scholarly journals Resistance of the Wheat Cultivar ‘Renan’ to Septoria Leaf Blotch Explained by a Combination of Strain Specific and Strain Non-Specific QTL Mapped on an Ultra-Dense Genetic Map

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 100
Author(s):  
Camilla Langlands-Perry ◽  
Murielle Cuenin ◽  
Christophe Bergez ◽  
Safa Ben Krima ◽  
Sandrine Gélisse ◽  
...  
Keyword(s):  
Genetic Map ◽  
Quantitative Resistance ◽  
Kinase Domain ◽  
Snp Markers ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Zymoseptoria Tritici ◽  
Major Resistance Genes ◽  
Pathogen Populations ◽  
Leucine Rich Repeats

Quantitative resistance is considered more durable than qualitative resistance as it does not involve major resistance genes that can be easily overcome by pathogen populations, but rather a combination of genes with a lower individual effect. This durability means that quantitative resistance could be an interesting tool for breeding crops that would not systematically require phytosanitary products. Quantitative resistance has yet to reveal all of its intricacies. Here, we delve into the case of the wheat/Septoria tritici blotch (STB) pathosystem. Using a population resulting from a cross between French cultivar Renan, generally resistant to STB, and Chinese Spring, a cultivar susceptible to the disease, we built an ultra-dense genetic map that carries 148,820 single nucleotide polymorphism (SNP) markers. Phenotyping the interaction was done with two different Zymoseptoria tritici strains with contrasted pathogenicities on Renan. A linkage analysis led to the detection of three quantitative trait loci (QTL) related to resistance in Renan. These QTL, on chromosomes 7B, 1D, and 5D, present with an interesting diversity as that on 7B was detected with both fungal strains, while those on 1D and 5D were strain-specific. The resistance on 7B was located in the region of Stb8 and the resistance on 1D colocalized with Stb19. However, the resistance on 5D was new, so further designated Stb20q. Several wall-associated kinases (WAK), nucleotide-binding and leucine-rich repeats (NB-LRR) type, and kinase domain carrying genes were present in the QTL regions, and some of them were expressed during the infection. These results advocate for a role of Stb genes in quantitative resistance and for resistance in the wheat/STB pathosystem being as a whole quantitative and polygenic.

scholarly journals Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch in European winter wheat

2018 ◽  
Author(s):  
Steven Yates ◽  
Alexey Mikaberidze ◽  
Simon Krattinger ◽  
Michael Abrouk ◽  
Andreas Hund ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Winter Wheat ◽  
High Throughput ◽  
Quantitative Resistance ◽  
Small Chromosome ◽  
Snp Markers ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Limiting Factor

Accurate, high-throughput phenotyping for quantitative traits is the limiting factor for progress in plant breeding. We developed automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform a GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four resistance traits. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.

Advances in breeding techniques for durable Septoria tritici blotch (STB) resistance in cereals

2021 ◽  
pp. 303-356
Author(s):  
Harsh Raman ◽  
Keyword(s):  
Quantitative Resistance ◽  
Durable Resistance ◽  
Genetic Resistance ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Zymoseptoria Tritici ◽  
Winter Cereal ◽  
Cereal Breeding ◽  
Qualitative Resistance ◽  
Breeding Techniques

Septoria tritici blotch (STB), caused by the hemibiotrophic fungus Zymoseptoria tritici, is one of the most important foliar diseases of winter cereal crops. Recent advances are helping to understand the genetic basis and architecture of resistance to STB. To date, at least 22 genes for qualitative resistance and over 200 quantitative trait loci (QTL) for quantitative resistance have been identified in cereals. This knowledge is enabling cereal breeding programs to develop varieties with more durable resistance to STB. This chapter reviews recent research on genetic resistance loci and breeding strategies based on both conventional and biotechnology-based breeding approaches (molecular marker/genomic-assisted breeding, genetic transformation, and gene-editing) to achieve achieving durable resistance to STB infection and minimise grain yield losses.

scholarly journals Ranking Quantitative Resistance to Septoria tritici Blotch in Elite Wheat Cultivars Using Automated Image Analysis

2018 ◽  
Vol 108 (5) ◽  
pp. 568-581 ◽  
Author(s):  
Petteri Karisto ◽  
Andreas Hund ◽  
Kang Yu ◽  
Jonas Anderegg ◽  
Achim Walter ◽  
...  
Keyword(s):  
Image Analysis ◽  
Quantitative Resistance ◽  
Major Gene ◽  
Growing Season ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Wheat Cultivars ◽  
Zymoseptoria Tritici ◽  
Breeding Programs

Quantitative resistance is likely to be more durable than major gene resistance for controlling Septoria tritici blotch (STB) on wheat. Earlier studies hypothesized that resistance affecting the degree of host damage, as measured by the percentage of leaf area covered by STB lesions, is distinct from resistance that affects pathogen reproduction, as measured by the density of pycnidia produced within lesions. We tested this hypothesis using a collection of 335 elite European winter wheat cultivars that was naturally infected by a diverse population of Zymoseptoria tritici in a replicated field experiment. We used automated image analysis of 21,420 scanned wheat leaves to obtain quantitative measures of conditional STB intensity that were precise, objective, and reproducible. These measures allowed us to explicitly separate resistance affecting host damage from resistance affecting pathogen reproduction, enabling us to confirm that these resistance traits are largely independent. The cultivar rankings based on host damage were different from the rankings based on pathogen reproduction, indicating that the two forms of resistance should be considered separately in breeding programs aiming to increase STB resistance. We hypothesize that these different forms of resistance are under separate genetic control, enabling them to be recombined to form new cultivars that are highly resistant to STB. We found a significant correlation between rankings based on automated image analysis and rankings based on traditional visual scoring, suggesting that image analysis can complement conventional measurements of STB resistance, based largely on host damage, while enabling a much more precise measure of pathogen reproduction. We showed that measures of pathogen reproduction early in the growing season were the best predictors of host damage late in the growing season, illustrating the importance of breeding for resistance that reduces pathogen reproduction in order to minimize yield losses caused by STB. These data can already be used by breeding programs to choose wheat cultivars that are broadly resistant to naturally diverse Z. tritici populations according to the different classes of resistance.

scholarly journals An Improved Method for Measuring Quantitative Resistance to the Wheat Pathogen Zymoseptoria tritici Using High-Throughput Automated Image Analysis

2016 ◽  
Vol 106 (7) ◽  
pp. 782-788 ◽  
Author(s):  
Ethan L. Stewart ◽  
Christina H. Hagerty ◽  
Alexey Mikaberidze ◽  
Christopher C. Mundt ◽  
Ziming Zhong ◽  
...  
Keyword(s):  
Image Analysis ◽  
Quantitative Resistance ◽  
Recombinant Inbred Lines ◽  
Continuous Distribution ◽  
Field Resistance ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Improved Method ◽  
Zymoseptoria Tritici

Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. An improved method of quantifying STB symptoms was developed based on automated analysis of diseased leaf images made using a flatbed scanner. Naturally infected leaves (n = 949) sampled from fungicide-treated field plots comprising 39 wheat cultivars grown in Switzerland and 9 recombinant inbred lines (RIL) grown in Oregon were included in these analyses. Measures of quantitative resistance were percent leaf area covered by lesions, pycnidia size and gray value, and pycnidia density per leaf and lesion. These measures were obtained automatically with a batch-processing macro utilizing the image-processing software ImageJ. All phenotypes in both locations showed a continuous distribution, as expected for a quantitative trait. The trait distributions at both sites were largely overlapping even though the field and host environments were quite different. Cultivars and RILs could be assigned to two or more statistically different groups for each measured phenotype. Traditional visual assessments of field resistance were highly correlated with quantitative resistance measures based on image analysis for the Oregon RILs. These results show that automated image analysis provides a promising tool for assessing quantitative resistance to Z. tritici under field conditions.

scholarly journals Precision Phenotyping Reveals Novel Loci for Quantitative Resistance to Septoria Tritici Blotch

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Steven Yates ◽  
Alexey Mikaberidze ◽  
Simon G. Krattinger ◽  
Michael Abrouk ◽  
Andreas Hund ◽  
...  
Keyword(s):  
Disease Resistance ◽  
High Throughput ◽  
Quantitative Resistance ◽  
Small Chromosome ◽  
Snp Markers ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Limiting Factor ◽  
Single Experiment

Accurate, high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding. We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform the GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four independent resistance traits. Sixteen of the intervals overlapped with known STB resistance intervals, suggesting that our phenotyping approach can identify simultaneously (i.e., in a single experiment) many previously defined STB resistance intervals. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance, perhaps representing resistance to pathogen strains that had not been tested in earlier experiments. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance.

scholarly journals Measurement of infection efficiency of a major wheat pathogen using time-resolved imaging of disease progress

2018 ◽  
Author(s):  
P. Karisto ◽  
S. Dora ◽  
A. Mikaberidze
Keyword(s):  
Quantitative Resistance ◽  
Control Measure ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Zymoseptoria Tritici ◽  
Time Resolved ◽  
Infection Efficiency ◽  
Disease Progress ◽  
Wheat Leaves ◽  
Time Resolved Imaging

AbstractInfection efficiency is a key epidemiological parameter that determines the proportion of pathogen spores able to infect and cause lesions once they have landed on a susceptible plant tissue. In this study, we present an improved method to measure infection efficiency of Zymoseptoria tritici using a replicated greenhouse experiment. Z. tritici is a fungal pathogen that infects wheat leaves and causes Septoria tritici blotch (STB), a major disease of wheat worldwide.We devised an original experimental setup, where we (i) attached living wheat leaves to metal plates allowing for time-resolved imaging of disease progress in planta. Since lesions were continuously appearing, expanding and merging during the period of up to three weeks, daily measurements were necessary for accurate counting of lesions. We also (ii) used reference membranes to characterize the density and the spatial distribution of inoculated spores on leaf surfaces. In this way, we captured the relationship between the number of lesions and the number of viable spores deposited on the leaves and estimated the infection efficiency of about 4 % from the slope of this relationship.Our study provides a proof of principle for an accurate and reliable measurement of infection efficiency of Z. tritici. The method opens opportunities for determining the genetic basis of the component of quantitative resistance that suppresses infection efficiency. This knowledge would improve breeding for quantitative resistance against STB, a control measure considered more durable than deployment of major resistance genes.

scholarly journals A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

2018 ◽  
Author(s):  
Lukas Meile ◽  
Daniel Croll ◽  
Patrick C. Brunner ◽  
Clémence Plissonneau ◽  
Fanny E. Hartmann ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Genomic Region ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Comparative Genomic ◽  
List Type ◽  
Avirulence Genes ◽  
Zymoseptoria Tritici ◽  
Strain Specificity ◽  
Evolutionary Trajectory

SummaryCultivar-strain specificity in the wheat-Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, of which many have been identified. However, on the pathogen side, the molecular determinants of specificity are largely unknown.We used genetic mapping, targeted gene disruption and allele swapping to characterize the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to estimate the evolutionary trajectory of Avr3D1.Avr3D1 is specifically recognized by cultivars harboring the resistance gene Stb7 and triggers a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a region populated by independent transposable element insertions. The gene is present in all 132 investigated strains and is highly polymorphic, with a total of 30 different protein variants. We demonstrated that certain amino acid mutations in Avr3D1 led to evasion of recognition.These results demonstrate that quantitative resistance and gene-for-gene interactions are not mutually exclusive per se. Location of avirulence genes in highly plastic genomic regions likely facilitates accelerated evolution that enables escape from recognition by resistance proteins.

scholarly journals Ranking quantitative resistance to Septoria tritici blotch in elite wheat cultivars using automated image analysis

2017 ◽  
Author(s):  
Petteri Karisto ◽  
Andreas Hund ◽  
Kang Yu ◽  
Jonas Anderegg ◽  
Achim Walter ◽  
...  
Keyword(s):  
Image Analysis ◽  
Quantitative Resistance ◽  
Major Gene ◽  
Growing Season ◽  
Automated Image Analysis ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Wheat Cultivars ◽  
Zymoseptoria Tritici ◽  
Breeding Programs

AbstractQuantitative resistance is likely to be more durable than major gene resistance for controlling Septoria tritici blotch (STB) on wheat. Earlier studies hypothesized that resistance affecting the degree of host damage, as measured by the percentage of leaf area covered by STB lesions, is distinct from resistance that affects pathogen reproduction, as measured by the density of pycnidia produced within lesions. We tested this hypothesis using a collection of 335 elite European winter wheat cultivars that was naturally infected by a diverse population of Zymoseptoria tritici in a replicated field experiment. We used automated image analysis (AIA) of 21420 scanned wheat leaves to obtain quantitative measures of conditional STB intensity that were precise, objective, and reproducible. These measures allowed us to explicitly separate resistance affecting host damage from resistance affecting pathogen reproduction, enabling us to confirm that these resistance traits are largely independent. The cultivar rankings based on host damage were different from the rankings based on pathogen reproduction, indicating that the two forms of resistance should be considered separately in breeding programs aiming to increase STB resistance. We hypothesize that these different forms of resistance are under separate genetic control, enabling them to be recombined to form new cultivars that are highly resistant to STB. We found a significant correlation between rankings based on automated image analysis and rankings based on traditional visual scoring, suggesting that image analysis can complement conventional measurements of STB resistance, based largely on host damage, while enabling a much more precise measure of pathogen reproduction. We showed that measures of pathogen reproduction early in the growing season were the best predictors of host damage late in the growing season, illustrating the importance of breeding for resistance that reduces pathogen reproduction in order to minimize yield losses caused by STB. These data can already be used by breeding programs to choose wheat cultivars that are broadly resistant to naturally diverse Z. tritici populations according to the different classes of resistance.

scholarly journals Characterisation of an antimicrobial and phytotoxic ribonuclease secreted by the fungal wheat pathogen Zymoseptoria tritici

2017 ◽  
Author(s):  
Graeme J. Kettles ◽  
Carlos Bayon ◽  
Caroline A. Sparks ◽  
Gail Canning ◽  
Kostya Kanyuka ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Effector Proteins ◽  
Yeast Cells ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
List Type ◽  
Expression Systems ◽  
Zymoseptoria Tritici ◽  
Loop Region

Abstract-The fungus Zymoseptoria tritici is the causal agent of Septoria Tritici Blotch (STB) disease of wheat leaves. Z. tritici secretes many functionally uncharacterised effector proteins during infection. Here we characterised a secreted ribonuclease (Zt6) with an unusual biphasic expression pattern.-Transient expression systems were used to characterise Zt6, and mutants thereof, in both host and non-host plants. Cell-free protein expression systems monitored impact of Zt6 protein on functional ribosomes, and in vitro assays of cells treated with recombinant Zt6 determined toxicity against bacteria, yeasts and filamentous fungi.-We demonstrated that Zt6 is a functional ribonuclease and that phytotoxicity is dependent on both the presence of a 22-amino acid N-terminal “loop” region and its catalytic activity. Zt6 selectively cleaves both plant and animal rRNA species, and is toxic to wheat, tobacco, bacterial and yeast cells but not to Z. tritici itself.-Zt6 is the first Z. tritici effector demonstrated to have a likely dual functionality. The expression pattern of Zt6 and potent toxicity towards microorganisms suggests that whilst it may contribute to the execution of wheat cell death, it is also likely to have an important secondary function in antimicrobial competition and niche protection.

scholarly journals Prevalence of QoI resistance and mtDNA diversity in the Irish Zymoseptoria tritici population

2019 ◽  
Vol 58 (1) ◽  
pp. 27-33
Author(s):  
S. Kildea ◽  
D.E. Bucar ◽  
F. Hutton ◽  
S. de la Rosa ◽  
T.E. Welch ◽  
...  
Keyword(s):  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Entire Group ◽  
Zymoseptoria Tritici ◽  
Qoi Fungicides ◽  
Quinone Outside Inhibitor ◽  
Strain Collection ◽  
Increased Sensitivity ◽  
Mtdna Diversity

Abstract The emergence and spread of Quinone outside Inhibitor (QoI) fungicide resistance in the Irish Zymoseptoria tritici population in the early 2000s had immediate impacts on the efficacy of the entire group of fungicides for the control of septoria tritici blotch. As a result, a dramatic reduction in the quantities applied to winter wheat occurred in the following seasons. Even in the absence of these fungicides, the frequency of the resistance allele, G143A in the pathogens mtDNA has remained exceptionally high (>97%), and as such, it can be anticipated that continued poor efficacy of current QoI fungicides will be observed. Amongst the isolates with G143A, differences in sensitivity to the QoI pyraclostrobin were observed in vitro. The addition of the alternative oxidase (AOX) inhibitor salicylhydroxamic acid increased sensitivity in these isolates, suggesting some continued impairment of respiration by the QoI fungicides, albeit weak. Interestingly, amongst those tested, the strains from a site with a high frequency of inserts in the MFS1 transporter gene known to enhance QoI efflux did not exhibit this increase in sensitivity. A total of 19 mtDNA haplotypes were detected amongst the 2017 strain collection. Phylogenetic analysis confirmed the suggestion of a common ancestry of all the haplotypes, even though three of the haplotypes contained at least one sensitive strain.

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