Norman Warthmann

Publications (32) View all

• Article: Artificial MicroRNAs for Specific Gene Silencing in Rice.

  Norman Warthmann, Stephan Ossowski, Rebecca Schwab, Detlef Weigel
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  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.
  Methods in molecular biology (Clifton, N.J.) 01/2013; 956:131-49.
• Source

  Available from: Detlef Weigel

  Article: Reference-guided assembly of four diverse Arabidopsis thaliana genomes.

  Korbinian Schneeberger, Stephan Ossowski, Felix Ott, Juliane D Klein, Xi Wang, Christa Lanz, Lisa M Smith, Jun Cao, Joffrey Fitz, Norman Warthmann, Stefan R Henz, Daniel H Huson, Detlef Weigel
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  ABSTRACT: We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html.
  Proceedings of the National Academy of Sciences 06/2011; 108(25):10249-54. · 9.68 Impact Factor
• Source

  Available from: Magnus Nordborg

  Article: Major-effect alleles at relatively few loci underlie distinct vernalization and flowering variation in Arabidopsis accessions.

  Amy Strange, Peijin Li, Clare Lister, Jillian Anderson, Norman Warthmann, Chikako Shindo, Judith Irwin, Magnus Nordborg, Caroline Dean
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  ABSTRACT: We have explored the genetic basis of variation in vernalization requirement and response in Arabidopsis accessions, selected on the basis of their phenotypic distinctiveness. Phenotyping of F2 populations in different environments, plus fine mapping, indicated possible causative genes. Our data support the identification of FRI and FLC as candidates for the major-effect QTL underlying variation in vernalization response, and identify a weak FLC allele, caused by a Mutator-like transposon, contributing to flowering time variation in two N. American accessions. They also reveal a number of additional QTL that contribute to flowering time variation after saturating vernalization. One of these was the result of expression variation at the FT locus. Overall, our data suggest that distinct phenotypic variation in the vernalization and flowering response of Arabidopsis accessions is accounted for by variation that has arisen independently at relatively few major-effect loci.
  PLoS ONE 01/2011; 6(5):e19949. · 4.09 Impact Factor
• Source

  Available from: Sang-Tae Kim

  Article: Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana.

  Kirsten Bomblies, Levi Yant, Roosa A Laitinen, Sang-Tae Kim, Jesse D Hollister, Norman Warthmann, Joffrey Fitz, Detlef Weigel
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  ABSTRACT: As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local "outcrossing hotspots" appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.
  PLoS Genetics 01/2010; 6(3):e1000890. · 8.69 Impact Factor
• Source

  Available from: Detlef Weigel

  Article: The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana.

  Stephan Ossowski, Korbinian Schneeberger, José Ignacio Lucas-Lledó, Norman Warthmann, Richard M Clark, Ruth G Shaw, Detlef Weigel, Michael Lynch
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  ABSTRACT: To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 x 10(-9) base substitutions per site per generation, the majority of which are G:C-->A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light-induced mutagenesis.
  Science 01/2010; 327(5961):92-4. · 31.20 Impact Factor