Mapping and Genetic Dissection of Novel Tar Spot Resistance QTL on Maize Chromosome 1

bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-06

Abstract Tar spot, caused by the obligately biotrophic fungus Phyllachora maydis , significantly threatens maize ( Zea mays L.) production across the Americas. Host genetic resistance offers the most viable long-term management strategy. Building on observed differential tar spot susceptibility, we utilized 92 recombinant-inbred lines (RILs) from the Intermated B73 × Mo17 (IBM-94) population to characterize the genetic architecture of resistance. Phenotypic analysis of 92 RILs plus the highly susceptible parent Mo17 and the moderately resistant parent B73 confirmed stable differences in susceptibility, with B73 consistently demonstrating moderate resistance compared to Mo17. Analysis of variance revealed highly significant genetic variation within the population (F = 12.96; p < 0.001). A high Pearson correlation (r = 0.8706, p < 0.0001) and coefficient of determination (R 2 = 0.7579) across environments indicated that 76% of the phenotypic variance is attributable to genetic factors. Linkage mapping identified a novel, consistent major QTL cluster on chromosome 1. This cluster comprises five regions (qTAR_1.1 through qTAR_1.5) exceeding the significance threshold (LOD 3.8) in both years. We identified 74 candidate genes including bZIP and RING/U-box proteins at significant SNP peaks. Additionally, gene annotations revealed a high concentration of wall-associated kinases and S-locus lectin protein kinases within the qTAR_1.4 and qTAR_1.5 regions, alongside potential defense-related transcription factors (MYB, bZIP, and C2H2 zinc fingers). These results provide a framework for high-resolution mapping and functional validation to accelerate the development of tar spot-resistant maize cultivars.

Genome-Wide Association study in a US soft winter wheat population reveals novel and known sources of resistance to the Septoria tritici blotch pathogen <i>Zymoseptoria tritici</i>

bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-02

Abstract Key message GWAS of 337 soft winter wheat genotypes from a breeding program in Indiana, USA identified marker-trait associations that likely correspond with existing and novel resistances to Septoria tritici blotch disease. Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici , is a major disease of wheat worldwide. To find additional sources of resistance, Genome-Wide Association (GWA) was used to analyze 337 soft winter wheat genotypes from Indiana, USA, by inoculating seedlings with two isolates of Z. tritici in a complete randomized design. Necrosis and pycnidia development were assessed at 14, 18 and 22 days post inoculation, enabling the calculation of area under the disease progress curve (AUDPC) for each parameter. Adjusted necrosis and pycnidia AUDPC scores were compared with 14,341 high-quality SNPs in a GWA analysis using the FarmCPU and GAPIT CMLM models to identify markers associated with the resistance. Significant (p &lt; 0.05) isolate ξ genotype interactions were identified, confirming that the phenotypic variation was caused by isolate-specific resistance genes. Overall, 9 marker-trait associations (MTAs) were identified with Z. tritici necrosis and pycnidia resistance. All mapped MTAs were isolate and necrosis/pycnidia specific. Distinct MTAs were mapped for necrosis and pycnidia on chromosome 6A, and for pycnidia on chromosomes 1A, 1D, 4A, 7A, 3B and 5B. The MTAs on chromosomes 4A, 6A, 5B and 1D likely corresponded with the known genes Stb7 , Stb15 , Stb1 and Stb19 , respectively. Those on chromosomes 1A, 7A and 3B were not associated with previously known genes and may be novel. Candidate genes near the marker locations have been identified for further investigations. Indiana soft winter wheat germplasm segregates for novel and known Stb genes and constitutes a valuable breeding resource for Z. tritici resistance.

Progression of Corn Tar Spot and Reproducibility Assessment of an Inoculation Protocol in Semicontrolled Environments

Plant Disease · 2025-07-08 · 1 citations

in maize, addressing variability across geographic regions. We tested a whorl inoculation method under semicontrolled environments in Ecuador and the United States, focusing on three objectives: (i) to develop a noninvasive inoculation protocol; (ii) to assess the effects of inoculum source, cultivar susceptibility, and leaf position on disease progression over time; and (iii) to evaluate the reproducibility of the protocol. Inoculum preparations from fresh or stored leaves were tested across multiple maize cultivars. Results indicated that the use of a fresh inoculum source led to faster disease onset (15 to 17 days after inoculation) and higher stromata counts compared with inoculum prepared from stored leaves. In Ecuador, fisheye lesions were prominent, whereas they were absent in the United States; however, the factors driving those differences remain unclear. Reproducibility was high in Ecuador and less consistent in the United States, likely because of environmental variability and inoculum quality. Future research should focus on optimizing artificial inoculation methods by exploring the interaction between environmental conditions, inoculum quality, and host susceptibility. Overall, the findings contribute to refining inoculation protocols for tar spot in maize.

Loop-Mediated Isothermal Amplification (LAMP) for the Detection and Quantification of Fungal Phytopathogens

2025-03-18

Accurate identification of fungal pathogens that are causal agents of plant diseases is necessary to make appropriate disease management. Loop-mediated isothermal amplification (LAMP) is a sensitive and specific tool for the detection of fungal pathogens in plants. LAMP is an isothermal technique for the amplification of nucleic acids. Four to six primers are used to amplify the target sequence of DNA. The result is a variety of DNA products of diverse sizes with a characteristic stem-loop structure and multiple loops. The amplified products are easily detected by fluorescence measurement and changes in the turbidity or color of the reaction by adding intercalating dyes. LAMP has been used to detect fungal phytopathogens in soybean, rice, grapes, cotton, banana, corn, and wheat, showing high specificity and sensitivity. Also, several portable devices for real-time LAMP have been developed and used under field conditions. One caveat is that this technique requires an extensive optimization process to be effective under field conditions due to cross-contamination.

Functional Characterization of <i>Zymoseptoria tritici</i> Candidate Effectors Reveals Their Role in Modulating Immunity in <i>Nicotiana benthamiana</i>

bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-23 · 1 citations

Abstract Zymoseptoria tritici is a significant wheat pathogen responsible for Septoria tritici blotch (STB) disease and can cause up to 50% yield losses globally. Despite its economic impact, understanding of the molecular interactions between Z. tritici and its host remains limited, particularly the functions of many uncharacterized candidate effectors. To explore the roles of candidate effectors in modulating host immune responses, we selected seven Z. tritici genes with elevated expression during the early biotrophic phase and the transition to necrotrophy in a susceptible interaction. These candidates were transiently expressed in Nicotiana benthamiana , both with and without their predicted signal peptides. AlphaFold structural predictions revealed that two candidates share similarity with proteins of known function: a sterol-binding protein from Saccharomyces cerevisiae and a necrosis-inducing effector from Valsa mali . Effector activity did not always correlate with expression timing, and the presence of a signal peptide significantly influenced the activity of candidate effectors on host defense responses. Several effectors consistently attenuate the production of reactive oxygen species (ROS), while none suppress PBR1-mediated cell death, indicating they do not target this NLR or its downstream signaling. Two candidate effectors, Mycgr3107904 and Mycgr394290, induce cell death in N. benthamiana while also modulating the ROS burst, suggesting potential dual functions at different stages of infection. These findings provide new insights into how Z. tritici effectors modulate plant immunity during disease progression, either to evade host recognition or establish infection. Our results show that effector functions may extend beyond what is inferred from expression profiles alone.

Native Bacillus subtilis strains cultivated in a low-cost medium enhance maize growth and suppress seed-borne fungi by defense activation and rhizosphere colonization

Biological Control · 2025-11-20

• Native Bacillus subtilis strains suppressed seed-borne fungi in maize. • Inoculation enhanced expression of plant growth and defense-related genes. • Auxin levels, chlorophyll content, and antioxidant activity increased. • Repeated applications improved rhizosphere colonization at root apex. • Low-cost bacterial cultivation supports sustainable maize production. We evaluated two native Bacillus subtilis strains (CtpxS2-1 and CtpxS3-5) cultivated in low-cost DSF40–MOL5 medium as seed inoculants for maize ( Zea mays ). This study extends previous work by integrating molecular, physiological, and ecological endpoints under greenhouse conditions. Seed treatment with these strains enhanced germination rates and seedling vigor, suppressed seed-borne fungal pathogens, and promoted systemic defense responses. Quantitative RT-qPCR revealed upregulation of defense-related genes ( PR-1, PR-4, SOD-2 ) and growth regulators ( ZmYUC1, PIN-3 ), while biochemical assays confirmed increased auxin, chlorophyll, and antioxidant enzyme activities resulting in greater shoot and root biomass. Longitudinal monitoring demonstrated sustained rhizosphere colonization at the root apex and improved plant height and chlorophyll index over 90 days. These findings highlight DSF40-MOL5 as a cost-effective formulation enabling scalable Bacillus -based bioinoculants for sustainable maize production.

P1203 Spatial mapping and geographic variation of inflammatory bowel disease in Canada: A population-based study using Statistics Canada data

Journal of Crohn s and Colitis · 2025-01-01 · 1 citations

Abstract Background Crohn’s Disease (CD) and Ulcerative Colitis (UC) pose significant challenges to patients and healthcare systems, with a rising incidence and prevalence globally1,2. To address the challenges of health resource allocation and understand the geographic distribution of these conditions in Canada, we conducted the spatial mapping of IBD across Canada using national population survey data available from Statistics Canada. Methods We utilized data from the 2009-2018 Canadian Community Health Survey (CCHS) to identify individuals with CD or UC. Prevalence rates, both crude and adjusted for age and sex, were calculated for each health region in Canada. Spatial dependencies between health regions were estimated using global Moran’s I and local indicators of spatial association (LISA) were used to identify clusters of health region (hot-spots) where the prevalence was significantly higher than in other areas. We further applied spatial simultaneous autoregressive lag models to explore the influence of region-level sociodemographic factors on identified spatial dependencies. Results A total of 492,560 individuals from 2010-2018 CCHS were included, representing 29,846,350 Canadians across 109 health regions. Survey data revealed that 0.38% of Canadians self-reported having CD and 0.47% reported having UC. The majority of respondents reported being urban-residing, middle-aged, and white. Across Canadian provinces, the age and sex-standardized prevalence of IBD ranged from 742 per 100,000 in Quebec to 1267 per 100,000 in Nova Scotia (Figure 1). Spatial analysis identified significant dependencies among health regions, but these spatial associations were explained by the differing distributions of sociodemographic characteristics in each health region (Table 1). Increased health region-level prevalence of CD and UC was associated with a larger proportion of individuals 30+ years, identifying as a female, immigrants, or as white (p&amp;lt;0.05 for each). Conclusion Data from this large, population-based Canadian national survey demonstrated significant geographic variation in the prevalence of CD and UC. However, after adjusting for patient demographic characteristics, the spatial dependency became non-significant. Key characteristics related to urbanization including the age distribution and proportion of immigrants in a health region were associated with increased prevalence rates. These results suggest that differences in CD and UC prevalence between geographic areas are primarily driven by individual demographics rather than differences in characteristics of local healthcare delivery systems and further support the notion that characteristics of urbanization increase the prevalence of IBD in an area1. References 1.Ng et al., 2017. Doi: 10.1016/s0140-6736(17)32448-0 2.Coward et al., 2023. Doi: 10.1093/jcag/gwad004

Comparative Transcriptomic Analysis of <i>Zymoseptoria tritici</i> Reveals Interaction-Specific Gene Expression Patterns During Susceptible, Resistant, and Nonhost Interactions

Molecular Plant-Microbe Interactions · 2025-01-01

Zymoseptoria tritici causes Septoria tritici blotch, which significantly reduces yields of wheat. To investigate infection phase-specific gene expression in the pathogen, we analyzed gene expression during infection of susceptible and resistant wheat cultivars, as well as the nonhost species barley, at 1, 3, 6, 10, 17, and 23 days postinoculation (DPI). There were dramatic differences in pathogen gene expression at 10 DPI in the susceptible compared with both resistant interactions. The most pronounced differences in pathogen gene expression were observed at 3 DPI in both the susceptible and resistant host interactions compared with the nonhost. Thirty-one putative effectors showed early expression during the susceptible compared with the nonhost interaction; six were selected for subcellular localization studies. Using Agrobacterium-mediated transient expression in Nicotiana benthamiana, subcellular localization assays revealed that two candidate effectors localized to putative mobile cytosolic bodies when expressed without their signal peptides, suggesting potential roles in intracellular signaling or host gene regulation. When expressed with their signal peptides, four candidate effectors localized to the cytosol, whereas one did not accumulate to detectable levels. Comparison of pathogen gene expression in the susceptible host with expression in the resistant hosts identified genes expressed during the transition from biotrophic to necrotrophic growth at 10 DPI. Comparison of pathogen gene expression in resistant and susceptible hosts, versus in the nonhost barley, identified genes involved in initial colonization and host recognition. These results contribute to understanding candidate effectors that are activated early during infection and may play a role in the suppression of plant immunity. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Improved Gene Annotation of the Fungal Wheat Pathogen Zymoseptoria tritici Based on Combined Iso-Seq and RNA-Seq Evidence

Repository for Publications and Research Data (ETH Zurich) · 2025-11-01

Despite large omics datasets, the prediction of eukaryotic genes is still challenging. We have developed a new method to improve the prediction of eukaryotic genes and demonstrate its utility using the genome of the fungal wheat pathogen Zymoseptoria tritici. From 10,933 to 13,260 genes were predicted by four previous annotations, but only one third were identical. A novel bioinformatics suite, InGenAnnot, was developed to improve Z. tritici gene annotation using Iso-Seq full-length transcript sequences. The best gene models were selected among different ab initio gene predictions, according to transcript and protein evidence. Overall, 13,414 reannotated gene models (RGMs) were predicted, improving previous annotations. Iso-Seq transcripts outlined 5' and 3' untranslated regions for 73% of the RGMs and alternative transcripts mainly due to intron retention. Our results showed that the combination of different ab initio gene predictions and evidence-driven curation improved gene annotation of a eukaryotic genome. It also provided new insights into the transcriptional landscape of this fungus.

Improved Gene Annotation of the Fungal Wheat Pathogen <i>Zymoseptoria tritici</i> Based on Combined Iso-Seq and RNA-Seq Evidence

Molecular Plant-Microbe Interactions · 2025-01-01 · 7 citations

Despite large omics datasets, the prediction of eukaryotic genes is still challenging. We have developed a new method to improve the prediction of eukaryotic genes and demonstrate its utility using the genome of the fungal wheat pathogen Zymoseptoria tritici. From 10,933 to 13,260 genes were predicted by four previous annotations, but only one third were identical. A novel bioinformatics suite, InGenAnnot, was developed to improve Z. tritici gene annotation using Iso-Seq full-length transcript sequences. The best gene models were selected among different ab initio gene predictions, according to transcript and protein evidence. Overall, 13,414 reannotated gene models (RGMs) were predicted, improving previous annotations. Iso-Seq transcripts outlined 5′ and 3′ untranslated regions for 73% of the RGMs and alternative transcripts mainly due to intron retention. Our results showed that the combination of different ab initio gene predictions and evidence-driven curation improved gene annotation of a eukaryotic genome. It also provided new insights into the transcriptional landscape of this fungus. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .