Natural selection drives population divergence for local adaptation in a wheat pathogen

Pereira, Daniel; Brunner, Patrick C.; McDonald, Bruce A.

doi:10.1101/805127

Cited by 3 publications

(2 citation statements)

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“…Three expressed sequence tag (EST) derived SSR loci SNOD1, SNOD3, SNOD5, one minisatellite locus SNOD8 (Stukenbrock et al, 2005) and 16 newly developed SSR loci ( Supplementary Table S1) were used for genotyping. The new SSR markers were designed by Dr. Patrick C. Brunner at ETH Zurich based on the reference genome SN15 and alignments with genome sequences of 164 global strains of P. nodorum (Pereira et al, 2019). PCR was carried out with M13 tailed (Schuelke, 2000) fluorescent labeled primers ( Supplementary Table S1), PCR products were separated by capillary electrophoresis using an ABI3730 Gene Analyzer (Applied Biosciences) and a GeneScan 500 LIZ dye Size Standard from Applied Biosystems (Life Technologies), and the resulting data analyzed using Software: GeneMapper v.5 (Applied Biosystems).…”

Section: Ssr Analysismentioning

confidence: 99%

Genetic Structure of the Norwegian Parastagonospora nodorum Population

et al. 2020

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The necrotrophic fungal pathogen Parastagonospora nodorum causes Septoria nodorum blotch (SNB), which is one of the dominating leaf blotch diseases of wheat in Norway. A total of 165 P. nodorum isolates were collected from three wheat growing regions in Norway from 2015 to 2017. These isolates, as well as nine isolates from other countries, were analyzed for genetic variation using 20 simple sequence repeat (SSR) markers. Genetic analysis of the isolate collection indicated that the P. nodorum pathogen population infecting Norwegian spring and winter wheat underwent regular sexual reproduction and exhibited a high level of genetic diversity, with no genetic subdivisions between sampled locations, years or host cultivars. A high frequency of the presence of necrotrophic effector (NE) gene SnToxA was found in Norwegian P. nodorum isolates compared to other parts of Europe, and we hypothesize that the SnToxA gene is the major virulence factor among the three known P. nodorum NE genes (SnToxA, SnTox1, and SnTox3) in the Norwegian pathogen population. While the importance of SNB has declined in much of Europe, Norway has remained as a P. nodorum hotspot, likely due at least in part to local adaptation of the pathogen population to ToxA sensitive Norwegian spring wheat cultivars.

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Section: Ssr Analysismentioning

confidence: 99%

Genetic Structure of the Norwegian Parastagonospora nodorum Population

et al. 2020

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“…This type of selection can only be possible when some of the phenotypic traits are favored by local environments such as climatic conditions or agricultural practices [58], for example, the density of fungicide application or trade-offs associated with fungicide resistant mutants [27,59]. Previous studies demonstrated that Q ST -F ST comparisons are a powerful approach to infer the importance of diversifying selection in the evolution of quantitative traits [44,60], and revealed that the evolutionary mechanism serves as main driver for the development of fungicide resistance and other ecological traits in pathogen populations including virulence, pesticide resistance, and temperature tolerance in Puccinia striiformis, Mycosphaerella graminicola, P. infestans, and Parastagonospora nodorum, [38,45,61,62]. On the contrary, stabilizing selection (Q ST < F ST ) was found to drive the adaptation of fungicide resistance in a barley pathogen Rhynchosporium commune [14].…”

Section: Sources Of Genetic Variation Contributing To Azoxystrobin Admentioning

confidence: 99%

Temperature-Mediated Plasticity Regulates the Adaptation of Phytophthora infestans to Azoxystrobin Fungicide

et al. 2020

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Fungicide is one of the main approaches used in agriculture to manage plant diseases for food production, but their effectiveness can be reduced due to the evolution of plant pathogens. Understanding the genetics and evolutionary processes responsible for the development of fungicide resistance is a key to food production and social sustainability. In this study, we used a common garden experiment to examine the source of genetic variation, natural selection, and temperature contributing to the development of azoxystrobin resistance in Phytophthora infestans and infer sustainable ways of plant disease management in future. We found that plasticity contributed to ~40% of phenotypic variation in azoxystrobin sensitivity while heritability accounted for 16%. Further analysis indicated that overall population differentiation in azoxystrobin sensitivity (QST) was significantly greater than the overall population differentiation in simple sequence repeat (SSR) marker (FST), and the P. infestans isolates demonstrated higher level of azoxystrobin sensitivity at the higher experimental temperature. These results suggest that changes in target gene expression, enzymatic activity, or metabolic rate of P. infestans play a more important role in the adaptation of the pathogen to azoxystrobin resistance than that of mutations in target genes. The development of azoxystrobin resistance in P. infestans is likely driven by diversifying selection for local adaptation, and elevated temperature associated with global warming in the future may increase the effectiveness of using azoxystrobin to manage P. infestans. The sustainable approaches for increasing disease control effectiveness and minimizing the erosion of the fungicide efficacy are proposed.

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The genetic architecture of emerging fungicide resistance in populations of a global wheat pathogen

Pereira

McDonald

Croll

2020

Preprint

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16Containing fungal diseases often depends on the application of fungicidal compounds. 17Fungicides can rapidly lose effectiveness due to the rise of resistant individuals in populations. 18However, the lack of knowledge about resistance mutations beyond known target genes 19 challenges investigations into pathways to resistance. We used whole-genome sequencing data 20 and association mapping to reveal the multilocus genetic architecture of fungicide resistance in 21 a global panel of 159 isolates of Parastagonospora nodorum, an important fungal pathogen of 22 wheat. We found significant differences in azole resistance among global field populations. The 23 populations evolved distinctive combinations of resistance alleles which can interact 24 synergistically. We identified 34 significantly associated SNPs located in close proximity to 25 genes associated with fungicide resistance in other fungi, including an MFS transporter. Using 26 fungal colony growth rates and melanin production at different temperatures as fitness proxies, 27we found no evidence that resistance was constrained by genetic trade-offs. Our study 28 demonstrates how genome-wide association studies of a global collection of pathogen strains 29 can recapitulate the emergence of fungicide resistance. The distinct complement of resistance 30 mutations found among populations illustrates how the evolutionary trajectory of fungicide 31 adaptation can be complex and challenging to predict. 32 33

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Natural selection drives population divergence for local adaptation in a wheat pathogen

Cited by 3 publications

References 83 publications

Genetic Structure of the Norwegian Parastagonospora nodorum Population

Genetic Structure of the Norwegian Parastagonospora nodorum Population

Temperature-Mediated Plasticity Regulates the Adaptation of Phytophthora infestans to Azoxystrobin Fungicide

The genetic architecture of emerging fungicide resistance in populations of a global wheat pathogen

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