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

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 representative P. nodorum isolates from Australia and South Africa. The presence of PE401 removed 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 wheat 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 complex NE-NE interaction that is occurring within the P. nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed.

Understanding the plant-pathogen interaction associated with Septoria nodorum blotch of wheat

This chapter discusses understanding the plant-pathogen interaction associated with septorium nodorum blotch of wheat. It begins by reviewing the necrotrophic effector-host sensitivity gene interactions in the wheat-P. nodorum system. It then reviews the genetic relationship between NE-sensitivity gene interactions and the importance of these interactions in the field. Additional QTL associated with susceptibility/resistance to P. nodorum is also discussed, followed by a section on the impact of genome sequencing in characterizing NE-sensitivity gene interactions.

Achievements in breeding cereals with durable disease resistance in Northwest Europe

Breeding cereals in Northwest Europe for durable resistance has made an important contribution to control of almost all economically significant diseases and pests of wheat, barley and oats. Durable resistance to fungal diseases is largely polygenic and quantitative, with the important exception of mlo resistance to powdery mildew of spring barley. Resistance to powdery mildew of winter wheat, spring barley and spring oats, brown rust of winter barley and Septoria nodorum blotch of wheat has been especially effective and durable. Resistance to Barley yellow mosaic virus and orange wheat blossom midge has used single genes which have so far been durable. Plant breeders are increasingly producing varieties with high or moderate resistance to all the most important diseases, and have successfully combined durable resistance with other traits which are important to farmers and end-users, including high yield, marketable grain quality and desirable agronomic properties.

Advances in genetic mapping of Septoria nodorum blotch resistance in wheat and applications in resistance breeding

Septoria nodorum blotch (SNB) caused by the necrotrophic fungus Parastagonospora nodorum is an important wheat disease in many high rainfall areas across the world. It reduces both yield and grain quality by causing symptoms on wheat leaves and glumes, and can cause yield losses up to 30% under warm and humid conditions. This book chapter gives an update on the recent progress in genetic mapping of SNB resistance in wheat, with focus on adult plant leaf blotch and glume blotch resistance with relevance to resistance breeding. This is followed by a case study on the investigation of the naturally occurring P. nodorum population in Norway and mapping of resistance loci in relevant wheat germplasm using MAGIC populations and GWAS panels as well as how this information can be used to improve resistance breeding and disease management. In the end, some future perspectives of SNB resistance breeding is provided.

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

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.

Evaluation of Septoria Nodorum Blotch (SNB) Resistance in Glumes of Wheat (Triticum aestivum L.) and the Genetic Relationship With Foliar Disease Response

Septoria nodorum blotch (SNB) is a necrotrophic disease of wheat prominent in some parts of the world, including Western Australia (WA) causing significant losses in grain yield. The genetic mechanisms for resistance are complex involving multiple quantitative trait loci. In order to decipher comparable or independent regulation, this study identified the genetic control for glume compared to foliar resistance across four environments in WA against 37 different isolates. High proportion of the phenotypic variation across environments was contributed by genotype (84.0% for glume response and 82.7% for foliar response) with genotype-by-environment interactions accounting for a proportion of the variation for both glume and foliar response (14.7 and 16.2%, respectively). Despite high phenotypic correlation across environments, most of the eight and 14 QTL detected for glume and foliar resistance using genome wide association analysis (GWAS), respectively, were identified as environment-specific. QTL for glume and foliar resistance neither co-located nor were in LD in any particular environment indicating autonomous genetic mechanisms control SNB response in adult plants, regulated by independent biological mechanisms and influenced by significant genotype-by- environment interactions. Known Snn and Tsn loci and QTL were compared with 22 environment-specific QTL. None of the eight QTL for glume or the 14 for foliar response were co-located or in linkage disequilibrium with Snn and only one foliar QTL was in LD with Tsn loci on the physical map. Therefore, glume and foliar response to SNB in wheat is regulated by multiple environment-specific loci which function independently, with limited influence of known NE-Snn interactions for disease progression in Western Australian environments. Breeding for stable resistance would consequently rely on recurrent phenotypic selection to capture and retain favorable alleles for both glume and foliar resistance relevant to a particular environment.

Genes Associated with Foliar Resistance to Septoria Nodorum Blotch of Hexaploid Wheat (Triticum aestivum L.)

The genetic control of host response to the fungal necrotrophic disease Septoria nodorum blotch (SNB) in bread wheat is complex, involving many minor genes. Quantitative trait loci (QTL) controlling SNB response were previously identified on chromosomes 1BS and 5BL. The aim of this study, therefore, was to align and compare the genetic map representing QTL interval on 1BS and 5BS with the reference sequence of wheat and identify resistance genes (R-genes) associated with SNB response. Alignment of QTL intervals identified significant genome rearrangements on 1BS between parents of the DH population EGA Blanco, Millewa and the reference sequence of Chinese Spring with subtle rearrangements on 5BL. Nevertheless, annotation of genomic intervals in the reference sequence were able to identify and map 13 and 12 R-genes on 1BS and 5BL, respectively. R-genes discriminated co-located QTL on 1BS into two distinct but linked loci. NRC1a and TFIID mapped in one QTL on 1BS whereas RGA and Snn1 mapped in the linked locus and all were associated with SNB resistance but in one environment only. Similarly, Tsn1 and WK35 were mapped in one QTL on 5BL with NETWORKED 1A and RGA genes mapped in the linked QTL interval. This study provided new insights on possible biochemical, cellular and molecular mechanisms responding to SNB infection in different environments and also addressed limitations of using the reference sequence to identify the full complement of functional R-genes in modern varieties.

GWAS analysis reveals distinct pathogenicity profiles of Australian Parastagonospora nodorum isolates and identification of marker-trait-associations to septoria nodorum blotch

The fungus Parastagonospora nodorum is the causal agent of septoria nodorum leaf blotch (SNB) and glume blotch which are common in many wheat growing regions in the world. The disease is complex and could be explained by multiple interactions between necrotrophic effectors secreted by the pathogen and matching susceptibility genes in wheat. An Australian P. nodorum population was clustered into five groups with contrasting properties. This study was set to identify their pathogenicity profiles using a diverse wheat panel of 134 accessions which are insensitive to SnToxA and SnTox1 in both in vitro and in vivo conditions. SNB seedling resistance/susceptibility to five representative isolates from the five clusters, responses to crude culture-filtrates (CFs) of three isolates and sensitivity to SnTox3 semi-purified effector together with 11,455 SNP markers have been used for linkage disequilibrium (LD) and association analyses. While quantitative trait loci (QTL) on 1D, 2A, 2B, 4B, 5B, 6A, 6B, 7A, 7D chromosomes were consistently detected across isolates and conditions, distinct patterns and isolate specific QTL were also observed among these isolates. In this study, SnTox3–Snn3-B1 interaction for the first time in Australia and SnTox3–Snn3-D1 interaction for the first time in bread wheat were found active using wild-type isolates. These findings could be due to new SnTox3 haplotype/isoform and exotic CIMMYT/ICARDA and Vavilov germplasm used, respectively. This study could provide useful information for dissecting novel and different SNB disease components, helping to prioritise research targets and contributing valuable information on genetic loci/markers for marker-assisted selection in SNB resistance wheat breeding programme.

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

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.

The Parastagonospora nodorum necrotrophic effector SnTox5 targets the wheat gene Snn5 and facilitates entry into the leaf mesophyll

Parastagonospora nodorum, causal agent of septoria nodorum blotch, is a destructive necrotrophic fungal pathogen of wheat. P. nodorum is known to secrete several necrotrophic effectors that target wheat susceptibility genes that trigger classical biotrophic resistance responses but resulting in susceptibility rather than resistance. SnTox5 targets the wheat susceptibility gene Snn5 to induce necrosis. In this study, we used full genome sequences of 197 P. nodorum isolates collected from the US and their disease phenotyping on the Snn5 differential line LP29, to perform genome wide association study analysis to localize the SnTox5 gene to chromosome 8 of P. nodorum. SnTox5 was validated using gene transformation and CRISPR-Cas9 based gene disruption. SnTox5 encoded a small secreted protein with a 22 and 45 amino acid secretion signal and a pro sequence, respectively. The SnTox5 gene is under purifying selection in the Upper Midwest but under strong diversifying selection in the South/East regions of the US. Comparison of wild type and SnTox5-disrupted strains on wheat lines with and without the susceptibility target Snn5 showed that SnTox5 has two functions, 1) facilitating colonization of the mesophyll layer, and 2) targeting Snn5 to induce programmed cell death to provide cellular nutrient to complete its necrotrophic life cycle.