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.

Novel homeotic genes in Drosophila melanogaster

Abstract: The generation of the anterior-posterior segment pattern in the Drosophila embryo requires two closely linked processes. First, the correct number of segments must be established. This is achieved by the concerted action of maternal coordinate genes and zygotic segmentation genes of the gap, pair-rule, and segment polarity classes. Second, each segment must acquire a unique identity depending on its position along the anterior-posterior axis. The latter process is controlled by the homeotic selector genes of the Antennapedia (ANT-C) and bithorax complexes (BX-C) (Akam, Development, 101, 1-22, 1987; Ingham, Nature, 335, 25-34, 1988). The members of the ANT-C and BX-C are among the best-characterized genes active in the Drosophila embryo. The basal units of their action are parasegments (PS) whose borders are out of phase with the borders of the segments which are seen in the mature embryo (see Fig. 1). The correct spatial expression of the homeotic selector genes of the ANT-C and BX-C is controlled at three different levels. Early in development, the maternal coordinate and the zygotic segmentation genes activate transcription of homeotic selector genes in a parasegmental frame. Later in development, the trans-regulatory Polycomb (PC) group genes repress the homeotic selector genes outside their domains. In addition, the homeotic selector genes repress each other, thereby maintaining the borders between their expression domains. Two observations suggested the existence of other homeotic genes active in the head and tail. First, loss-offunction mutations in the homeotic selector genes cause transformations only in the overtly segmented body region of the Drosophila embryo from PS 0 to 15, which correspond to posterior head, thorax, abdomen, and anterior tail. The extreme ends of the embryo, the anterior head and the posterior tail, are not affected in any homeotic selector gene mutation (Fig. 1). Second, the general rule that certain PS are simply transformed into anteriorly adjacent ones in selector gene mutations does not hold true for the posterior head and the anterior tail. Recently, two novel homeotic genes, spalt (sal) and fork head W h ) , have been identified for which the term regionspecific homeotic genes has been coined. In contrast to the homeotic selector genes of the ANT-C and BX-C, these genes act in two separate regions of the embryo. Both genes map outside the ANT-C and BX-C regions of the genome, and they do not share the homeodomain characteristic for the protein products of homeotic selector genes. Here, we review the genetic and molecular analysis of this class of homeotic genes. sal andflh mutations cause transformations in the head and tail of the Drosophila embryo

Image-based methods for phenotyping growth dynamics and fitness in large plant populations

Abstract: With the development of next-generation sequencing technologies, high-throughput phenotyping has become the new bottleneck of quantitative genetics analyses. The model species Arabidopsis thaliana offers extensive resources to investigate intraspecific trait variability and the genetic bases of ecologically relevant traits, such as growth dynamics and reproductive allocation. However, reproducible and cost-effective methods need to be developed for the measurement of growth and especially fitness related traits in large populations. Here we describe image-based methods that can be adapted to a wide range of laboratory conditions, and enable the reliable estimation of biomass accumulation and fruit production in thousands of A. thaliana individuals. We propose a semi-invasive approach, where part of a population is used to predict plant biomass from image analysis. The other part of the population is daily imaged during three weeks, then harvested at the end of the life cycle where rosette and inflorescence are separately imaged. We developed ImageJ macros and R codes for image segmentation, 2D skeletonization and subsequent statistical analysis. First, ontogenetic growth is modelled from estimated and measured dry mass for all individuals with non-linear regressions, from which the dynamics of absolute growth rate (GR) and relative growth rate (RGR) are calculated. Second, analysis of the 2D inflorescence skeleton allows the estimation of fruit production, an important component of plant fitness. Our method was evaluated across 451 natural accessions of A. thaliana. Cross-validation revealed that our image-based method allows predicting approximately 90% of biomass variation and 70% of fruit production. Furthermore, estimated traits - like measured traits - showed high heritabilities and inter-experiment reproducibility. We propose a flexible toolkit for the measurement of growth and fitness related traits in large plant populations. It is based on simple imaging, making the method reproducible at low cost in different facilities. However, as manual imaging of large plant populations can quickly become a limiting factor, we also describe an automated high-throughput imaging coupled with micro-computers that enables large phenotypic screening for genome-wide association studies and stress experiments.

A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina

Abstract: The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A. thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500-km2-area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species. Whole-genome resequencing revealed that plants from the four sites and a Patagonia herbarium specimen collected in 1967 formed a single haplogroup (Pat), indicating that the phenotypic variation observed in the field reflected plastic responses to the environment. ADMIXTURE and principal components analyses suggest that the ancestor of the Pat haplogroup either came from Italy or the Balkan/Caucasus regions of Eurasia. In the laboratory, plants from the Pat haplogroup were hyposensitive to continuous red (Rc) and shade light, with corresponding changes in expression of phytochrome signaling genes. Pat had higher PIF3 and PIF5 and lower HY5 expression under Rc light; and lower expression of PIL1, ATHB2 and HFR1 under shade compared to Col-0. In addition, Pat plants had a strong vernalization requirement associated with high levels of FLC expression. We conclude that including Pat in studies of natural variation and in comparisons with other introduced populations will provide additional information for genome-wide association studies and allow for a more detailed assessment of the demographic events following colonization. This article is protected by copyright. All rights reserved.

Pigment Pattern Formation in the Guppy, Poecilia reticulata, Involves the Kita and Csf1ra Receptor

Abstract: Males of the guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting on the color patterns of the guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, were described, both of which play a decisive role in the formation of the guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryogenesis and after birth is affected. Here, we show that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of guppy males, which in the case of csf1ra might be mediated by xanthophore-melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early appearing and kita-dependent and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides the first molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics.

A map of climate change-driven natural selection in Arabidopsis thaliana

Abstract: Through the lens of evolution, climate change is an agent of directional selection that forces populations to change and adapt, or face extinction. Current assessments of the risks associated with climate change, however, do not typically take into account that natural selection can dramatically impact the genetic makeup of populations. We made use of extensive genome information in Arabidopsis thaliana and measured how rainfall-manipulation affected the fitness of 517 natural lines grown in Spain and Germany. This allowed us to directly infer selection at the genetic level. Natural selection was particularly strong in the hot-dry Spanish location, killing 63% of lines and significantly changing the frequency of ~5% of all genome-wide variants. A significant proportion of this selection over variants could be predicted from climate (mis)match between experimental sites and the geographic areas of where variants are found (R2=29-52%). Field-validated predictions across the species range indicated that Mediterranean and Western Siberia populations -- at the edges of the species' environmental limits -- currently experience the strongest climate-driven selection, and Central Europeans the weakest. With rapidly increasing droughts and rising temperatures in Europe, we forecast a wave of directional selection moving North, putting many native A. thaliana populations at evolutionary risk.

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.