Identification and Genomic Analysis of Stagonospora Nodorum Blotch Susceptibility Genes in Wheat

Parastagonospora nodorum is a necrotrophic fungal pathogen that causes the disease Stagonospora nodorum blotch (SNB) on wheat. The fungus produces necrotrophic effectors (NEs), that when recognized by corresponding host genes, cause cell death leading to disease. A novel NE, designated SnTox7, was identified from culture filtrates of isolate Sn6 of P. nodorum. SnTox7 is a small protein with estimated size less than 30 kDa. The interaction between SnTox7 and its corresponding host sensitivity gene, Snn7, explained 33% of the disease variation among a segregating F2 population. The Snn7 gene governs sensitivity to SnTox7 and was delineated to a 2.7 cM interval on the long arm of wheat chromosome 2D. Another host sensitivity gene Snn3- B1, conferring sensitivity to SnTox3, was previously mapped on the short arm of wheat chromosome 5B. Forty-four molecular markers were added to the genetic map to saturate the Snn3-B1 gene region. High-resolution mapping of the Snn3-B1 locus in 5,600 gametes delineated the gene to a 1.5 cM interval. The closely linked markers should be very useful for marker-assisted selection against Snn3-B1. A third host gene, Snn1, confers sensitivity to the NE Tox1. Snn1 was isolated through map-based cloning, and its structure, expression and allelic diversity were further characterized. A bacterial artificial chromosome (BAC) contig of about 2.5 Mb in size was identified to span the Snn1 locus through screening of Chinese Spring chromosome arm 1BS minimum tiling path (MTP) pools. Additional markers developed from BAC end sequences (BESs) delineated the Snn1 gene to a physical segment consisting of four BAC clones. Sequencing and bioinformatic analysis of these clones led to the identification of seven candidate genes. Six of the seven candidates were excluded through critical recombinants. The seventh gene, a cell wall-associated kinase (WAK), was verified as Snn1 through comparative sequence analysis with ethylmethane sulfonate (EMS)-induced mutants. The Snn1 transcription profile showed that it was regulated by light and possibly circadian rhythms. These results demonstrate that P. nodorum can hijack multiple host pathways driven by different classes of genes that typically confer resistance to biotrophic pathogens, thus demonstrating the surprisingly intricate nature of plant-necrotrophic pathogen interactions

Identification and Genomic Analysis of Stagonospora Nodorum Blotch Susceptibility Genes in Wheat

Video summarizing Ph.D. dissertation for a non-specialist audience.Genomics and BioinformaticsPlant SciencesCollege of Agriculture, Food Systems and Natural Resource

Characterizing Virulence of the Pyrenophora tritici-repentis Isolates Lacking Both ToxA and ToxB Genes

The fungus Pyrenophora tritici-repentis (Ptr) causes tan spot of wheat crops, which is an important disease worldwide. Based on the production of the three known necrotrophic effectors (NEs), the fungal isolates are classified into eight races with race 4 producing no known NEs. From a laboratory cross between 86–124 (race 2 carrying the ToxA gene for the production of Ptr ToxA) and DW5 (race 5 carrying the ToxB gene for the production of Ptr ToxB), we have obtained some Ptr isolates lacking both the ToxA and ToxB genes, which, by definition, should be classified as race 4. In this work, we characterized virulence of two of these isolates called B16 and B17 by inoculating them onto various common wheat (Triticum aestivum L.) and durum (T. turgidum L.) genotypes. It was found that the two isolates still caused disease on some genotypes of both common and durum wheat. Disease evaluations were also conducted in recombinant inbred line populations derived from two hard red winter wheat cultivars: Harry and Wesley. QTL mapping in this population revealed that three genomic regions were significantly associated with disease, which are different from the three known NE sensitivity loci. This result further indicates the existence of other NE-host sensitivity gene interactions in the wheat tan spot disease system

Quantitative interactions:The disease outcome of Botrytis cinerea across the plant kingdom

Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host resistance or pathogen virulence. However, the specific interactions between host and pathogen account for 16% of the disease outcome. Furthermore, the disease outcomes cluster among genotypes of a species but are independent of the relatedness between hosts. When analyzing the host specificity and virulence of B. cinerea, generalist strains are predominant. In this fungal necrotroph, specialization may happen by a loss in virulence on most hosts rather than an increase of virulence on a specific host. To uncover the genetic architecture of Botrytis host specificity and virulence, a genome-wide association study (GWAS) was performed and revealed up to 1492 genes of interest. The genetic architecture of these traits is widespread across B. cinerea genome. The complexity of the disease outcome might be explained by hundreds of functionally diverse genes putatively involved in adjusting the infection to diverse hosts.Accession list = all plant genotypes. isolate host origin = list of isolates with info. SNP data = SNP matrix for B. cinerea strains used for GWAS. LSmean files = least-square means of lesion area in either the column or row format to do plotting and linear modeling. Full meta data = all lesion area data. Lmer = full results of the linear mixed models for each of the 7 crops. Rnotebook = explanation on the R pipelines and associated R codes. Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: IOS1339125Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: IOS1021861This study is based on a collection of 98 strains of Botrytis cinerea that samples fourteen plant hosts and to a smaller degree geographical origins. We generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants, resulting in a dataset of 51,920 visible lesions at 72hpi. Least-square means and linear modeling was applied. GWAS was performed to assess the genetic architecture in Botrytis

A conserved hypothetical gene is required but not sufficient for Ptr ToxC production in Pyrenophora tritici-repentis.

The fungus Pyrenophora tritici-repentis (Ptr) causes tan spot, an important foliar disease of wheat worldwide. The fungal pathogen produce three necrotrophic effectors, namely Ptr ToxA, Ptr ToxB and Ptr ToxC to induce necrosis or chlorosis in wheat. Both Ptr ToxA and Ptr ToxB are proteins, and their encoding genes have been cloned. Ptr ToxC was characterized as a low-molecular-weight molecule 20 years ago but the gene(s) controlling its production in Ptr are unknown. Here, we report the genetic mapping, molecular cloning and functional analysis of a fungal gene that is required for Ptr ToxC production. The genetic locus controlling the production of Ptr ToxC, termed as ToxC, was mapped to a subtelomeric region using segregating bi-parental populations, genome sequencing, and association analysis. Additional marker analysis further delimited ToxC to a 173 kb region. The predicted genes in the region were examined for presence/absence polymorphism in different races/isolates leading to the identification of a single candidate gene. Functional validation showed that this gene was required but not sufficient for Ptr ToxC production, thus it is designated as ToxC1. ToxC1 encoded a conserved hypothetical protein likely located on the vacuole membrane. The gene was highly expressed during infection, and only one haplotype was identified among 120 isolates sequenced. Our work suggests that Ptr ToxC is not a protein and is likely produced through a cascade of biosynthetic pathway. The identification of ToxC1 is a major first step towards revealing the Ptr ToxC biosynthetic pathway and studying its molecular interactions with host factors