Detlef Weigel

Detlef Weigel
Max Planck Institute for Developmental Biology · Department of Molecular Biology

PhD

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1,364
Publications
172,423
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85,447
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Publications

Publications (1,364)
Article
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Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate th...
Article
Full-text available
Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences ¹ . Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana . In contrast to expectations, we find that mutations occur less often in functi...
Article
Full-text available
Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and...
Preprint
Full-text available
Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Many WGBS-based studies aim to identify biologically relevant loci that display differential methylation between genotypes, treatment groups, tissues, or developmental stages. Over the years, different tools have been devel...
Article
Although rapid phenotypic evolution has been documented often, the genomic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations that...
Preprint
Full-text available
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 opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occu...
Article
Full-text available
Plants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana , a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogen...
Article
Full-text available
Plants deploy cell-surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens¹. LRR receptor kinases and LRR receptor proteins at the plasma membrane recognize microorganism-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR proteins detect microbial effectors inside cel...
Article
Full-text available
Motivation: Genome-wide association study (GWAS) requires a researcher to perform a multitude of different actions during analysis. From editing and formatting genotype and phenotype information to running the analysis software to summarizing and visualizing the results. A typical GWAS workflow poses a significant challenge of utilizing the comman...
Article
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. While human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical con...
Preprint
Full-text available
Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and...
Article
Full-text available
The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whol...
Preprint
Full-text available
We present a new software package vcf2gwas to perform reproducible genome-wide association studies (GWAS). vcf2gwas is a Python API for bcftools, PLINK and GEMMA. Before running the analysis a traditional GWAS workflow requires the user to edit and format the genotype information from commonly used Variant Call Format (VCF) file and phenotype infor...
Article
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Research in many different areas of medicine will benefit from new approaches to peer review and publishing.
Article
Full-text available
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demogr...
Preprint
Causal mutations and their frequency in nature are well-characterized for herbicide resistance. However, we still lack understanding of the extent of parallelism in the mutational origin of target-site resistance (TSR), the role of standing variation and gene flow in the spread of TSR variants, and allelic interactions that mediate their selective...
Article
Hybrid necrosis in plants refers to a genetic autoimmunity syndrome in the progeny of interspecific or intraspecific crosses. Although the phenomenon was first documented in 1920, it has been unequivocally linked to autoimmunity only recently, with the discovery of the underlying genetic and biochemical mechanisms. The most common causal loci encod...
Preprint
Full-text available
Pseudomonas and Sphingomonas are among the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana . Relative to Pseudomonas , the ecology of Sphingomonas and its interaction with plants remains elusive, despite its global ubiquity and known representatives of plant-beneficial strains. We analyzed the genomic features of ove...
Preprint
Full-text available
The plant microbiome is a rich biotic environment, comprising numerous taxa. The community structure of these colonizers is constrained by multiple factors, including host-microbe and microbe-microbe interactions, as well as the interplay between the two. While much can be learned from pairwise relationships between individual hosts and microbes, o...
Article
Full-text available
Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germinat...
Article
Full-text available
Much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target‐sites, despite the increasingly recognized importance of polygenic resistance. Little work has been done to characterize the broader genomic basis of herbicide resistance, including the number and distri...
Preprint
Full-text available
Pattern-triggered immunity (PTI) is a central component of plant immunity. Activation of PTI relies on the recognition of microbe-derived structures, termed patterns, through plant encoded surface-resident pattern recognition receptors (PRRs). We have identified proteobacterial translation initiation factor 1 (IF1) as an immunogenic pattern that tr...
Preprint
Pattern-triggered immunity (PTI) is a central component of plant immunity. Activation of PTI relies on the recognition of microbe-derived structures, termed patterns, through plant encoded surface-resident pattern recognition receptors (PRRs). We have identified proteobacterial translation initiation factor 1 (IF1) as an immunogenic pattern that tr...
Preprint
Full-text available
It is now accepted that phenotypic evolution can occur quickly but the genetic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations t...
Article
Full-text available
Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of...
Article
Full-text available
BACKGROUND Before 2010, Amaranthus tuberculatus (Moq.) J. D. Sauer was barely known to farmers and stakeholders in Italy. Since then, several populations resistant to ALS‐inhibiting herbicides have been collected. In most populations, a known target site resistance‐endowing mutation was found, a Trp to Leu substitution at position 574 of the ALS ge...
Preprint
Full-text available
The quantitative resistance gene ACCELERATED CELL DEATH 6 ( ACD6 ), which encodes a transmembrane protein with intracellular ankyrin repeats, has been implicated in a trade-off between growth and defense among wild strains of Arabidopsis thaliana . Naturally hyperactive alleles of the ACD6 -Est-1 type can lead to spontaneous activation of immune re...
Preprint
Full-text available
New combinations of genetic material brought together through hybridization can lead to unfit offspring as a result of outbreeding or inbreeding depression. In selfing plants such as Arabidopsis thaliana, outbreeding depression is typically the result of pairwise deleterious epistatic interactions between two alleles that can geographically co-occu...
Preprint
Full-text available
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can contribute to observed patterns of genetic diversity and our understanding of the adaptive spread of alleles. While human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influ...
Article
Full-text available
Genome editing with the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated protein) system allows mutagenesis of a targeted region of the genome using a Cas endonuclease and an artificial guide RNA. Both because of variable efficiency with which such mutations arise and because the repair process produces a spec...
Article
Full-text available
Amaranthus tuberculatus and Amaranthus palmeri are agronomically important weed species, both with stable dioecious reproductive systems. An understanding of the genetic basis of sex determination may lead to new methods of managing these troublesome weeds. Previous research identified genomic sequences associated with maleness in each species. Mal...
Preprint
Plants use both cell surface and intracellular immune receptors with leucine rich-repeat (LRRs) to detect pathogens. LRR receptor kinases (LRR-RKs) and LRR receptor-like proteins (LRR-RPs) recognize extracellular microbe-derived molecules to confer pattern-triggered immunity (PTI), while nucleotide-binding LRR (NLR) proteins detect microbial effect...
Article
Full-text available
From July 2021 eLife will only review manuscripts already published as preprints, and will focus its editorial process on producing public reviews to be posted alongside the preprints.
Article
Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human Exportin-5, has been considered as a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report HST functions in the miRNA...
Article
Full-text available
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K...
Article
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same spe...
Preprint
Full-text available
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demogr...
Article
Full-text available
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies three weeks after sowing. Massive transcriptional changes ta...
Article
Full-text available
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome asse...
Article
Full-text available
Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. pal...
Preprint
Full-text available
Although much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, the importance of polygenic resistance has been increasingly recognized. Despite this, little work has been done to characterize the genomic basis of herbicide resistance, including the n...
Preprint
Full-text available
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome asse...
Article
Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factor...
Preprint
Full-text available
Background Genome editing with the CRISPR/Cas9 system allows the user to mutate a targeted region of the genome using an endonuclease (Cas9) and an artificial single-guide RNA (sgRNA). Both because of variable efficiency with which such mutations arise and because the repair process produces a spectrum of mutations, one needs to ascertain the genom...
Preprint
Full-text available
Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness and evolutionary optimization of genic mutation rates remains controversial. However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities, which is predicted by...
Preprint
Full-text available
The microbial population size, or load, in a host is a fundamental metric of colonization by commensals or infection by pathogens. Sequence-based measurement of DNA amount contributed by host and microbes in a sample provides a simple way of measuring microbial load, and it also has the ability to estimate microbiome diversity. Unfortunately, it is...
Preprint
Full-text available
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies three weeks after sowing. Massive transcriptional changes ta...
Article
Full-text available
Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, support the acquisition of nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing...
Article
Full-text available
Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the type of genetic variants detected in GWAS to include major deletions, insertions and rearrangements. We first use raw sequencing data directly to derive short sequences,...
Preprint
Full-text available
Motivation: New DNA sequencing technologies have enabled the rapid analysis of many thousands of genomes from a single species. At the same time, the conventional approach of mapping sequencing reads against a single reference genome sequence is no longer adequate. However, even where multiple high-quality reference genomes are available, the probl...
Article
Full-text available
Protein‐protein interactions, including oligomerization, are involved in regulation of many cellular processes. Unfortunately, many proteins are expressed at a very low level in vivo, making it challenging to observe oligomerization by size‐exclusion chromatography, also known as gel filtration. In this protocol, we present detailed steps to perfor...
Article
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eLife is making changes to its policies on peer review in response to the impact of COVID-19 on the scientific community.
Preprint
Full-text available
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development and adaptation to environmental fluctuations in most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K2...
Article
Full-text available
After the ice caps, tropical forests are globally the most threatened terrestrial environments. Modern trees are not just witnesses to growing contemporary threats but also legacies of past human activity. Here, we review the use of dendrochronology, radiocarbon analysis, stable isotope analysis, and DNA analysis to examine ancient tree management....
Article
In certain plant hybrids, immunity signaling is initiated when immune components interact in the absence of a pathogen trigger. In Arabidopsis thaliana, such autoimmunity and cell death are linked to variants of the NLR RPP7 and the RPW8 proteins involved in broad-spectrum resistance. We uncover the molecular basis for this autoimmunity and demonst...