Association mapping and meta-analysis: two complementary approaches for the detection of reliable Septoria tritici blotch quantitative resistance in bread wheat (Triticum aestivum L.)

Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola, is one of the most ubiquitous and important diseases of bread wheat worldwide. The aim of this study was to identify markers linked to loci conferring resistance to STB from seven biparental populations. Linkage analysis, meta-analysis and association mapping were combined to identify robust quantitative trait loci (QTLs) for resistance. Linkage analysis led to the detection of 115 QTLs for resistance to STB and 66 QTLs linked to plant height and/or earliness. Meta-analysis clustered these 115 QTLs into 27 Meta-QTLs (MQTLs) of pathogen resistance, of which 14 were found to be linked to plant height and/or earliness. Both the relationship between dwarfing and susceptibility to STB and the significant negative correlation between earliness and STB symptoms were confirmed. Eleven loci were linked to STB resistance by association mapping using a general linear model and/or a mixed linear model, of which eight co-located with STB MQTLs and two co-located with individual QTLs. Associated markers located in MQTL regions enhanced the relevance of the results and validated the potential of an association mapping approach. With several biparental populations, meta-analysis is the most relevant form of genetic analysis study, but association mapping can be used as a validation method. Regions linked to resistance in both methods should be relevant for use in breeding programs for improving resistance to STB in wheat varieties. The main interest in comparing both approaches is to detect robust loci that will be functional in many genetic backgrounds rather than just in one or a few specific backgrounds.     

New broad-spectrum resistance to septoria tritici blotch derived from synthetic hexaploid wheat

Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola, is one of the most devastating foliar diseases of wheat. We screened five synthetic hexaploid wheats (SHs), 13 wheat varieties that represent the differential set of cultivars and two susceptible checks with a global set of 20 isolates and discovered exceptionally broad STB resistance in SHs. Subsequent development and analyses of recombinant inbred lines (RILs) from a cross between the SH M3 and the highly susceptible bread wheat cv. Kulm revealed two novel resistance loci on chromosomes 3D and 5A. The 3D resistance was expressed in the seedling and adult plant stages, and it controlled necrosis (N) and pycnidia (P) development as well as the latency periods of these parameters. This locus, which is closely linked to the microsatellite marker Xgwm494, was tentatively designated Stb16q and explained from 41 to 71% of the phenotypic variation at seedling stage and 28–31% in mature plants. The resistance locus on chromosome 5A was specifically expressed in the adult plant stage, associated with SSR marker Xhbg247, explained 12–32% of the variation in disease, was designated Stb17, and is the first unambiguously identified and named QTL for adult plant resistance to M. graminicola. Our results confirm that common wheat progenitors might be a rich source of new Stb resistance genes/QTLs that can be deployed in commercial breeding programs.     

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.     

Terminal Heat Tolerance in Bread Wheat Determined by Agronomical Traits and SSR Markers

Since global warming affects wheat cropping systems, more has yet to be indicated on the parameters, which control terminal heat tolerance, and severely influence wheat (Triticum aestivum L.) productivity. Identification of tolerant wheat genotypes by heat tolerance-linked molecular markers is a rapid and cost-effective screening tool in plant breeding. Accordingly, in a four-year field experiment (2015–2019), 44 wheat genotypes were selected out of 100 genotypes, and were examined in timely and late planting (mid-January resulting in heat stress). Stress decreased yield components, including 1000-kernel weight (TKW), grains per spike, and plants per square meter, and the physiological traits, including days to heading and days to maturity, grain filling duration, and greenness, and eventually decreased grain yield up to?~?28%. The early maturity genotypes resulted in higher yields under stress conditions by a stress-avoidance mechanism. Among 14 SSR markers, GWM577 was positively correlated with yield, and WMS3062, GWM261, and WMS1025 had positive correlations with longevity under stress. Accordingly, WMS3062 and GWM261 can be used to determine high yield and early maturity genotypes. Furthermore, GWM114 showed a positive correlation with TKW, indicating their usefulness for grouping wheat genotypes and for identifying heat-related markers. Since the crossing of the genetically distant genotypes can create more diverse populations, the results could be applied to plan breeding projects to establish more diverse populations for different chromosomal locations and traits under heat stress conditions. Moreover, our findings demonstrated that the morphological and molecular analyses could be useful for describing wheat genetic variation of heat tolerance.

     

The genetic architecture of seedling resistance to Septoria tritici blotch in the winter wheat doubled-haploid population Solitär × Mazurka

Breeding for resistance to Septoria tritici blotch (STB), caused by Mycosphaerella graminicola (anamorph: Septoria tritici), is an essential component in controlling this important foliar disease of wheat. Inheritance of seedling resistance to seven worldwide pathogen isolates has been studied in a doubled-haploid (DH) population derived from a cross between the field resistant cultivar Solitär and the susceptible cultivar Mazurka. Multiple quantitative trait locus (QTL) mapping revealed major and minor genetic effects on resistance as well as several epistatic relationships in the seedling stage. Solitär conferred resistance to isolate IPO323, governed by Stb6 on chromosome 3A, as well as to IPO99015, IPO92034, Hu1 and Hu2 controlled by a QTL on chromosome arm 1BS, possibly corresponding to Stb11 and minor QTL on chromosomes 1B, 3D, 6B and 7D. Resistance of Mazurka to IPO90015 and BBA22 was caused by a QTL located in a region on 4AL which harbours Stb7 or Stb12. QTL specific to pycnidial coverage on 3B and specific to necrosis on 1A could be discovered for isolate IPO92034. Pairwise epistatic interactions were reliably detected with five isolates. Although their contributions to the total variance are generally low, the genotypic effect of the QTL by QTL interaction of 4AL (Stb7 or Stb12) and 3AS (Stb6) made up almost 15% of disease expression. Altogether, the results suggest a complex inheritance of resistance to STB in the seedling stage in terms of isolate-specificity and resistance mechanisms, which have implications for marker-assisted breeding in an attempt to pyramid STB resistance genes.