Identification of a locus conferring dominant susceptibility to Pyrenophora tritici-repentis in barley

The fungus Pyrenophora tritici-repentis (Ptr) causes tan spot, a destructive foliar disease of wheat worldwide. The pathogen produces several necrotrophic effectors, which induce necrosis or chlorosis on susceptible wheat lines. Multiple races of Ptr have been identified, based on their ability to produce one or more of these effectors. Ptr has a wide host range of cereal and non-cereal grasses, but is known to cause damage only on wheat. Previously, we showed that Ptr can interact specifically with cultivated barley (Hordeum vulgare ssp. vulgare), and that the necrotrophic effector Ptr ToxB induces mild chlorosis in a highly selective manner when infiltrated into certain barley genotypes. In the present study, a barley doubled-haploid (DH) population was evaluated for reaction to Ptr race 5, a Ptr ToxB-producer. Then a comprehensive genetic map composed of 381 single nucleotide polymorphism (SNP) markers was used to map the locus conditioning this chlorosis. The F1 seedlings, and 92 DH lines derived from a cross between the resistant Japanese malting barley cultivar Haruna Nijo and the susceptible wild barley (H. vulgare ssp. spontaneum) OUH602 were inoculated with a conidial suspension of Ptr race 5 isolate at the two-leaf stage. The seedlings were monitored daily for symptoms and assessed for chlorosis development on the second leaf, 6 days after inoculation. All tested F1 seedlings exhibited chlorosis symptoms similar to the susceptible parent, and the DH lines segregated 1:1 for susceptible:resistant phenotypes, indicating the involvement of a single locus. Marker-trait linkage analysis based on interval mapping identified a single locus on the distal region of the short arm of chromosome 2H. We designate this locus Susceptibility to P. tritici-repentis1 (Spr1). The region encompassing this locus has 99 high confidence gene models, including membrane receptor-like kinases (RLKs), intracellular nucleotide-binding, leucine-rich repeat receptors (NLRs), and ankyrin-repeat proteins (ANKs). This shows the involvement of a dominant locus conferring susceptibility to Ptr in barley. Further work using high-resolution mapping and transgenic complementation will be required to identify the underlying gene

The pangenome of the wheat pathogen <i>Pyrenophora tritici-repentis</i> reveals novel transposons associated with necrotrophic effectors <i>ToxA</i> and <i>ToxB</i>

BACKGROUND: In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements. RESULTS: A comparative genome analysis revealed an open pangenome, with an abundance of accessory genes (~ 57%) reflecting Ptr’s adaptability. A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated in this work in addition to previously assembled genomes. We also discovered the involvement of large mobile elements associated with Ptr’s effectors: ToxA, the gene encoding for the necrosis effector, was found as a single copy within a 143-kb ‘Starship’ transposon (dubbed ‘Horizon’) with a clearly defined target site and target site duplications. ‘Horizon’ was located on different chromosomes in different isolates, indicating mobility, and the previously described ToxhAT transposon (responsible for horizontal transfer of ToxA) was nested within this newly identified Starship. Additionally, ToxB, the gene encoding the chlorosis effector, was clustered as three copies on a 294-kb element, which is likely a different putative ‘Starship’ (dubbed ‘Icarus’) in a ToxB-producing isolate. ToxB and its putative transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and ‘Icarus’ were both present in a different non-coding isolate. This suggests that ToxB may have been mobile at some point during the evolution of the Ptr genome which is contradictory to the current assumption of ToxB vertical inheritance. Finally, the genome architecture of Ptr was defined as ‘one-compartment’ based on calculated gene distances and evolutionary rates. CONCLUSIONS: These findings together reflect on the highly plastic nature of the Ptr genome which has likely helped to drive its worldwide adaptation and has illuminated the involvement of giant transposons in facilitating the evolution of virulence in Ptr. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-022-01433-w

Genomic Prediction Accuracy of Stripe Rust in Six Spring Wheat Populations by Modeling Genotype by Environment Interaction

Some previous studies have assessed the predictive ability of genome-wide selection on stripe (yellow) rust resistance in wheat, but the effect of genotype by environment interaction (GEI) in prediction accuracies has not been well studied in diverse genetic backgrounds. Here, we compared the predictive ability of a model based on phenotypic data only (M1), the main effect of phenotype and molecular markers (M2), and a model that incorporated GEI (M3) using three cross-validations (CV1, CV2, and CV0) scenarios of interest to breeders in six spring wheat populations. Each population was evaluated at three to eight field nurseries and genotyped with either the DArTseq technology or the wheat 90K single nucleotide polymorphism arrays, of which a subset of 1,058- 23,795 polymorphic markers were used for the analyses. In the CV1 scenario, the mean prediction accuracies of the M1, M2, and M3 models across the six populations varied from 0.11 to 0.07, from 0.22 to 0.49, and from 0.19 to 0.48, respectively. Mean accuracies obtained using the M3 model in the CV1 scenario were significantly greater than the M2 model in two populations, the same in three populations, and smaller in one population. In both the CV2 and CV0 scenarios, the mean prediction accuracies of the three models varied from 0.53 to 0.84 and were not significantly different in all populations, except the Attila/CDC Go in the CV2, where the M3 model gave greater accuracy than both the M1 and M2 models. Overall, the M3 model increased prediction accuracies in some populations by up to 12.4% and decreased accuracy in others by up to 17.4%, demonstrating inconsistent results among genetic backgrounds that require considering each population separately. This is the first comprehensive genome-wide prediction study that investigated details of the effect of GEI on stripe rust resistance across diverse spring wheat populations

Identification of Disease Resistance Parents and Genome-Wide Association Mapping of Resistance in Spring Wheat

The likelihood of success in developing modern cultivars depend on multiple factors, including the identification of suitable parents to initiate new crosses, and characterizations of genomic regions associated with target traits. The objectives of the present study were to (a) determine the best economic weights of four major wheat diseases (leaf spot, common bunt, leaf rust, and stripe rust) and grain yield for multi-trait restrictive linear phenotypic selection index (RLPSI), (b) select the top 10% cultivars and lines (hereafter referred as genotypes) with better resistance to combinations of the four diseases and acceptable grain yield as potential parents, and (c) map genomic regions associated with resistance to each disease using genome-wide association study (GWAS). A diversity panel of 196 spring wheat genotypes was evaluated for their reaction to stripe rust at eight environments, leaf rust at four environments, leaf spot at three environments, common bunt at two environments, and grain yield at five environments. The panel was genotyped with the Wheat 90K SNP array and a few KASP SNPs of which we used 23,342 markers for statistical analyses. The RLPSI analysis performed by restricting the expected genetic gain for yield displayed significant (p \u3c 0.05) differences among the 3125 economic weights. Using the best four economic weights, a subset of 22 of the 196 genotypes were selected as potential parents with resistance to the four diseases and acceptable grain yield. GWAS identified 37 genomic regions, which included 12 for common bunt, 13 for leaf rust, 5 for stripe rust, and 7 for leaf spot. Each genomic region explained from 6.6 to 16.9% and together accounted for 39.4% of the stripe rust, 49.1% of the leaf spot, 94.0% of the leaf rust, and 97.9% of the common bunt phenotypic variance combined across all environments. Results from this study provide valuable information for wheat breeders selecting parental combinations for new crosses to develop improved germplasm with enhanced resistance to the four diseases as well as the physical positions of genomic regions that confer resistance, which facilitates direct comparisons for independent mapping studies in the future

Influence of nitrogen sources on growth and mycotoxin production by isolates of Pyrenophora tritici-repentis from wheat

The fungus Pyrenophora tritici-repentis (Died.) Drechs. infects the leaves and kernels of wheat, causing tan spot and red smudge, respectively. Isolates of P. tritici-repentis have been reported to be both phytopathogenic and mycotoxigenic. This research investigates the influence of nitrogen sources on growth and production of mycotoxins by eight different isolates of P. tritici-repentis. A synthetic agar medium (SAM) was used with different nitrogen sources, both inorganic [(NH4Cl, NH4NO3 and (NH4)2SO4)] and organic (l-alanine, l-histidine, and l-lysine), at a concentration of 37.5 mmol L− 1. Individual isolates exhibited different growth rates that varied according to the nitrogen source added to the medium. The choice of nitrogen source also had a major effect on production of the mycotoxins emodin, catenarin and islandicin. The highest concentrations of emodin, 54.40 ± 4.46 μg g− 1, 43.07 ± 23.39 μg g− 1 and 28.91 ± 4.64 μg g− 1 of growth medium, were produced on the complex medium (V8-potato dextrose agar) by the isolates Alg-H2, 331-2 and TS93-71B, respectively. A relatively high concentration of emodin also was produced by isolates Az35-5 (28.29 ± 4.71 μg g− 1 of medium) and TS93-71B (27.03 ± 4.09 μg g− 1 of medium) on synthetic medium supplemented with l-alanine. The highest concentrations of catenarin (174.54 ± 14.46 μg g− 1 and 104.87 ± 6.13 μg g− 1 of medium) were recorded for isolates TS93-71B and Alg-H2 on synthetic medium supplemented with l-alanine and NH4Cl, respectively. The highest concentration of islandicin (4.64 ± 0.36 μg g− 1 medium) was observed for isolate 331-2 in the presence of l-lysine. There was not a close relationship between mycelial growth and mycotoxin production by the fungal isolates. This is the first report on the influence of nitrogen sources on the production of mycotoxins by P. tritici-repentis

AAC Magnet Canada Western Red Spring wheat

AAC Magnet (BW1045) is an awned, hollow-stemmed, high-yielding Canada Western Red Spring (CWRS) wheat adapted to growing conditions in the Canadian Prairies. AAC Magnet was 5% higher yielding than Glenn and yielded 2% more than Carberry, a popular CWRS wheat variety across the Canadian Prairies. AAC Magnet matured 2 d earlier than Carberry and a day later than Unity, the earliest maturing check. AAC Magnet had the same height as Glenn and was shorter with better stem strength compared with Unity. AAC Magnet had better lodging scores compared with Unity. Over the 3 yr of testing (2015–2017), the test weight of AAC Magnet was slightly lower than the lowest checks, whereas the 1000-kernel weight of AAC Magnet was higher than all of the checks. The grain protein content of AAC Magnet was 0.3% lower than Carberry. AAC Magnet was rated moderately resistant to Fusarium head blight (Fusarium graminearum Schwabe), resistant to leaf rust (Puccinia triticina Erikss.) and stem rust (Puccinia graminis Pers. f. sp. tritici Erikss. & E. Henn). AAC Magnet was moderately susceptible/susceptible to resistant to the Ug99 family of stem rusts, resistant to loose smut [Ustilago tritici (Pers.) Rostr.], intermediately resistant to stripe rust (Puccinia striiformis Westend.), susceptible to common bunt [Tilletia caries (DC.) Tul. & C. Tul.], and moderately susceptible to leaf spot complex. AAC Magnet was susceptible to orange wheat blossom midge (Sitodiplosis mosellana Géhin). Based on the milling and baking performance over 3 yr (2015–2017) evaluated by the Grain Research Laboratory, Canadian Grain Commission, AAC Magnet was classified as CWRS wheat.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

AAC LeRoy Canada Western Red Spring wheat

AAC LeRoy (BW1049) is a hollow stemmed, awned, high-yielding Canada Western Red Spring (CWRS) wheat suited to the growing conditions in western Canada. AAC LeRoy was 10% higher yielding than Unity, the highest yielding check in the Central Bread Wheat Cooperative registration trials (2015–2017). Within the same test, AAC LeRoy was 13% higher yielding than Carberry, a popular CWRS wheat variety across the Canadian Prairies. AAC LeRoy matured 2 d earlier than Carberry and 1 d later than Unity, the earliest maturing check suited for eastern prairie growing conditions. AAC LeRoy was 6 cm shorter with better stem strength than Unity. The lodging score for AAC LeRoy was lower than the mean of the checks. The test weight of AAC LeRoy was similar to the mean of the checks. Over the 3 yr of testing (2015–2017), the 1000-kernel weight of AAC LeRoy was higher than all of the checks, with a grain protein content 0.6% units lower than Carberry. AAC LeRoy was rated as moderately resistant to Fusarium head blight (Fusarium graminearum Schwabe), leaf rust (Puccinia triticina Erikss.), stripe rust (Puccinia striiformis Westend.), and stem rust (Puccinia graminis Pers. f. sp. tritici Erikss. & E. Henn), including the Ug99 family of stem rusts. It also had a resistant reaction to loose smut [Ustilago tritici (Pers.) Rostr.] and an intermediately resistant reaction to common bunt [Tilletia caries (DC.) Tul. & C. Tul.]. AAC LeRoy was resistant to orange wheat blossom midge (Sitodiplosis mosellana Géhin). AAC LeRoy was registered under the CWRS market class.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

AAC Hodge Canada Western Red Spring wheat

AAC Hodge (BW1069) is a hollow-stemmed, awned and high yielding Canada Western Red Spring (CWRS) wheat cultivar suited to the growing conditions in Western Canada. AAC Hodge was 6% higher yielding than AAC Viewfield, the highest yielding check in the Central Bread Wheat Cooperative (CBWC) registration trials (2017-2019). Within the same test, AAC Hodge was 16% higher yielding than Carberry. AAC Hodge matured 1 d earlier than Carberry and 2 d later than Unity; Unity is the earliest maturing check in the eastern prairie growing conditions. AAC Hodge was 7 cm shorter with better lodging resistance than Unity. The lodging score for AAC Hodge was lower than the mean of the checks. The test weight of AAC Hodge was similar to the mean of the checks. Over the 3 yr of testing (2017-2019), the 1000-kernel weight of AAC Hodge was equal to, or higher than all the checks. The grain protein content of AAC Hodge was equal to that of AAC Viewfield. AAC Hodge was rated moderately resistant to Fusarium head blight (FHB; Fusarium graminearum Schwabe) and resistant to leaf rust (Puccinia triticina Erikss.), stripe rust (Puccinia striiformis Westend), stem rust (Puccinia graminis Pers. f. sp. tritici Eriks. E. Henn), and common bunt [Tilletia caries (DC) Tul. C. Tul.]. AAC Hodge ranged from resistant to moderately susceptible for its reaction to the Ug99 family of stem rusts. AAC Hodge was resistant to orange wheat blossom midge (OBWM) (Sitodiplosis mosellana Ghin). AAC Hodge was registered under the CWRS class.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

AAC Warman Canada Western Red Spring wheat

AAC Warman is a high yielding Canada Western Red Spring (CWRS) wheat adapted to production in Western Canada. AAC Warman was 3% higher yielding than Unity, the highest yielding check in the Central Bread Wheat Cooperative registration trials (2014-2016). Within the same test, AAC Warman was 11% higher yielding than Carberry, a popular CWRS wheat variety across the Canadian prairies. AAC Warman matured 3 days earlier than Carberry and a day later than Unity, the earliest maturing check. AAC Warman was shorter than Unity and had better stem strength compared to Unity, however, the lodging score for AAC Warman was higher than the mean of the checks. Over three years of testing (2014-2016), the test weight and thousand kernel weight of AAC Warman was similar to Carberry. The grain protein content of AAC Warman was 0.3% lower than both Unity and Carberry. AAC Warman was rated moderately resistant to Fusarium head blight (Fusarium graminearum Schwabe), resistant to leaf rust (Puccinia triticina Erikss.) and stem rust (Puccinia graminis f. sp. tritici), but was moderately susceptible to stripe rust (Puccinia striiformis Westend) and common bunt [Tilletia caries (DC) Tul. C. Tul.]. It was rated moderately resistant to loose smut [Ustilago tritici (Pers.) Rostr.] and intermediate resistant to the leaf spot complex. AAC Warman was resistant to orange wheat blossom midge (Sitodiplosis mosellana GĂŠhin). Based on the milling and baking performance over three years (2014-2016) evaluated by the Grain Research Laboratory, Canadian Grain Commission, AAC Warman was registered under the CWRS class.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Evolution of the ToxB gene in Pyrenophora tritici-repentis and related species

Pyrenophora tritici-repentis (tan spot) is a destructive foliar pathogen of wheat with global impact. This ascomycete fungus possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene ToxB across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Within the ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a, ∼5.6-kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in P. tritici-repentis. Additionally, a microsatellite with 25 nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation. Exploring ToxB-like protein distribution in other ascomycetes revealed the presence of ToxB-like proteins in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared with a phylogenetic tree, suggesting a past horizontal gene transfer event during the evolution of the ToxB gene. [Graphic: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food. This is an open access article distributed under the CC BY-NC-ND 4.0 International license