Karl Schmid
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View article: Rapid replacement of established by exotic genetic lineages of the fungal maize pathogen <i>Exserohilum turcicum</i> in the Swiss Rhine valley
Rapid replacement of established by exotic genetic lineages of the fungal maize pathogen <i>Exserohilum turcicum</i> in the Swiss Rhine valley Open
The fungal maize pathogen Exserohilum turcicum , the causative agent of Northern Corn Leaf Blight (NCLB) was introduced to Europe in the late 19th century, E. turcicum where it rapidly expanded. It persisted in four major clonal lineages a…
View article: Investigating the <scp>bHLH</scp> transcription factor <scp><i>TSARL1</i></scp> as marker and regulator of saponin biosynthesis in <i>Chenopodium quinoa</i>
Investigating the <span>bHLH</span> transcription factor <span><i>TSARL1</i></span> as marker and regulator of saponin biosynthesis in <i>Chenopodium quinoa</i> Open
BACKGROUND Quinoa ( Chenopodium quinoa ) is valued for its nutritional benefits and resilience to abiotic stresses. However, its commercial use is limited by bitter‐tasting saponins on the seeds, necessitating resource‐intensive removal pr…
View article: Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies
Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies Open
Genome-environment association (GEA) is an approach for identifying adaptive loci by combining genetic variation with environmental parameters, offering potential for improving crop resilience. However, its application to genebank accessio…
View article: A High‐Throughput Phenotyping Pipeline for Quinoa (<scp><i>Chenopodium quinoa</i></scp>) Panicles Using Image Analysis With Convolutional Neural Networks
A High‐Throughput Phenotyping Pipeline for Quinoa (<span><i>Chenopodium quinoa</i></span>) Panicles Using Image Analysis With Convolutional Neural Networks Open
Quinoa is a grain crop with excellent nutritional properties that has attracted global attention for its potential contribution to future food security in a changing climate. Despite its long history of cultivation, quinoa has been improve…
View article: Regional diversity and leaf microbiome interactions of the fungal maize pathogen <i>Exserohilum turcicum</i> in Switzerland: A metagenomic analysis
Regional diversity and leaf microbiome interactions of the fungal maize pathogen <i>Exserohilum turcicum</i> in Switzerland: A metagenomic analysis Open
The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco‐evolutionary dynamics and interactions between host, p…
View article: Regional Diversity and Leaf Microbiome Interactions of the Fungal Maize Pathogen<i>Exserohilum turcicum</i>in Switzerland: A Metagenomic Analysis
Regional Diversity and Leaf Microbiome Interactions of the Fungal Maize Pathogen<i>Exserohilum turcicum</i>in Switzerland: A Metagenomic Analysis Open
The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allows to monitor eco-evolutionary dynamics and interactions betwen host, pathog…
View article: GGoutlieR: an R package to identify and visualizeunusual geo-genetic patterns of biological samples
GGoutlieR: an R package to identify and visualizeunusual geo-genetic patterns of biological samples Open
Chang et al., (2023). GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples. Journal of Open Source Software, 8(91), 5687, https://doi.org/10.21105/joss.05687
View article: Population Genomic Evidence for a Repeated Introduction and Rapid Expansion of the Fungal Maize Pathogen <i>Setosphaeria turcica</i> in Europe
Population Genomic Evidence for a Repeated Introduction and Rapid Expansion of the Fungal Maize Pathogen <i>Setosphaeria turcica</i> in Europe Open
Modern agricultural practices, climate change, and globalization foster the rapid spread of plant pathogens, such as the maize fungal pathogen Setosphaeria turcica, which causes Northern corn leaf blight and expanded into Central Europe du…
View article: Population genomic evidence for a repeated introduction and rapid expansion of the fungal maize pathogen Setospheria turcica in Europe
Population genomic evidence for a repeated introduction and rapid expansion of the fungal maize pathogen Setospheria turcica in Europe Open
Northern corn leaf blight (NCLB) is a devastating fungal disease of maize and caused by the fungal pathogen Setosphaeria turcica. We show by sequencing of S. turcica isolates and evolutionary modeling that over the last 30 years different …
View article: Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass
Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass Open
Repeated herbicide applications in agricultural fields exert strong selection on weeds such as blackgrass ( Alopecurus myosuroides ), which is a major threat for temperate climate cereal crops. This inadvertent selection pressure provides …
View article: GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples
GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples Open
Summary Landscape genomics is an emerging field of research that integrates genomic and environmental information to explore the drivers of evolution. Reliable data on the geographical origin of biological samples is a prerequisite for acc…
View article: Deep haplotype analyses of target‐site resistance locus <i>ACCase</i> in blackgrass enabled by pool‐based amplicon sequencing
Deep haplotype analyses of target‐site resistance locus <i>ACCase</i> in blackgrass enabled by pool‐based amplicon sequencing Open
Summary Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the…
View article: Additional Files for "Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass"
Additional Files for "Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass" Open
This dataset contains additional supporting files referenced by the following publication: • Kersten S, Chang J, Huber CD, Voichek Y, Lanz C, Hagmaier T, Lang P, Lutz U, Hirschberg I, Lerchl J, Porri A, Van de Peer Y, Schmid K, Weigel D, R…
View article: Additional Files for "Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass"
Additional Files for "Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass" Open
This dataset contains additional supporting files referenced by the following publication: • Kersten S, Chang J, Huber CD, Voichek Y, Lanz C, Hagmaier T, Lang P, Lutz U, Hirschberg I, Lerchl J, Porri A, Van de Peer Y, Schmid K, Weigel D, R…
View article: Enhancing quinoa cultivation in the Andean highlands of Peru: a breeding strategy for improved yield and early maturity adaptation to climate change using traditional cultivars
Enhancing quinoa cultivation in the Andean highlands of Peru: a breeding strategy for improved yield and early maturity adaptation to climate change using traditional cultivars Open
Quinoa ( Chenopodium quinoa Willd.) is an ancient food crop that originated in the Andes. It has good nutritional properties that increasingly attract interest around the world and it is considered as a future crop for food security and cl…
View article: Population genomic evidence for a repeated introduction and rapid expansion of the fungal maize pathogen Setospheria turcica in Europe
Population genomic evidence for a repeated introduction and rapid expansion of the fungal maize pathogen Setospheria turcica in Europe Open
Northern corn leaf blight (NCLB) is a devastating fungal disease of maize and caused by the fungal pathogen Setosphaeria turcica. We show by sequencing of S. turcica isolates and evolutionary modeling that over the last 30 years different …
View article: Population genomic evidence for a repeated introduction and rapid expansion of the fungal maize pathogen Setospheria turcica in Europe
Population genomic evidence for a repeated introduction and rapid expansion of the fungal maize pathogen Setospheria turcica in Europe Open
Northern corn leaf blight (NCLB) is a devastating fungal disease of maize and caused by the fungal pathogen Setosphaeria turcica. We show by sequencing of S. turcica isolates and evolutionary modeling that over the last 30 years different …
View article: Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history
Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history Open
Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of qu…
View article: Deep haplotype analyses of target-site resistance locus<i>ACCase</i>in blackgrass enabled by pool-based amplicon sequencing
Deep haplotype analyses of target-site resistance locus<i>ACCase</i>in blackgrass enabled by pool-based amplicon sequencing Open
Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potenti…
View article: High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (Chenopodium quinoa Willd.)
High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (Chenopodium quinoa Willd.) Open
Quinoa is a pseudocereal originating from the Andean regions. Despite quinoa’s long cultivation history, genetic analysis of this crop is still in its infancy. We aimed to localize quantitative trait loci (QTL) contributing to the phenotyp…
View article: High-density mapping of QTL controlling agronomically important traits in quinoa (<i>Chenopodium quinoa</i>Willd.)
High-density mapping of QTL controlling agronomically important traits in quinoa (<i>Chenopodium quinoa</i>Willd.) Open
Quinoa is a pseudocereal originating from the Andean regions. In spite of quinoa’s long cultivation history, genetic analysis of this crop is still in its infancy. We aimed to localize QTL contributing to the phenotypic variation of agrono…
View article: Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions
Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions Open
Understanding how crops adapt to specific environmental conditions is becoming increasingly important in the face of accelerating climate change, but the genetics of local adaptation remain little understood for many crops. Landscape genom…
View article: Supplementary Data - Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions
Supplementary Data - Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions Open
File: 50K_GenotypesEU_raw_UHOH_SoySNP50K.csv.tgz Genotyping data of SoySNP50k SNP array of 170 European soybean varieties. The array includes 51.955 SNP markers. Genotypes of each variety are in columns and each row is a SNP marker. Namin…
View article: Supplementary Data - Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions
Supplementary Data - Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions Open
File: 50K_GenotypesEU_raw_UHOH_SoySNP50K.csv.tgz Genotyping data of SoySNP50k SNP array of 170 European soybean varieties. The array includes 51.955 SNP markers. Genotypes of each variety are in columns and each row is a SNP marker. Namin…
View article: Characterization of Flowering Time in Genebank Accessions of Grain Amaranths and Their Wild Relatives Reveals Signatures of Domestication and Local Adaptation
Characterization of Flowering Time in Genebank Accessions of Grain Amaranths and Their Wild Relatives Reveals Signatures of Domestication and Local Adaptation Open
Grain amaranths (Amaranthus spp.) are ancient crops from the Americas that are consumed as pseudo-cereals and vegetables. Two grain amaranths, A. cruentus and A. hypochondriacus, originated in Central America, and A. caudatus in South Amer…
View article: Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (Hordeum vulgare L. ssp. spontaneum) in the Southern Levant
Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (Hordeum vulgare L. ssp. spontaneum) in the Southern Levant Open
Determining the extent of genetic variation that reflects local adaptation in crop-wild relatives is of interest for the purpose of identifying useful genetic diversity for plant breeding. We investigated the association of genomic variati…
View article: Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass
Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass Open
Repeated herbicide applications exert enormous selection on blackgrass ( Alopecurus myosuroides ), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunit…