spectra of healthy and SLB-infected corn leaves. Fluorescence emission spectra of healthy and diseased leaves were used to train an Autoencoder (AE) anomaly detection algorithm—an unsupervised machine learning model—to quantify the phenotype associated with SLB-infected leaves. For all samples, the signature of corn leaves consisted of two prominent peaks around 450 nm and 325 nm. However, SLB-infected leaves showed a higher response at 325 nm compared to healthy leaves, which was correlated to the presence of C. heterostrophus based on disease severity ratings from Visual Scores (VS). Specifically, we observed a linear inverse relationship between the AE error and the VS (R2 = 0.94 and RMSE = 0.935). With improved hardware, this method may enable improved quantification of SLB infection versus visual scoring based on e.g., fungal spore concentration per unit area and spatial localization. [ABSTRACT FROM AUTHOR]

The pattern‐triggered immunity (PTI) response is triggered at the plant cell surface by the recognition of microbe‐derived molecules known as microbe‐ or pathogen‐associated molecular patterns or molecules derived from compromised host cells called damage‐associated molecular patterns. Membrane‐localized receptor proteins, known as pattern recognition receptors, are responsible for this recognition. Although much of the machinery of PTI is conserved, natural variation for the PTI response exists within and across species with respect to the components responsible for pattern recognition, activation of the response, and the strength of the response induced. This review describes what is known about this variation. We discuss how variation in the PTI response can be measured and how this knowledge might be utilized in the control of plant disease and in developing plant varieties with enhanced disease resistance. [ABSTRACT FROM AUTHOR]

The article discusses the potential for manipulating the plant mycobiome to enhance plant resilience. It explains that there are two main methods for manipulating the mycobiome: leveraging existing fungal communities or introducing novel taxa. The article also highlights the challenges and opportunities for mycobiome management, emphasizing the need for a broad understanding of plant-fungal interactions. It discusses the importance of community assembly processes, host defense mechanisms, and the maintenance of beneficial mycobiomes. The article concludes by stating that successful mycobiome manipulation will require a combination of molecular and genetic tools, as well as an understanding of the ecology and evolution of plant-fungal interactions. [Extracted from the article]

Metagenomics is a powerful tool for understanding organismal interactions; however, classification, profiling and detection of interactions at the strain level remain challenging. We present an automated pipeline, quantitative metagenomic alignment and taxonomic exact matching (Qmatey), that performs a fast exact matching-based alignment and integration of taxonomic binning and profiling. It interrogates large databases without using metagenome-assembled genomes, curated pan-genes or k-mer spectra that limit resolution. Qmatey minimizes misclassification and maintains strain level resolution by using only diagnostic reads as shown in the analysis of amplicon, quantitative reduced representation and shotgun sequencing datasets. Using Qmatey to analyze shotgun data from a synthetic community with 35% of the 26 strains at low abundance (0.01–0.06%), we revealed a remarkable 85–96% strain recall and 92–100% species recall while maintaining 100% precision. Benchmarking revealed that the highly ranked Kraken2 and KrakenUniq tools identified 2–4 more taxa (92–100% recall) than Qmatey but produced 315–1752 false positive taxa and high penalty on precision (1–8%). The speed, accuracy and precision of the Qmatey pipeline positions it as a valuable tool for broad-spectrum profiling and for uncovering biologically relevant interactions. [ABSTRACT FROM AUTHOR]

These papers cover established and emerging viral tools for functional genomics in maize, a genomic study of maize resistance genes, and the identification and detailed characterization of maize genes involved in pathogen resistance and microbial genes involved in pathogenicity. The first identification of a plant disease resistance gene, I Hm1 i (Johal & Briggs, [12]), and of a plant disease susceptibility gene, I T-urf13 i (Dewey et al., [7]), occurred in maize. Thatcher, Jung et al. ([35], this issue) took advantage of the recent availability of a set of diverse maize genome sequences to characterize the diversity of NLR genes in maize as well as the maize relative I Zea luxurians i . Maize ( I Zea mays i ) is an annual grass belonging to the tribe Andropogoneae of the family Gramineae. [Extracted from the article]

Summary: Blumeria graminis f. sp. tritici (Bgt) is a globally important fungal pathogen of wheat that can rapidly evolve to defeat wheat powdery mildew (Pm) resistance genes. Despite periodic regional deployment of the Pm1a resistance gene in US wheat production, Bgt strains that overcome Pm1a have been notably nonpersistent in the United States, while on other continents, they are more widely established.A genome‐wide association study (GWAS) was conducted to map sequence variants associated with Pm1a virulence in 216 Bgt isolates from six countries, including the United States. A virulence variant apparently unique to Bgt isolates from the United States was detected in the previously mapped gene AvrPm1a (BgtE‐5612) on Bgt chromosome 6; an in vitro growth assay suggested no fitness reduction associated with this variant.A gene on Bgt chromosome 8, Bgt‐51526, was shown to function as a second determinant of Pm1a virulence, and despite < 30% amino acid identity, BGT‐51526 and BGTE‐5612 were predicted to share > 85% of their secondary structure. A co‐expression study in Nicotiana benthamiana showed that BGTE‐5612 and BGT‐51526 each produce a PM1A‐dependent hypersensitive response.More than one member of a B. graminis effector family can be recognized by a single wheat immune receptor, and a two‐gene model is necessary to explain virulence to Pm1a. [ABSTRACT FROM AUTHOR]

Summary: Southern leaf blight (SLB), caused by the necrotrophic fungal pathogen Cochliobolus heterostrophus (anamorph Bipolaris maydis), is a major foliar disease which causes significant yield losses in maize worldwide. A major quantitative trait locus, qSLB3.04, conferring recessive resistance to SLB was previously mapped on maize chromosome 3.Using a combination of map‐based cloning, association analysis, ethyl methanesulfonate and transposon mutagenesis, and CRISPR‐Cas9 editing, we demonstrate that a leucine‐rich repeat receptor‐like kinase gene which we have called ChSK1 (Cochliobolus heterostrophus Susceptibility Kinase 1) at qSLB3.04 causes increased susceptibility to SLB. Genes of this type have generally been associated with the defense response.We present evidence that ChSK1 may be associated with suppression of the basal immune response.These findings contribute to our understanding of plant disease susceptibility genes and the potential to use them for engineering durable disease resistance. [ABSTRACT FROM AUTHOR]

In contrast to large‐effect qualitative disease resistance, quantitative disease resistance (QDR) exhibits partial and generally durable resistance and has been extensively utilized in crop breeding. The molecular mechanisms underlying QDR remain largely unknown but considerable progress has been made in this area in recent years. In this review, we summarize the genes that have been associated with plant QDR and their biological functions. Many QDR genes belong to the canonical resistance gene categories with predicted functions in pathogen perception, signal transduction, phytohormone homeostasis, metabolite transport and biosynthesis, and epigenetic regulation. However, other "atypical" QDR genes are predicted to be involved in processes that are not commonly associated with disease resistance, such as vesicle trafficking, molecular chaperones, and others. This diversity of function for QDR genes contrasts with qualitative resistance, which is often based on the actions of nucleotide‐binding leucine‐rich repeat (NLR) resistance proteins. An understanding of the diversity of QDR mechanisms and of which mechanisms are effective against which classes of pathogens will enable the more effective deployment of QDR to produce more durably resistant, resilient crops. [ABSTRACT FROM AUTHOR]

Northern leaf blight [NLB; caused by Exserohilum turcicum (Pass) K.J. Leonard and E.G. Suggs] is an important fungal disease of maize (Zea mays L.) in the United States and worldwide. The IBM population, an advanced intercross recombinant inbred line population derived from a cross between the lines Mo17 and B73, was evaluated in three environments (Aurora, NY, in 2006 and 2007 and Clayton, NC in 2007) for two traits related to NLB resistance, weighted mean disease (WMD) and incubation period (IP), and for days to anthesis (DTA). Two WMD quantitative trait loci (QTL) in bins 2.00/2.01 and 4.08 were detected from the overall analysis; of these, only the QTL in bin 4.08 was detected in all three environments analyzed separately. Likewise, only one IP QTL, in bin 2.02, was detected in all three environments and from the overall analysis. Several environment-specific QTL for each trait were also detected. Several DTA QTL were detected with the strongest effect detected in bin 8.05. Correlations between disease resistance traits and days to anthesis were uniformly low. The results from this study were compared to those of previous studies that used the IBM population to identify QTL for two other maize foliar diseases, southern leaf blight {causal agent Cochliobolus heterostrophus (Drechs.) Drechs. [anamorph = Bipolaris maydis (Nisikado and Miyake) Shoemaker; synonym = Helminthosporium maydis (Nisikado and Miyake)]} and gray leaf spot [causal agent Cercospora zeae-maydis (Tehon and E.Y. Daniets)]. Although we did not find QTL conferring resistance to all three diseases, significant correlations between resistances to these diseases in the IBM population were identified, implying the existence of loci (and possibly genes) affecting resistance to all three diseases. doi: 10.2135/cropsci2009.02.0066

Peas (Pisum sativum) are the second most cultivated pulse crop in the world. They can serve as human food, fodder, and cover crop. The most serious foliar disease of pea cultivars worldwide is Ascochyta blight, which can be caused by several pathogens. Of these, Peyronella pinodes is the most aggressive and prevalent worldwide. Several traits, including resistance to Peyronella pinodes, stem diameter, internode length between nodes 2–3 and 5–6, and area of 7th leaf, were measured in 269 entries of the pea single plant plus collection. The heritability (H2) of the morphological traits was relatively high, while disease resistance had low heritability. Using 53,196 single-nucleotide polymorphism markers to perform a genome-wide association study to identify genomic loci associated with variation in all the traits measured, we identified 27 trait–locus associations, 5 of which were associated with more than 1 trait. [ABSTRACT FROM AUTHOR]

The success of a breeding program depends on having adequate diversity in the germplasm. However, as advanced breeding stocks and materials are generated, one casualty is the diversity itself. As a result, breeding programs in many crop species have reached a point of diminishing returns and it is feared that unless new diversity is infused into the breeding germplasm, we face catastrophic reductions in crop productivity if the climate turns adverse. Although some scientists favor transgenic approaches, a 'back to nature' approach to genetic diversity may prove faster and more effective. Wild and exotic relatives of crop plants hold a wealth of alleles that, if we can find them, can help break yield barriers and enhance tolerance to stresses. Many approaches, based largely on quantitative trait loci genetics, have been proposed and used for this purpose, but most are either highly laborious or discover relevant variation inefficiently. Here, we propose a gene-centered approach, dubbed MAGIC (mutant-assisted gene identification and characterization), that uses Mendelian mutants or other genetic variants in a trait of interest as reporters to identify novel genes and variants for that trait. MAGIC is similar to enhancer--suppressor screens, but rather than relying on variation created in the laboratory, it reveals variation created and refined by nature over millions of years of evolution. This approach could be an effective tool for exploring novel variation and a valuable means to harness natural diversity and define genetic networks.

Gray leaf spot [GLS, causal agent Cercospora zeae-maydis (Tehon and E. Y. Daniels)] is an important fungal disease of maize in the U.S. and worldwide. The IBM population, an advanced intercross recombinant inbred line population derived from a cross between the maize lines Mo17 (resistant) and B73 (susceptible), was evaluated in three environments (Andrews, NC in 2005, 2006, and 2007) for resistance to GLS and for days from planting to anthesis (DTA). A conventional recombinant inbred line population derived from the same two parents (the 'Stuber' population) was also assessed for GLS resistance in two environments (Andrews NC, 2004 and 2005). Quantitative trait loci (QTL) for GLS resistance were detected in each population. Five significant QTL were detected in the IBM population in bins 1.05, 2.04, 4.05, 9.03, and 9.05. In each case the QTL were localized to regions less than 3 centiMorgans (cM). Two QTL for GLS resistance were identified in the Stuber population in bins 2.04 and 7.05. The GLS QTL in bin 2.04 was previously identified as a QTL for southern leaf blight resistance in the IBM population. These results were compared with results from five previous GLS QTL studies and two potential GLS QTL 'hotspots' were identified in bins 1.05-1.06 and 2.03-2.05. As expected, QTL were identified with much more precision in the IBM population compared to the Stuber population and to previous studies. There was no significant correlation between disease resistance and days to anthesis. Three DTA QTL were detected in bins 4.09, 8.05, and 9.02, which did not co-localize with GLS QTL.

Fusarium verticillioides (Sacc.) Nirenberg (synonym F. moniliforme Sheldon) (teleomorph: Gibberella moniliformis) and F. proliferatum (Matsushima) Nirenberg (teleomorph: G. intermedia) are fungal pathogens of maize (Zea mays L.) that cause ear rot and contaminate grain with fumonisins, mycotoxins that can harm animals and humans. The objective of this study was to identify quantitative trait loci (QTL) for resistance to Fusarium ear rot and fumonisin contamination in two maize populations, comprised of 213 B[C.sub.1][F.sub.1:2] families from the first backcross of GE440 to FR1064 (GEFR) and 143 recombinant inbred lines from the cross of NC300 to B104 (NCB). QTL mapping was used to study the genetic relationships between resistances to ear rot and fumonisin contamination and to investigate consistency of QTL across populations. In the GEFR population, seven QTL explained 47% of the phenotypic variation for mean ear rot resistance and nine QTL with one epistatic interaction explained 67% of the variation for mean fumonisin concentration. In the NCB population, five QTL explained 31% of the phenotypic variation for mean ear rot resistance and six QTL and three epistatic interactions explained 81% of the phenotypic variation for mean fumonisin concentration. Eight QTL in the GEFR population and five QTL in the NCB population affected both disease traits. At least three ear rot and two fumonisin contamination resistance QTL mapped to similar positions in the two populations. Two QTL, localized to chromosomes four and five, appeared to be consistent for both traits across both populations.