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Detlef Weigel

Bio: Detlef Weigel is an academic researcher from Max Planck Society. The author has contributed to research in topics: Arabidopsis & Arabidopsis thaliana. The author has an hindex of 142, co-authored 516 publications receiving 84670 citations. Previous affiliations of Detlef Weigel include Ludwig Maximilian University of Munich & California Institute of Technology.


Papers
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Posted ContentDOI
20 Aug 2020-bioRxiv
TL;DR: In this paper, the authors implemented genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate resistance in the problematic agricultural weed, Amaranthus tuberculatus.
Abstract: 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 number and distribution of involved genes, their effect sizes, allele frequencies, and signatures of selection Here we implement genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate resistance in the problematic agricultural weed, Amaranthus tuberculatus GWA correctly identifies the gene targeted by glyphosate, and additionally finds more than 100 genes across all 16 chromosomes associated with resistance The encoded proteins have relevant non-target-site resistance and stress-related functions, with potential for pleiotropic roles in resistance to other herbicides and diverse life history traits Resistance-related alleles are enriched for large effects and intermediate frequencies, implying that strong selection has shaped the genetic architecture of resistance despite potential pleiotropic costs The range of common and rare allele involvement implies a partially shared genetic basis of non-target-site resistance across populations, complemented by population-specific alleles Resistance-related alleles show evidence of balancing selection, and suggest a long-term maintenance of standing variation at stress-response loci that have implications for plant performance under herbicide pressure By our estimates, genome-wide SNPs explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, indicating the potential for an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations

6 citations

Journal ArticleDOI
19 Mar 2004-Cell
TL;DR: An intricate arrangement of different cell types is required for the spring-loaded mechanism of spontaneous seed dispersal typical for many fruits.

6 citations

Posted ContentDOI
30 Jan 2017-bioRxiv
TL;DR: Unexpectedly, the vast majority of regulatory sites that differed in chromatin accessibility among strains show little variation in the underlying DNA sequence, implicating variation in upstream regulators.
Abstract: Variation in regulatory DNA is thought to drive evolution. Cross-species comparisons of regulatory DNA have provided evidence for both weak purifying selection and substantial turnover in regulatory regions. However, disruption of transcription factor binding sites can affect the expression of neighboring genes. Thus, the base-pair level functional annotation of regulatory DNA has proven challenging. Here, we explore regulatory DNA variation and its functional consequences in genetically diverse strains of the plant Arabidopsis thaliana, which largely maintain the positional homology of regulatory DNA. Using chromatin accessibility to delineate regulatory DNA genome-wide, we find that 15% of approximately 50,000 regulatory sites varied in accessibility among strains. Some of these accessibility differences are associated with extensive underlying sequence variation, encompassing many deletions and dramatically hypervariable sequence. For the majority of such regulatory sites, nearby gene expression was similar, despite this large genetic variation. However, among all regulatory sites, those with both high levels of sequence variation and differential chromatin accessibility are the most likely to reside near genes with differential expression among strains. Unexpectedly, the vast majority of regulatory sites that differed in chromatin accessibility among strains show little variation in the underlying DNA sequence, implicating variation in upstream regulators.

6 citations

Book ChapterDOI
TL;DR: This chapter describes the generation and application of amiRNAs as a gene silencing tool in rice.
Abstract: Artificial microRNAs (amiRNAs) have been shown to facilitate efficient gene silencing with high specificity to the intended target gene(s). For the plant breeder, gene silencing by artificial miRNAs will certainly accelerate gene discovery, because it allows targeting of all genes in a mapping interval, independent of the genetic background. In addition, beneficial knockout phenotypes can easily be transferred between varieties and across incompatibility barriers. This chapter describes the generation and application of amiRNAs as a gene silencing tool in rice.

6 citations

Journal ArticleDOI
TL;DR: This protocol describes freeze substitution of plant tissues that provides better conservation of certain intracellular components, including microtubules and membranes, than do the standard sample preparation procedures for TEM.
Abstract: INTRODUCTION Transmission electron microscopy (TEM) requires extensive preparation of plant tissues to achieve optimal results. Samples must be fixed to preserve ultrastructure, dehydrated to withstand the high vacuum of an electron microscope, and embedded in a suitable resin to permit very thin sections to be produced. This protocol describes freeze substitution of plant tissues. It provides better conservation of certain intracellular components, including microtubules and membranes, than do the standard sample preparation procedures for TEM.

6 citations


Cited by
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Journal ArticleDOI
23 Jan 2004-Cell
TL;DR: Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.

32,946 citations

Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations

01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal Article
TL;DR: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

9,847 citations

Journal ArticleDOI
14 Dec 2000-Nature
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
Abstract: The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

8,742 citations