Parastagonospora nodorum and Related Species in Western Canada: Genetic Variability and Effector Genes

Parastagonospora nodorum is an important fungal pathogen that causes Septoria nodorum blotch (SNB) in wheat. This pathogen produces several necrotrophic effectors that act as virulence factors; three have been cloned, SnToxA, SnTox1, and SnTox3. In this study, P. nodorum and its sister species P. avenaria f. tritici (Pat1) were isolated from wheat node and grain samples collected from distanced sites in western Canada during 2018. The presence of effector genes and associated haplotypes were determined by PCR and sequence analysis. An internal transcribed spacer-restriction fragment length polymorphism test was developed to distinguish between leaf spotting pathogens (P. nodorum, Pat1, Pyrenophora tritici-repentis, and Bipolaris sorokiniana). P. nodorum was mainly recovered from wheat nodes and to a lesser extent from the grains, while Pat1 was exclusively isolated from grain samples. The effector genes were present in almost all P. nodorum isolates, with the ToxA haplotype 5 (H5) being most prevalent, while a novel ToxA haplotype (denoted here H21) is reported for the first time. In Pat1, only combinations of SnTox1 and SnTox3 genes were present. A ToxA haplotype network was also constructed to assess the evolutionary relationship among globally found haplotypes to date. Finally, cultivars representing wheat development in Canada for the last century were tested for sensitivity to Sn-effectors and to the presence of Tsn1, the ToxA sensitivity gene. Of tested cultivars, 32.9 and 56.9% were sensitive to SnTox1 and SnTox3, respectively, and Tsn1 was present in 59% of the cultivars. In conclusion, P. nodorum and Pat1 were prevalent wheat pathogens in Canada with a potential tissue-specific colonization capacity, while producing necrotrophic effectors to which wheat is sensitive.

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SnToxA, SnTox1 and SnTox3 originated in Parastagonospora nodorum in the Fertile Crescent

10.1101/2020.03.11.987214 ◽

2020 ◽

Author(s):

Fariba Ghaderi ◽

Bahram Sharifnabi ◽

Mohammad Javan-Nikkhah ◽

Patrick C. Brunner ◽

Bruce A. McDonald

Keyword(s):

Spatial Scales ◽

Bipolaris Sorokiniana ◽

Center Of Origin ◽

Pyrenophora Tritici Repentis ◽

Effector Genes ◽

A Genome ◽

Fertile Crescent ◽

Genes Encoding ◽

Parastagonospora Nodorum ◽

Necrotrophic Effectors

ABSTRACTThe center of origin of the globally distributed wheat pathogen Parastagnospora nodorum has remained uncertain because only a small number of isolates from the Fertile Crescent, a region in the Middle East where wheat was domesticated from wild grasses, were included in earlier population genetic and phylogeographic studies. We isolated and genetically analyzed 193 P. nodorum strains from three naturally infected wheat fields distributed across Iran, a country located within the Fertile Crescent, using eleven neutral microsatellite loci. Compared to previous studies that included populations from North America, Europe, Africa, Australia and China, the populations from Iran had the highest genetic diversity globally and also exhibited greater population structure over smaller spatial scales, patterns typically associated with a species’ center of origin. Genes encoding the necrotrophic effectors SnToxA, SnTox1 and SnTox3 were found at a high frequency in the Iranian population. By sequencing 96 randomly chosen Iranian strains, we detected new alleles for all three effector genes. Analyses of allele diversity showed that all three effector genes had higher diversity in Iran than in any population included in previous studies, with Iran acting as a hub for the effector diversity that was found in other global populations. Taken together, these findings support the hypothesis that P. nodorum originated either within or nearby the Fertile Crescent with a genome that already encoded all three necrotrophic effectors during its emergence as a pathogen on wheat. Our findings also suggest that P. nodorum was the original source of the ToxA genes discovered in the wheat pathogens Phaeosphaeria avenaria f. sp. tritici 1, Pyrenophora tritici-repentis and Bipolaris sorokiniana.

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Sensitivity genes in wheat and corresponding effector genes in necrotrophs exhibiting inverse gene-for-gene relationship

10.21203/rs.3.rs-223024/v1 ◽

2021 ◽

Author(s):

Pushpendra Kumar Gupta ◽

Neeraj Kumar Vasistha ◽

Pawan Kumar Singh

Keyword(s):

Bipolaris Sorokiniana ◽

Relevant Information ◽

Tan Spot ◽

Future Research ◽

Disease Symptoms ◽

Septoria Nodorum Blotch ◽

Effector Genes ◽

Necrotrophic Effectors ◽

S Genes ◽

Gene For Gene

Abstract In wheat, genes for resistance (R) as well as susceptibility (S) are now known for several diseases. The S genes also include sensitivity genes like Tsn1 in wheat. R genes follow a gene-for-gene (GFG) relationship and generally involve biotrophs and S genes particularly sensitivity genes, follow an inverse gene-for-gene relationship (IGFG), generally involving necrotroph or hemi-biotroph pathogens. The toxin (virulence factor) genes of the pathogen and the corresponding sensitivity genes have been described in some detail for the following three pathogens: (i) Paratagonospora nodorum (causing Septoria nodorum blotch or SNB); (ii) Pyrenophora tritici-repentis (tan spot) and (iii) Bipolaris sorokiniana (spot blotch). These and some other pathogens produce several necrotrophic effectors (NEs), which interact directly or indirectly with the products of S genes in the host and produce disease symptoms like necrosis and/or chlorosis. In this article we present a critical review of all the relevant information about the interactions between NEs of the above three pathogens and the corresponding S genes in wheat. The gaps in knowledge and possibilities for future research are also discussed.

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Sensitivity to three Parastagonospora nodorum necrotrophic effectors in current Australian wheat cultivars and the presence of further fungal effectors

Crop and Pasture Science ◽

10.1071/cp13443 ◽

2014 ◽

Vol 65 (2) ◽

pp. 150 ◽

Cited By ~ 20

Author(s):

Kar-Chun Tan ◽

Ormonde D. C. Waters ◽

Kasia Rybak ◽

Eva Antoni ◽

Eiko Furuki ◽

...

Keyword(s):

Fungal Pathogen ◽

Gene Interactions ◽

Wheat Cultivars ◽

Septoria Nodorum Blotch ◽

Effector Genes ◽

Australian Wheat ◽

Parastagonospora Nodorum ◽

Necrotrophic Effector ◽

Necrotrophic Effectors ◽

Western Australian

Parastagonospora nodorum is a major fungal pathogen of wheat in Australia, causing septoria nodorum blotch (SNB). Virulence of P. nodorum is quantitative and depends largely on multiple effector–host sensitivity gene interactions. The pathogen utilises a series of proteinaceous, necrotrophic effectors to facilitate disease development on wheat cultivars that possess appropriate dominant sensitivity loci. Thus far, three necrotrophic effector genes have been cloned. Proteins derived from these genes were used to identify wheat cultivars that confer effector sensitivity. The goal of this study was to determine whether effector sensitivity could be used to enhance breeding for SNB resistance. We have demonstrated that SnTox1 effector sensitivity is common in current commercial Western Australian wheat cultivars. Thirty-three of 46 cultivars showed evidence of sensitivity to SnTox1. Of these, 19 showed moderate or strong chlorotic/necrotic responses to SnTox1. Thirteen were completely insensitive to SnTox1. Disease susceptibility was most closely associated with SnTox3 sensitivity. We have also identified biochemical evidence of a novel chlorosis-inducing protein or proteins in P. nodorum culture filtrates unmasked in strains that lack expression of ToxA, SnTox1 and SnTox3 activities.

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New Insights into the Roles of Host Gene-Necrotrophic Effector Interactions in Governing Susceptibility of Durum Wheat to Tan Spot and Septoria nodorum Blotch

G3 Genes|Genome|Genetics ◽

10.1534/g3.116.036525 ◽

2016 ◽

Vol 6 (12) ◽

pp. 4139-4150 ◽

Cited By ~ 19

Author(s):

Simerjot K Virdi ◽

Zhaohui Liu ◽

Megan E Overlander ◽

Zengcui Zhang ◽

Steven S Xu ◽

...

Keyword(s):

Durum Wheat ◽

Common Wheat ◽

Tan Spot ◽

Septoria Nodorum ◽

Pyrenophora Tritici Repentis ◽

Septoria Nodorum Blotch ◽

Necrotrophic Fungi ◽

Host Genetic ◽

Parastagonospora Nodorum ◽

Necrotrophic Effector

Abstract Tan spot and Septoria nodorum blotch (SNB) are important diseases of wheat caused by the necrotrophic fungi Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively. The P. tritici-repentis necrotrophic effector (NE) Ptr ToxB causes tan spot when recognized by the Tsc2 gene. The NE ToxA is produced by both pathogens and has been associated with the development of both tan spot and SNB when recognized by the wheat Tsn1 gene. Most work to study these interactions has been conducted in common wheat, but little has been done in durum wheat. Here, quantitative trait loci (QTL) analysis of a segregating biparental population indicated that the Tsc2-Ptr ToxB interaction plays a prominent role in the development of tan spot in durum. However, analysis of two biparental populations indicated that the Tsn1-ToxA interaction was not associated with the development of tan spot, but was strongly associated with the development of SNB. Pa. nodorum expressed ToxA at high levels in infected Tsn1 plants, whereas ToxA expression in P. tritici-repentis was barely detectable, suggesting that the differences in disease levels associated with the Tsn1-ToxA interaction were due to differences in pathogen expression of ToxA. These and previous results together indicate that: (1) the effects of Tsn1-ToxA on tan spot in common wheat can range from nonsignificant to highly significant depending on the host genetic background; (2) Tsn1-ToxA is not a significant factor for tan spot development in durum wheat; and (3) Tsn1-ToxA plays a major role in SNB development in both common and durum wheat. Durum and common wheat breeders alike should strive to remove both Tsc2 and Tsn1 from their materials to achieve disease resistance.

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Identification and Characterization of the SnTox6-Snn6 Interaction in the Parastagonospora nodorum–Wheat Pathosystem

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-12-14-0396-r ◽

2015 ◽

Vol 28 (5) ◽

pp. 615-625 ◽

Cited By ~ 35

Author(s):

Y. Gao ◽

J. D. Faris ◽

Z. Liu ◽

Y. M. Kim ◽

R. A. Syme ◽

...

Keyword(s):

Disease Development ◽

Host Interaction ◽

Septoria Nodorum Blotch ◽

Polymerase Chain ◽

Trait Locus ◽

Parastagonospora Nodorum ◽

Wheat Lines ◽

Necrotrophic Effectors ◽

Sensitivity Gene

Parastagonospora nodorum is a necrotrophic fungal pathogen that causes Septoria nodorum blotch (SNB) (formerly Stagonospora nodorum blotch) on wheat. P. nodorum produces necrotrophic effectors (NE) that are recognized by dominant host sensitivity gene products resulting in disease development. The NE–host interaction is critical to inducing NE-triggered susceptibility (NETS). To date, seven NE–host sensitivity gene interactions, following an inverse gene-for-gene model, have been identified in the P. nodorum–wheat pathosystem. Here, we used a wheat mapping population that segregated for sensitivity to two previously characterized interactions (SnTox1-Snn1 and SnTox3-Snn3-B1) to identify and characterize a new interaction involving the NE designated SnTox6 and the host sensitivity gene designated Snn6. SnTox6 is a small secreted protein that induces necrosis on wheat lines harboring Snn6. Sensitivity to SnTox6, conferred by Snn6, was light-dependent and was shown to underlie a major disease susceptibility quantitative trait locus (QTL). No other QTL were identified, even though the P. nodorum isolate used in this study harbored both the SnTox1 and SnTox3 genes. Reverse transcription-polymerase chain reaction showed that the expression of SnTox1 was not detectable, whereas SnTox3 was expressed and, yet, did not play a significant role in disease development. This work expands our knowledge of the wheat–P. nodorum interaction and further establishes this system as a model for necrotrophic specialist pathosystems.

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Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat

10.1101/2021.07.28.454099 ◽

2021 ◽

Author(s):

Evan John ◽

Silke Jacques ◽

Huyen Phan ◽

Lifang Liu ◽

Danilo Pereira ◽

...

Keyword(s):

Regulatory Region ◽

Gene Promoter ◽

Epistatic Effect ◽

Start Codon ◽

Septoria Nodorum Blotch ◽

Trait Locus ◽

Repressor Molecule ◽

Wheat Leaves ◽

Parastagonospora Nodorum ◽

Necrotrophic Effectors

The fungus Parastagonospora nodorum uses proteinaceous necrotrophic effectors (NEs) to induce tissue necrosis on wheat leaves during infection, leading to the symptoms of septoria nodorum blotch (SNB). The NEs Tox1 and Tox3 induce necrosis on wheat possessing the dominant susceptibility genes Snn1 and Snn3B1/Snn3D1, respectively. We previously observed that Tox1 is epistatic to the expression of Tox3 and a quantitative trait locus (QTL) on chromosome 2A that contributes to SNB resistance/susceptibility. The expression of Tox1 is significantly higher in the Australian strain SN15 compared to the American strain SN4. Inspection of the Tox1 promoter region revealed a 401 bp promoter genetic element in SN4 positioned 267 bp upstream of the start codon that is absent in SN15, called PE401. Analysis of the world-wide P. nodorum population revealed that a high proportion of Northern Hemisphere isolates possess PE401 whereas the opposite was observed in the Southern Hemisphere. The presence of PE401 ablates the epistatic effect of Tox1 on the contribution of the SNB 2A QTL but not Tox3. PE401 was introduced into the Tox1 promoter regulatory region in SN15 to test for direct regulatory roles. Tox1 expression was markedly reduced in the presence of PE401. This suggests a repressor molecule(s) binds PE401 and inhibits Tox1 transcription. Infection assays also demonstrated that P. nodorum which lacks PE401 is more pathogenic on Snn1 varieties than P. nodorum carrying PE401. An infection competition assay between P. nodorum isogenic strains with and without PE401 indicated that the higher Tox1-expressing strain rescued the reduced virulence of the lower Tox1-expressing strain on Snn1 wheat. Our study demonstrated that Tox1 exhibits both selfish and altruistic characteristics. This offers an insight into a NE arms race that is occurring within the P. nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed.

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ToxA–Tsn1 Interaction for Spot Blotch Susceptibility in Indian Wheat: An Example of Inverse Gene-for-Gene Relationship

Plant Disease ◽

10.1094/pdis-05-19-1066-re ◽

2020 ◽

Vol 104 (1) ◽

pp. 71-81 ◽

Cited By ~ 6

Author(s):

Sudhir Navathe ◽

Punam Singh Yadav ◽

Ramesh Chand ◽

Vinod Kumar Mishra ◽

Neeraj Kumar Vasistha ◽

...

Keyword(s):

Fungal Pathogens ◽

Bipolaris Sorokiniana ◽

Spot Blotch ◽

Wheat Cultivars ◽

Pyrenophora Tritici Repentis ◽

Necrotic Spots ◽

Parastagonospora Nodorum ◽

Necrotrophic Effector ◽

Selection Of ◽

Gene For Gene

The ToxA–Tsn1 system is an example of an inverse gene-for-gene relationship. The gene ToxA encodes a host-selective toxin (HST) which functions as a necrotrophic effector and is often responsible for the virulence of the pathogen. The genomes of several fungal pathogens (e.g., Pyrenophora tritici-repentis, Parastagonospora nodorum, and Bipolaris sorokiniana) have been shown to carry the ToxA gene. Tsn1 is a sensitivity gene in the host, whose presence generally helps a ToxA-positive pathogen to cause spot blotch in wheat. Cultivars lacking Tsn1 are generally resistant to spot blotch; this resistance is attributed to a number of other known genes which impart resistance in the absence of Tsn1. In the present study, 110 isolates of B. sorokiniana strains, collected from the ME5A and ME4C megaenvironments of India, were screened for the presence of the ToxA gene; 77 (70%) were found to be ToxA positive. Similarly, 220 Indian wheat cultivars were screened for the presence of the Tsn1 gene; 81 (36.8%) were found to be Tsn1 positive. When 20 wheat cultivars (11 with Tsn1 and 9 with tsn1) were inoculated with ToxA-positive isolates, seedlings of only those carrying the Tsn1 allele (not tsn1) developed necrotic spots surrounded by a chlorotic halo. No such distinction between Tsn1 and tsn1 carriers was observed when adult plants were inoculated. This study suggests that the absence of Tsn1 facilitated resistance against spot blotch of wheat. Therefore, the selection of wheat genotypes for the absence of the Tsn1 allele can improve resistance to spot blotch.

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ToxA Is Present in the U.S. Bipolaris sorokiniana Population and Is a Significant Virulence Factor on Wheat Harboring Tsn1

Plant Disease ◽

10.1094/pdis-03-18-0521-re ◽

2018 ◽

Vol 102 (12) ◽

pp. 2446-2452 ◽

Cited By ~ 16

Author(s):

T. L. Friesen ◽

D. J. Holmes ◽

R. L. Bowden ◽

J. D. Faris

Keyword(s):

Winter Wheat ◽

Bipolaris Sorokiniana ◽

Selective Advantage ◽

The United States ◽

Tan Spot ◽

Single Spore ◽

Pyrenophora Tritici Repentis ◽

Culture Filtrates ◽

Parastagonospora Nodorum ◽

Mutant Lines

ToxA, a necrotrophic effector originally identified from the tan spot fungus Pyrenophora tritici-repentis in 1987, was subsequently identified from Parastagonospora nodorum in 2006. More recently, the ToxA gene was identified in the spot blotch fungus Bipolaris sorokiniana in Australia. Here we show that the ToxA gene is also present in the B. sorokiniana population in the winter wheat region of southcentral Texas. Leaves from ‘Duster’ wheat showing strong necrotic lesions were collected in Castroville, TX. Fifteen single-spore isolates were collected from separate lesions, and 13 of them harbored the BsToxA gene and secreted ToxA in culture based on sensitivity of BG261, the differential line containing the dominant ToxA sensitivity gene, Tsn1. Four isolates harboring BsToxA and one deficient in BsToxA were used to infiltrate two wheat lines harboring Tsn1 as well as their corresponding tsn1 mutant lines. Culture filtrates of the isolate lacking BsToxA did not induce necrosis on any of the lines. Culture filtrates of the four BsToxA-containing isolates induced necrosis on the wild type (Tsn1) lines but not on the corresponding tsn1 mutant lines. Sensitivity to these culture filtrates also mapped to the previously identified location for Tsn1 in the winter wheat mapping population Arina × Forno. Inoculation of one of these ToxA-producing isolates on the same population showed that the Tsn1 locus accounted for 24.4% of the disease variation. All 13 isolates harbored the same BsToxA nucleotide sequence, which was identical to one of the two haplotypes previously identified in Australia. Sensitivity to ToxA is prevalent in popular hard winter wheat cultivars in the central and southcentral winter wheat regions of the United States, showing the potential of a selective advantage for B. sorokiniana isolates that harbor the ToxA gene.

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Co-infection of wheat by Pyrenophora tritici-repentis and Parastagonospora nodorum in the wheatbelt of Western Australia

Crop and Pasture Science ◽

10.1071/cp19412 ◽

2020 ◽

Vol 71 (2) ◽

pp. 119

Author(s):

Araz S. Abdullah ◽

Mark R. Gibberd ◽

John Hamblin

Keyword(s):

Empirical Studies ◽

Triticum Aestivum L ◽

Fungal Species ◽

Tan Spot ◽

Robust Methods ◽

Pyrenophora Tritici Repentis ◽

Septoria Nodorum Blotch ◽

Fungal Abundance ◽

Wheat Leaves ◽

Parastagonospora Nodorum

The pathogenic fungal species Pyrenophora tritici-repentis (Ptr) and Parastagonospora nodorum (Pan) are common in many wheat-producing parts of the world. These two fungi cause tan spot and septoria nodorum blotch, respectively, frequently co-infecting wheat leaves. Empirical studies of this and other co-infections are rare because of the visual similarity of symptoms and the lack of robust methods for quantifying the abundance of pathogens associated with the co-infection. Here, we use a recently developed molecular method that simultaneously distinguishes and quantifies, in DNA equivalent, the abundance of Ptr and Pan, thereby allowing the prevalence of co-infection to be determined. The study examines the prevalence of co-infection under field conditions, at three widely spaced sites and on three wheat (Triticum aestivum L.) cultivars varying in disease resistance. Co-infection by Ptr and Pan was almost ubiquitous (overall prevalence 94%), and Pan DNA was detected only in association with Ptr. Although Ptr and Pan commonly co-infected, Ptr was more abundant during early and mid-season, at 80% of total fungal abundance when crops were tillering and 67% at booting stage. Pan became as abundant as Ptr when crops reached flowering. Variability in total fungal abundance and disease severity was primarily determined by cultivar; however, Ptr was the more abundant despite differences in cultivar resistance to this pathogen.

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

Pathogens ◽

10.3390/pathogens7030074 ◽

2018 ◽

Vol 7 (3) ◽

pp. 74 ◽

Cited By ~ 2

Author(s):

Jingwei Guo ◽

Gongjun Shi ◽

Zhaohui Liu

Keyword(s):

Triticum Aestivum L ◽

Tan Spot ◽

Pyrenophora Tritici Repentis ◽

Tan Spot Disease ◽

Hard Red Winter Wheat ◽

Winter Wheat Cultivars ◽

Race 2 ◽

Genomic Regions ◽

Race 4 ◽

Necrotrophic Effectors

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.

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