Genome-wide association mapping of resistance to the foliar diseases septoria nodorum blotch and tan spot in a global winter wheat collection

Septoria nodorum blotch (SNB) and tan spot, caused by the necrotrophic fungal pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis, respectively, often occur together as a leaf spotting disease complex on wheat (Triticum aestivum L.). Both pathogens produce necrotrophic effectors (NEs) that contribute to the development of disease. Here, genome-wide association analysis of a diverse panel of 264 winter wheat lines revealed novel loci on chromosomes 5A and 5B associated with sensitivity to the NEs SnTox3 and SnTox5 in addition to the known sensitivity genes for NEs Ptr/SnToxA, SnTox1, SnTox3, and SnTox5. Sensitivity loci for SnTox267 and Ptr ToxB were not detected. Evaluation of the panel with five P. nodorum isolates for SNB development indicated the Snn3-SnTox3 and Tsn1-SnToxA interactions played significant roles in disease development along with additional QTL on chromosomes 2A and 2D, which may correspond to the Snn7-SnTox267 interaction. For tan spot, the Tsc1-Ptr ToxC interaction was associated with disease caused by two isolates, and a novel QTL on chromosome 7D was associated with a third isolate. The Tsn1-ToxA interaction was associated with SNB but not tan spot. Therefore some, but not all, of the previously characterized host gene-NE interactions in these pathosystems play significant roles in disease development in winter wheat. Based on these results, breeders should prioritize the selection of resistance alleles at the Tsc1, Tsn1, Snn3, and Snn7 loci as well as the 2A and 7D QTL to obtain good levels of resistance to SNB and tan spot in winter wheat.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01400-5.

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

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.

The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing

Objectives

The assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived from short reads only. Here, a necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) isolate 134 (Ptr134), which causes tan spot disease on wheat, was sequenced on a MinION using Oxford Nanopore Technologies (ONT), to improve on a previous Illumina short-read genome assembly and provide a more complete genome resource for pan-genomic analyses of Ptr.

Results

The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses.

An optimized sporulation method for the wheat fungal pathogen Pyrenophora tritici-repentis

BACKGROUND

The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) causes tan (syn. yellow) spot of wheat and accounts for significant yield losses worldwide. Understanding the molecular mechanisms of this economically important crop disease is crucial to counteract the yield and quality losses of wheat globally. Substantial progress has been made to comprehend the race structure of this phytopathogen based on its production of necrotrophic effectors and genomic resources of Ptr. However, one limitation for studying Ptr in a laboratory environment is the difficulty to isolate high spore numbers from vegetative growth with mycelial contamination common. These limitations reduce the experimental tractability of Ptr.

RESULTS

Here, we optimized a multitude of parameters and report a sporulation method for Ptr that yields robust, high quality and pure spores. Our methodology encompasses simple and reproducible plugging and harvesting techniques, resulting in spore yields up to 1500 fold more than the current sporulation methods and was tested on multiple isolates and races of Ptr as well as an additional seven modern Australian Ptr isolates. Moreover, this method also increased purity and spore harvest numbers for two closely related fungal pathogens (Pyrenophora teres f. maculata and f. teres) that cause net blotch diseases in barley (Hordeum vulgare), highlighting the usability of this optimized sporulation protocol for the wider research community.

CONCLUSIONS

Large-scale spore infection and virulence assays are essential for the screening of wheat and barley cultivars and combined with the genetic mapping of these populations allows pinpointing and exploiting sources of host genetic resistance. We anticipate that improvements in spore numbers and purity will further advance research to increase our understanding of the pathogenicity mechanisms of these important fungal pathogens.

Resistance of winter wheat varieties to tan spot in the North Caucasus region of Russia

Tan spot caused by Pyrenophora tritici-repentis (Died.) Drechsler, in recent years, occupies an increasingly large area on the territory of Russia. Due to the wide distribution and economic significance of this disease, the search for resistant plants to the pathogen is relevant. This paper presents the results of a field assessment for 2017–2019 of 34 regionally distributed winter wheat varieties of Russian selection for resistance to P. tritici-repentis in the North Caucasus region of Russia. Field resistance - the development of the disease up to 30% against the background of artificial infection for three years was shown by 20.5% of the studied varieties. Wheat varieties were assessed for resistance to isolates of tan spot identified as races 1, 3, and 4 in the greenhouse at the seedling stage. The number of resistant accessions for each race was different and ranged from 12 to 20. The 12 varieties showed resistance to race 1, 14 varieties to race 3, 20 varieties to race 4. This research showed that the resistance to tan spot of studied varieties was race-specific. A functional allele of the susceptibility gene Tsn1 to P. tritici-repentis isolates, producing the toxin Ptr ToxA, was diagnosed by PCR method. Of the analyzed 34 varieties, 13 had a dominant allele of the Tsn1 (Tsn1⁺), and 21 had a recessive allele in the tsn1tsn1 homozygous state. All Tsn1⁺ varieties, and most varieties with recessive alleles tsn1tsn1, were susceptible to tan spot in the field. Varieties Dolya, Gurt, Lebed and Sila, which showed field resistance, had the tsn1tsn1 genotype. The expected reaction of varieties with different allelic composition of the Tsn1 gene to inoculation with the isolate of race 1, according to the generally accepted model of “gene-to-gene” interaction, did not coincide with that observed in reality, which confirms the results obtained by other authors. Research results demonstrate the effect of weather conditions on the susceptibility of wheat varieties to tan spot. In years with higher humidity and higher average air temperatures, the susceptibility response to the disease was observed in more varieties than in drier years. The studies show that the main part (79.5%) of winter wheat varieties of Russian selection widely zoned in the North Caucasus region of Russia are susceptible to P. tritici-repentis. Varieties that have been resistant to the pathogen in the adult phase in the field for three years and to the pathogen races in which the recessive allele of the tsn1 gene has been identified may be of interest as sources of resistance for developing new disease-resistant varieties.

PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis

Background

Necrotrophic effector proteins secreted by fungal pathogens are important virulence factors that mediate the development of disease in wheat. Pyrenophora tritici-repentis (Ptr), the causal agent of wheat tan spot, has a race structure dependent on the combination of effectors. In Ptr, ToxA and ToxB are known proteinaceous effectors responsible for necrosis and chlorosis respectively. While Ptr ToxA is encoded by the single gene ToxA, ToxB has multiple loci in the Ptr genome, which is postulated to be directly related to the level of ToxB production and leaf chlorosis. Although previous analysis has indicated that the majority of the ToxB loci lie on a single chromosome, the exact number and chromosomal locations for all the ToxB loci have not been fully identified.

Results

In this study, we have sequenced the genome of a race 5 ToxB-producing isolate (DW5), using PacBio long read technology, and found that ToxB duplications are nested in the complex subtelomeric chromosomal regions. A total of ten identical ToxB gene copies were identified and based on flanking sequence identity, nine loci appeared associated with chromosome 11 and a single copy with chromosome 5. Chromosome 11 multiple ToxB gene loci were separated by large sequence regions between 31 and 66 kb within larger segmental duplications in an alternating pattern related to loci strand, and flanked by transposable elements.

Conclusion

This work provides for the first time the full accompaniment of ToxB loci and surrounding regions, and identifies the organization and distribution of ten ToxB loci to subtelomeric regions. To our knowledge, this is the first report of an interwoven strand-related duplication pattern event. This study further highlights the importance of resolving the highly complex distal chromosomal regions, that remain difficult to assemble, and can harbour important effectors and virulence factors.

Supplementary information

Supplementary information accompanies this paper at 10.1186/s12864-020-07029-4.

Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces

BACKGROUND

In the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivum L.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB).

RESULTS

A diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition to Tsn1, several novel genomic regions Q.Ts1.sdsu-4BS and Q.Ts1.sdsu-5BS (tan spot Ptr race 1) and Q.Ts5.sdsu-1BL, Q.Ts5.sdsu-2DL, Q.Ts5.sdsu-3AL, and Q.Ts5.sdsu-6BL (tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms.

CONCLUSION

Our results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.

A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate

OBJECTIVES

The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) is the causal agent of tan spot a major disease of wheat. We have generated a new genome resource for an Australian Ptr race 1 isolate V1 to support comparative 'omics analyses. In particular, the V1 PacBio Biosciences long-read sequence assembly was generated to confirm the stability of large-scale genome rearrangements of the Australian race 1 isolate M4 when compared to the North American race 1 isolate Pt-1C-BFP.

RESULTS

Over 1.3 million reads were sequenced by PacBio Sequel small-molecule real-time sequencing (SRMT) cell to yield 11.4 Gb for the genome assembly of V1 (285X coverage), with median and maximum read lengths of 8959 bp and 72,292 bp respectively. The V1 genome was assembled into 33 contiguous sequences with a of total length 40.4 Mb and GC content of 50.44%. A total of 14,050 protein coding genes were predicted and annotated for V1. Of these 11,519 genes were orthologous to both Pt-1C-BFP and M4. Whole genome alignment of the Australian long-read assemblies (V1 to M4) confirmed previously identified large-scale genome rearrangements between M4 and Pt-1C-BFP and presented small scale variations, which included a sequence break within a race-specific region for ToxA, a well-known necrotrophic effector gene.

Transcriptomic changes in wheat during tan spot (Pyrenophora tritici-repentis) disease

OBJECTIVES

Tan spot is a yield-reducing disease that affects wheat and is caused by the fungus Pyrenophora tritici-repentis (Ptr). Eight races of Ptr have been identified based upon production of the effectors Ptr ToxA, Ptr ToxB, and Ptr ToxC. Wheat cultivars have also been characterized by their resistance and susceptibility to races of Ptr and sensitivity to the effectors. The objective of this research was to assess differences in gene expression between Ptr resistant and susceptible wheat cultivars when either inoculated with Ptr race 2 spores or directly infiltrated with Ptr ToxA.

DATA DESCRIPTION

A greenhouse experiment was used to assess wheat-Ptr interaction. Wheat seedlings were grown for two weeks prior to the experiment under greenhouse conditions. Four treatments were used: (1) spray-inoculation with a suspension of Ptr spores (3000 spores/mL) (2) spray inoculation with water as a control (3) needleless syringe injection with Ptr ToxA, and (4) needleless syringe injection with water as a control. Plants were transferred to a humidity chamber and leaf sample were taken at 0, 8, and 16 h. After RNA extraction and sequencing, 48 RNA datasets are reported. This data will be useful in understanding how resistant wheat responds to Ptr compared to susceptible wheat.

Genetic Dissection of Resistance to the Three Fungal Plant Pathogens Blumeria graminis, Zymoseptoria tritici, and Pyrenophora tritici-repentis Using a Multiparental Winter Wheat Population

Bread wheat (Triticum aestivum L.) is one of the world’s most important crop species. The development of new varieties resistant to multiple pathogens is an ongoing task in wheat breeding, especially in times of increasing demand for sustainable agricultural practices. Despite this, little is known about the relations between various fungal disease resistances at the genetic level, and the possible consequences for wheat breeding strategies. As a first step to fill this gap, we analyzed the genetic relations of resistance to the three fungal diseases – powdery mildew (PM), septoria tritici blotch (STB), and tan spot (TS) – using a winter wheat multiparent advanced generation intercross population. Six, seven, and nine QTL for resistance to PM, STB, and TS, respectively, were genetically mapped. Additionally, 15 QTL were identified for the three agro-morphological traits plant height, ear emergence time, and leaf angle distribution. Our results suggest that resistance to STB and TS on chromosome 2B is conferred by the same genetic region. Furthermore, we identified two genetic regions on chromosome 1AS and 7AL, which are associated with all three diseases, but not always in a synchronal manner. Based on our results, we conclude that parallel marker-assisted breeding for resistance to the fungal diseases PM, STB, and TS appears feasible. Knowledge of the genetic co-localization of alleles with contrasting effects for different diseases, such as on chromosome 7AL, allows the trade-offs of selection of these regions to be better understood, and ultimately determined at the genic level.

Exploration of wheat and pathogen transcriptomes during tan spot infection

Objectives

The fungus Pyrenophora tritici-repentis is the causal agent of tan spot, a major disease of wheat (Triticum aestivum). Here, we used RNA sequencing to generate transcriptional datasets for both the host and pathogen during infection and during in vitro pathogen growth stages.

Data description

To capture gene expression during wheat infection with the P. tritici-repentis isolate M4, RNA datasets were generated for wheat inoculated with P. tritici-repentis (infection) and a mock (control) at 3 and 4 days post-infection, when scorable leaf disease symptoms manifest. The P. tritici-repentis isolate M4 was also RNA sequenced to capture gene expression in vitro at two different growth stages: 7-day old vegetative mycelia and 9-day old sporulating mycelia, to coincide with a latent growth stage and early sporulation respectively. In total, 6 RNA datasets are available to aid in the validation of predicted genes of P. tritici-repentis and wheat. The datasets generated offer an insight into the transcriptomic profile of the host–pathogen interaction and can be used to investigate the expression of a subset of transcripts or targeted genes prior to designing cost-intensive RNA sequencing experiments, that would be best further explored with replication and a time series analysis.

Proteomics of the wheat tan spot pathogen Pyrenophora tritici-repentis

Objectives

The fungus Pyrenophora tritici-repentis is a major pathogen of wheat worldwide, causing the leaf spotting disease tan spot. To best inform approaches for plant genetic resistance, an understanding of the biology and pathogenicity mechanisms of this fungal pathogen is essential. Here, intracellular and extracellular proteins of P. tritici-repentis were extracted, and peptides analysed via high-resolution mass spectrometry. Our objective was to generate a useful proteomics resource for P. tritici-repentis. A survey of proteins secreted by the pathogen into culture filtrate is especially useful, as these are likely to come in direct contact with the wheat host and may play important roles in infection/pathogenicity. The peptide data presented herein, has also been used to successfully verify and refine in silico predicted P. tritici-repentis gene annotations, through the validation of alternative splicing and reading frame shifts.

Data description

The data sets presented consist of peptide spectra of the extracellular and intracellular proteomes of three P. tritici-repentis isolates. Peptide matches to translated transcripts of the North American reference isolate Pt-1C-BFP are also provided.

Proteome changes induced by Pyrenophora tritici-repentis ToxA in both insensitive and sensitive wheat indicate senescence-like signaling

BACKGROUND

Pyrenophora tritici-repentis is a phytopathogenic fungus which causes tan spot on wheat. Some races of P. tritici-repentis produce host-specific toxins which present symptoms of chlorosis or necrosis on susceptible wheat cultivars. One such toxin is Ptr ToxA, which enters mesophyll cells through a putative toxin-receptor and localizes with chloroplasts, ultimately causing damage and necrosis on leaves. These symptoms can occur even in the absence of the pathogen. Insensitive cultivars lack the receptor and Ptr ToxA cannot enter cells. The molecular mechanisms surrounding this plant-pathogen interaction are still largely unknown, although some details have begun to emerge.

RESULTS

Using 2-D electrophoresis, fifteen protein changes were identified reproducibly in the leaf proteomes of a sensitive and an insensitive cultivar over three days after inoculation of purified Ptr ToxA. Functional analysis of the proteins indicated that senescence signals may be induced in the sensitive cultivar. In the insensitive cultivar proteins involved in some features of senescence inhibition were seen. Complementary responses at the biochemical level may be actively promoting a localized senescence-like response in sensitive wheat cultivars whilst actively inhibiting this response in insensitive cultivars.

CONCLUSION

This is the first report of a biochemical response in an insensitive cultivar in this plant-pathogen interaction. Findings support the involvement of ethylene, and the activation of complementary pathways in sensitive versus insensitive wheat cultivars responding to Ptr ToxA. The nature of the system permits using purified toxin to mimic disease, which eliminates the pathogen proteome and ensures a synchronous response in inoculated leaves.