Genetic architecture is more complex for resistance to Septoria tritici blotch than to Fusarium head blight in Central European winter wheat

Background

Fusarium head blight (FHB) and Septoria tritici blotch (STB) severely impair wheat production. With the aim to further elucidate the genetic architecture underlying FHB and STB resistance, we phenotyped 1604 European wheat hybrids and their 135 parental lines for FHB and STB disease severities and determined genotypes at 17,372 single-nucleotide polymorphic loci.

Results

Cross-validated association mapping revealed the absence of large effect QTL for both traits. Genomic selection showed a three times higher prediction accuracy for FHB than STB disease severity for test sets largely unrelated to the training sets.

Conclusions

Our findings suggest that the genetic architecture is less complex and, hence, can be more properly tackled to perform accurate prediction for FHB than STB disease severity. Consequently, FHB disease severity is an interesting model trait to fine-tune genomic selection models exploiting beyond relatedness also knowledge of the genetic architecture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1628-8) contains supplementary material, which is available to authorized users.     

Stability of Adult‐plant Resistance to Septoria tritici blotch in 24 European Winter Wheat Varieties Across Nine Field Environments

Septoria tritici blotch (STB) is one of the most important leaf diseases in wheat worldwide. Objectives of this study were (i) to compare inoculation and natural infection; (ii) to evaluate the level of adult‐plant resistance to STB using four isolates; and (iii) to analyse environmental stability of 24 winter wheat (Triticum aestivum L.) varieties in inoculated vs. non‐inoculated field trials across 3 years including nine environments (location × year combinations). Field trials were sown in split‐plot design inoculated with four aggressive isolates of S. tritici plus one non‐inoculated variant as main factor and 24 wheat varieties as subfactor. Septoria tritici blotch severity was visually scored as percentage flag leaves covered with lesions bearing pycnidia. Overall STB rating ranged from 8% (Solitär) to 63% (Rubens) flag leaf area affected, resulting in significant (P < 0.01) genotypic variance. Variance of genotype × environment interaction amounted to approximately 50% of the genotypic variance. Genotype × isolate interaction variance was significant too (P < 0.01) but of minor importance. Therefore, environmental stability of varieties should be a major breeding goal. The varieties Solitär, History and Florett were most resistant and stable as revealed by a regression approach, and the susceptible varieties were generally unstable. Hence, STB resistance and stability are correlated (P < 0.01), but there were some exceptions (Tuareg, Ambition). Promising candidates for an environmentally stable, effective adult‐plant resistance have been identified.     

Genetic architecture of resistance to Septoria tritici blotch in European wheat

Background

Septoria tritici blotch is an important leaf disease of European winter wheat. In our survey, we analyzed Septoria tritici blotch resistance in field trials with a large population of 1,055 elite hybrids and their 87 parental lines. Entries were fingerprinted with the 9 k SNP array. The accuracy of prediction of Septoria tritici blotch resistance achieved with different genome-wide mapping approaches was evaluated based on robust cross validation scenarios.

Results

Septoria tritici blotch disease severities were normally distributed, with genotypic variation being significantly (P < 0.01) larger than zero. The cross validation study revealed an absence of large effect QTL for additive and dominance effects. Application of genomic selection approaches particularly designed to tackle complex agronomic traits allowed to double the accuracy of prediction of Septoria tritici blotch resistance compared to calculation methods suited to detect QTL with large effects.

Conclusions

Our study revealed that Septoria tritici blotch resistance in European winter wheat is controlled by multiple loci with small effect size. This suggests that the currently achieved level of resistance in this collection is likely to be durable, as involvement of a high number of genes in a resistance trait reduces the risk of the resistance to be overcome by specific pathogen isolates or races.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-858) contains supplementary material, which is available to authorized users.     

Trichoderma spp. as elicitors of wheat plant defense responses against Septoria tritici

Leaf blotch of wheat is a widespread and highly active disease that affects wheat production. In addition to the use of chemicals and proper cultivation methods, microbial antagonists are used to control plant pathogens. Trichoderma spp. stimulate a systemic induced response in plants. Therefore, the efficacy of Trichoderma spp. against wheat leaf blotch was evaluated under greenhouse conditions. The susceptible plants were sprayed with Septoria tritici conidiospores. In order to select an efficient method of pretreatment with Trichoderma spp., leaf spraying and seed coating with 14 isolates were tested in 2003 and 2004. The extent of leaf necrosis area and pycnidial coverage was estimated. Antagonism was assessed by the capacity of each Trichoderma spp. isolate to restrict the progress of leaf blotch, 21 days after inoculation. Of the two methods, seed coating was more efficacious against leaf blotch than leaf spraying. Amongst the 14 isolates tested, the isolate prepared from T. harzianum (Th5) produced the highest level of protection. None of the treatments caused changes in plant stem diameter or dry weight. Trichoderma spp. did not get into leaves while S. tritici was present, even in asymptomatic leaf extracts. In addition, the leaf apoplast antifungal proteolytic activity was measured in plants 7, 15, and 22 days after sowing. This antifungal action decreased in plants only inoculated with S. tritici, but increased in those grown from seeds coated with the T. harzianum (Th5) isolate. This increase conferred resistance to the susceptible wheat cultivar. The endogenous germin-like protease inhibitor coordinated the proteolytic action. These results suggest that T. harzianum stimulates a biochemical systemic induced response against leaf blotch.     

Effector discovery in the fungal wheat pathogen Zymoseptoria tritici

Fungal plant pathogens, such as Zymoseptoria tritici (formerly known as Mycosphaerella graminicola), secrete repertoires of effectors to facilitate infection or trigger host defence mechanisms. The discovery and functional characterization of effectors provides valuable knowledge that can contribute to the design of new and effective disease management strategies. Here, we combined bioinformatics approaches with expression profiling during pathogenesis to identify candidate effectors of Z. tritici. In addition, a genetic approach was conducted to map quantitative trait loci (QTLs) carrying putative effectors, enabling the validation of both complementary strategies for effector discovery. In planta expression profiling revealed that candidate effectors were up‐regulated in successive waves corresponding to consecutive stages of pathogenesis, contrary to candidates identified by QTL mapping that were, overall, expressed at low levels. Functional analyses of two top candidate effectors (SSP15 and SSP18) showed their dispensability for Z. tritici pathogenesis. These analyses reveal that generally adopted criteria, such as protein size, cysteine residues and expression during pathogenesis, may preclude an unbiased effector discovery. Indeed, genetic mapping of genomic regions involved in specificity render alternative effector candidates that do not match the aforementioned criteria, but should nevertheless be considered as promising new leads for effectors that are crucial for the Z. tritici–wheat pathosystem.     

Sexual reproduction of Zymoseptoria tritici on durum wheat in Tunisia revealed by presence of airborne inoculum,fruiting bodies and high levels of genetic diversity

Septoria tritici blotch (STB) caused by the heterothallic ascomycete Zymoseptoria tritici is currently one of the most devastating diseases of wheat worldwide. The extent of sexual reproduction of this pathogen is well documented on bread wheat, but not on durum wheat. The objective of the present study was to quantify the occurrence of Z. tritici sexual reproduction on durum wheat in the Tunisian environment. The assessment was undertaken using a triple approach combining fruiting body assessment, ascospore trapping and population genetic analyses. The results highlighted the formation of pseudothecia on leaves and stubble from the autumn until the end of the growing season. Likewise, qPCR monitoring highlighted a constant release of Z. tritici airborne inoculum during the wheat-growing season, with a peak of production at the end of the season. Genetic investigations using microsatellites revealed high levels of gene and genotypic diversities, an equal distribution of mating types, and a lack of genetic clustering within and between growing seasons. Taken together, these findings indicate that Z. tritici undergoes sexual reproduction on durum wheat in Tunisia at least to the same extent than on bread wheat in Western Europe, and that the dry and warm climate does not affect the mating process of the fungus. Frequent occurrence of sexual reproduction is a valuable knowledge to take into account in STB control strategies on durum wheat.     

Inheritance of resistance to leaf and glume blotch caused by Septoria nodorum Berk. in winter wheat

Sixteen crosses between eight winter wheat cultivars were screened for resistance to Septoria nodorum leaf and glume blotch in the F₁ and F₄ generations using artificial inoculation in the field. The F₁ of most crosses showed dominance for susceptibility on both ear and leaf. The effects of general combining ability were of similar magnitude as the effects for specific combining ability. On the basis of the phenotypic difference of the parents, no prediction was possible about the amount and the direction of genetic variance in the segregating populations. The variation observed in this study both within and among the segregating populations suggests a quantitative inheritance pattern influencing the expression of the two traits. The components of variance between F₂ families within a population were as high as (for S. nodorum blotch on the ear) or higher (for S. nodorum blotch on the leaf) than those between populations. Therefore, strong selection within a few populations may be as effective to obtain new resistant genotypes as selection in a large number of populations. In almost all crosses, progenies were found that were more resistant than the better parent. Thus transgression breeding may be a tool to breed for higher levels of resistance to S. nodorum blotch. Highly resistant genotypes were found even in combination with two susceptible parents. The genetic source for Septoria resistance is probably broader than is generally assumed and could be used to improve S. nodorum resistance by combination breeding followed by strong selection in large populations. Received: 18 January / Accepted: 30 April 1999     

Role of hydrogen peroxide during the interaction between the hemibiotrophic fungal pathogen Septoria tritici and wheat

Hydrogen peroxide (H(2)O(2)) is reported to inhibit biotrophic but benefit necrotrophic pathogens. Infection by necrotrophs can result in a massive accumulation of H(2)O(2) in hosts. Little is known of how pathogens with both growth types are affected (hemibiotrophs). The hemibiotroph, Septoria tritici, infecting wheat (Triticum aestivum) is inhibited by H(2)O(2) during the biotrophic phase, but a large H(2)O(2) accumulation occurs in the host during reproduction. Here, we infiltrated catalase, H(2)O(2) or water into wheat during the biotrophic or the necrotrophic phase of S. tritici and studied the effect of infection on host physiology to get an understanding of the survival strategy of the pathogen. H(2)O(2) removal by catalase at both early and late stages made plants more susceptible, whereas H(2)O(2) made them more resistant. H(2)O(2) is harmful to S. tritici throughout its life cycle, but it can be tolerated. The late accumulation of H(2)O(2) is unlikely to result from down-regulation of photosynthesis, but probably originates from damage to the peroxisomes during the general tissue collapse, which is accompanied by release of soluble sugars in a susceptible cultivar.     

Molecular mapping and physical location of major gene conferring seedling resistance to Septoria tritici blotch in wheat

Septoria tritici blotch (STB) caused by Mycosphaerella graminicola (anamorph: Septoria tritici), is one of the most important foliar diseases of wheat. We assessed three doubled-haploid (DH) populations derived from Chara (STB-susceptible)/WW2449 (STB-resistant), Whistler (STB-susceptible)/WW1842 (STB-resistant) and Krichauff (STB susceptible)/WW2451 (STB-resistant) for resistance to a single-pycnidium isolate 79.2.1A of M. graminicola at the seedling stage. STB resistance in each of the three DH populations was conditioned by a single major gene designated as StbWW2449, StbWW1842 and StbWW2451. Linkage analyses and physical mapping indicated that the StbWW loci were located on the short arm of chromosome 1B (IBS). Four simple sequence repeat (SSR) markers linked with STB resistance: Xwmc230, Xbarc119b, Xksum045 and Xbarc008 were located to the distal bin of 1BS.sat1BS-4 (FL: 0.52–1.00) in the 1BS physical map. Xwmc230, Xbarc119b and Xksum045 markers, mapped within 7 cM from StbWW were validated for their linkage and predicted the STB resistance with over 94% accuracy in the 79 advanced breeding lines having WW2449 as one of the parents. The marker interval Xwmc230/Xksum045-Xbarc119b also explained up to 38% of the phenotypic variance at the adult plant stage in all three DH mapping populations. These results have proven that SSR markers are useful in monitoring STB resistance both at seedling and adult plant stages and hence are suitable for routine marker-assisted selection in the wheat breeding programs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic architecture of resistance to Septoria tritici blotch (Mycosphaerella graminicola) in European winter wheat

Genome-wide marker–trait associations (MTA) were established in a population of 358 European winter wheat cultivars and 14 spring wheat cultivars (Triticum aestivum L.) for resistance to Septoria tritici blotch caused by the fungal pathogen Mycosphaerella graminicola. The MTA were based on field data in two consecutive years and genotypic data on 732 microsatellite markers. Best linear unbiased estimations (BLUEs) for resistance were calculated across the trials and ranged from 0.67 (most resistant) to 19.63 (most susceptible) with an average value of 4.93. A total of 115 MTA relating to 68 molecular markers was discovered for the two trials and BLUEs by using a mixed linear model corrected by a kinship matrix. In addition, two candidate genes, Ppd-D1 for photoperiodism and the dwarfing gene Rht-D1, were significantly associated with resistance to Septoria tritici blotch. Several MTA co-located with known resistance genes, e.g. Stb1, 3, 4, 6 and 8, while multiple additional MTA were discovered on several chromosomes, such as 2A, 2D, 3A, 5B, 7A and 7D. The results provide proof of concept for the method of genome-wide association analysis and indicate the presence of further Stb resistance genes in the European winter wheat pool.     

Identification of molecular markers for resistance to Septoria nodorum blotch in durum wheat

The development of Septoria nodorum blotch-resistant cultivars has become a high priority objective for durum wheat breeding programs. Marker-assisted selection enables breeders to improve selection efficiency. In order to develop markers for resistance to Septoria nodorum blotch, a set of F₅ recombinant inbred lines, derived from the crosses Sceptre/3–6, Sceptre/S9–10 and Sceptre/S12–1, was developed based on the F₂-derived family method. Two RAPD markers, designated UBC521₆₅₀ and RC37₅₁₀, were detected by bulked segregant analysis and located approximately 15 and 13.1 centiMorgans (cM) from the resistance gene snbTM, respectively. A SCAR marker was also successfully developed for marker-assisted selection in breeding programs based on the sequence of the RAPD marker UBC521₆₅₀. This is the first report of DNA-based markers linked to resistance for Septoria nodorum blotch in durum wheat. Received: 8 March 2000 / Accepted: 25 June 2000     

Effects of alien cytoplasm substitution on the response of wheat cultivars to Septoria nodorum

The effects of alien cytoplasm substitution on the response of wheat to Septoria nodorum were studied, using alloplasmic series of two cultivars, Chris and Selkirk. In general, cytoplasmic substitution caused unidirectional effects on Septoria-response, alloplasmic lines of both cultivars expressing lower levels of partial resistance (in leaf and head tissue) but higher levels of yield tolerance than the corresponding euplasmic line. The reduced resistance in alloplasmics was closely associated with reduced incubation periods of Septoria infection in both leaf and head tissue. Cytoplasmic substitution resulted in increased yield tolerance to Septoria-infection in both the non-tolerant Selkirk and the relatively tolerant Chris. Unlike their effects on partial resistance, specific cytoplasms exerted similar effects on tolerance in the two parental cultivars, several cytoplasms of the D plasmatype being particularly effective in increasing Septoria-tolevance. The potential for the development of Septoria-toterant cultivars by the incorporation of alien cytoplasms is discussed, in view of the observed neutral effects of D plasmatype cytoplasms on other agronomic traits.     

Genetic analysis of resistance to septoria tritici blotch in the French winter wheat cultivars Balance and Apache

The ascomycete Mycosphaerella graminicola is the causal agent of septoria tritici blotch (STB), one of the most destructive foliar diseases of bread and durum wheat globally, particularly in temperate humid areas. A screening of the French bread wheat cultivars Apache and Balance with 30 M. graminicola isolates revealed a pattern of resistant responses that suggested the presence of new genes for STB resistance. Quantitative trait loci (QTL) analysis of a doubled haploid (DH) population with five M. graminicola isolates in the seedling stage identified four QTLs on chromosomes 3AS, 1BS, 6DS and 7DS, and occasionally on 7DL. The QTL on chromosome 6DS flanked by SSR markers Xgpw5176 and Xgpw3087 is a novel QTL that now can be designated as Stb18. The QTLs on chromosomes 3AS and 1BS most likely represent Stb6 and Stb11, respectively, and the QTLs on chromosome 7DS are most probably identical with Stb4 and Stb5. However, the QTL identified on chromosome 7DL is expected to be a new Stb gene that still needs further characterization. Multiple isolates were used and show that not all isolates identify all QTLs, which clearly demonstrates the specificity in the M. graminicola–wheat pathosystem. QTL analyses were performed with various disease parameters. The development of asexual fructifications (pycnidia) in the characteristic necrotic blotches of STB, designated as parameter P, identified the maximum number of QTLs. All other parameters identified fewer but not different QTLs. The segregation of multiple QTLs in the Apache/Balance DH population enabled the identification of DH lines with single QTLs and multiple QTL combinations. Analyses of the marker data of these DH lines clearly demonstrated the positive effect of pyramiding QTLs to broaden resistance spectra as well as epistatic and additive interactions between these QTLs. Phenotyping of the Apache/Balance DH population in the field confirmed the presence of the QTLs that were identified in the seedling stage, but Stb18 was inconsistently expressed and might be particularly effective in young plants. In contrast, an additional QTL for STB resistance was identified on chromosome 2DS that is exclusively and consistently expressed in mature plants over locations and time, but it was also strongly related with earliness, tallness as well as resistance to Fusarium head blight. Although to date no Stb gene has been reported on chromosome 2D, the data provide evidence that this QTL is only indirectly related to STB resistance. This study shows that detailed genetic analysis of contemporary commercial bread wheat cultivars can unveil novel Stb genes that can be readily applied in marker-assisted breeding programs.     

Comparative virulence of Pyrenophora teres f. teres from Syria and Tunisia and screening for resistance sources in barley: implications for breeding

Aims: The aim of this study is to investigate the pathogenic diversity and virulence groups among Pyrenophora teres f. teres isolates, sampled from Syria and Tunisia, and to identify the most effective source of resistance in barley that could be used in breeding programmes to control net blotch in both countries. Methods and Results: One hundred and four isolates of P. teres f. teres were collected from barley in different agroecological zones of Tunisia and Syria. Their virulence was evaluated using 14 barley genotypes as differential hosts. The upgma clustering identified high pathogenic variability; the isolates were clustered onto 20 pathotypes that were sheltered under three virulence groups, with high, intermediate and low disease scores. According to susceptibility/resistance frequencies and mean disease ratings, CI05401 cultivar ranked as the best differential when inoculated with the Syrian isolates. However, CI09214 cultivar was classified as the best effective source of resistance in Tunisia. Conclusions: All P. teres f. teres isolates were differentially pathogenic. CI09214 and CI05401 cultivars were released as the most effective sources of resistance in Syria and Tunisia. Significance and Impact of the Study: National and international barley breeding programmes that seek to develop resistance against P. teres f. teres in barley should strongly benefit from this study. This resistance cannot be achieved without the proper knowledge of the pathogen virulence spectrum and the sources of host resistance.     

Diagnostics of phytopathogen fungi <Emphasis Type="Italic">Septoria tritici</Emphasis> and <Emphasis Type="Italic">Stagonospora nodorum</Emphasis> by fluorescent amplification-based specific hybridization (FLASH) PCR

A PCR system in the fluorescent amplification-based specific hybridization (FLASH) format was developed for the detection and identification of two important wheat pathogenic fungi Septoria tritici (teleomorph of Mycosphaerella graminicola) and Stagonospora nodorum (teleomorph of Phaeosphaeria nodorum), which cause spots on leaves and glumes, respectively. The pathogen detection system is based on the amplification of a genome fragment in the internal transcribed spacer 1 (ITS1) region and a site encoding the 5.8S ribosomal RNA. The forward primers to ITS1 and a universal reverse primer and a beacon type probe to the 5.8S ribosomal RNA region were chosen to provide the detection of the products in the FLASH format. This system was tested on different isolates of the pathogens, and on infected soil, leaf, and seed samples.