Detlef Weigel

Bio: Detlef Weigel is an academic researcher from Max Planck Society. The author has contributed to research in topics: Arabidopsis & Gene. 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.

The MicroRNA miR773 Is Involved in the Arabidopsis Immune Response to Fungal Pathogens.

Abstract: MicroRNAs (miRNAs) are 21- to 24-nucleotide short noncoding RNAs that trigger gene silencing in eukaryotes. In plants, miRNAs play a crucial role in a wide range of developmental processes and adaptive responses to abiotic and biotic stresses. In this work, we investigated the role of miR773 in modulating resistance to infection by fungal pathogens in Arabidopsis thaliana. Interference with miR773 activity by target mimics (in MIM773 plants) and concomitant upregulation of the miR773 target gene METHYLTRANSFERASE 2 (MET2) increased resistance to infection by necrotrophic (Plectosphaerrella cucumerina) and hemibiotrophic (Fusarium oxysporum, Colletototrichum higginianum) fungal pathogens. By contrast, both MIR773 overexpression and MET2 silencing enhanced susceptibility to pathogen infection. Upon pathogen challenge, MIM773 plants accumulated higher levels of callose and reactive oxygen species than wild-type plants. Stronger induction of defense-gene expression was also observed in MIM773 plants in response to fungal infection. Expression analysis revealed an important reduction in miR773 accumulation in rosette leaves of plants upon elicitor perception and pathogen infection. Taken together, our results show not only that miR773 mediates pathogen-associated molecular pattern-triggered immunity but also demonstrate that suppression of miR773 activity is an effective approach to improve disease resistance in Arabidopsis plants.

Image-based methods for phenotyping growth dynamics and fitness components in Arabidopsis thaliana

Abstract: The model species Arabidopsis thaliana has extensive resources to investigate intraspecific trait variability and the genetic bases of ecologically relevant traits However, the cost of equipment and software required for high-throughput phenotyping is often a bottleneck for large-scale studies, such as mutant screening or quantitative genetics analyses Simple tools are needed for the measurement of fitness-related traits, like relative growth rate and fruit production, without investment in expensive infrastructures Here, we describe methods that enable the estimation of biomass accumulation and fruit number from the analysis of rosette and inflorescence images taken with a regular camera We developed two models to predict plant dry mass and fruit number from the parameters extracted with the analysis of rosette and inflorescence images Predictive models were trained by sacrificing growing individuals for dry mass estimation, and manually measuring a fraction of individuals for fruit number at maturity Using a cross-validation approach, we showed that quantitative parameters extracted from image analysis predicts more 90% of both plant dry mass and fruit number When used on 451 natural accessions, the method allowed modeling growth dynamics, including relative growth rate, throughout the life cycle of various ecotypes Estimated growth-related traits had high heritability (065 < H2 < 093), as well as estimated fruit number (H2 = 068) In addition, we validated the method for estimating fruit number with rev5, a mutant with increased flower abortion The method we propose here is an application of automated computerization of plant images with ImageJ, and subsequent statistical modeling in R It allows plant biologists to measure growth dynamics and fruit number in hundreds of individuals with simple computing steps that can be repeated and adjusted to a wide range of laboratory conditions It is thus a flexible toolkit for the measurement of fitness-related traits in large populations of a model species

MSQT for choosing SNP assays from multiple DNA alignments

Abstract: Motivation: One challenging aspect of genotyping and association mapping projects is often the identification of markers that are informative between groups of individuals and to convert these into genotyping assays. Results: The Multiple SNP Query Tool (MSQT) extracts SNP information from multiple sequence alignments, stores it in a database, provides a web interface to query the database and outputs SNP information in a format directly applicable for SNP-assay design. MSQT was applied to Arabidopsis thaliana sequence data to develop SNP genotyping assays that distinguish a recurrent parent (Col-0) from five other strains. SNPs with intermediate allele frequencies were also identified and developed into markers suitable for efficient genetic mapping among random pairs of wild strains. Availability: The source code for MSQT is available at http://msqt.weigelworld.org, together with an online instance of MSQT containing data on 1214 sequenced fragments from 96 ecotypes (wild inbred strains) of the reference plant A.thaliana. All SNP genotyping assays are available in several formats for broad community use. Contact: weigel@weigelworld.org Supplementary information: Supplementary data are available at Bioinformatics online.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

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.

Human biochemical genetics

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

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

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.