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In Genetics: over 1,000 spontaneous mutations

Posted on December 10, 2018

New resource for understanding mutational processes in plants read more

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

Mao-Lun Weng, Claude Becker, Julia Hildebrandt, Matthew T. Rutter, Ruth G. Shaw, Detlef Weigel and Charles B. Fenster

Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the Arabidopsis thaliana reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for A. thaliana is 6.95 × 10?9 (s.e. ±2.68 × 10?10) per site per generation with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10?9 (±1.07 × 10?10) per site per generation, with deletions being more frequent and larger than insertions. Among the 1,694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that de novo mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.

On bioRxiv: Balancing selection in Capsella

Posted on November 30, 2018

Long-term balancing selection & evolution of immunity genes read more

Long-term balancing selection drives evolution of immunity genes in Capsella

Daniel Koenig et al. bioRxiv https://doi.org/10.1101/477612

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

Appeal to Federal Ministries of Research and Ag

Posted on November 26, 2018

German plant scientists: gene technology law is outdated read more

Leading German plant scientists agree that the gene technology law, which has been interpreted by the European Court of Justice to include genome edited organisms, is outdated and must be changed. They appeal to the Federal ministers of research and science and of agriculture to lead the charge in this matter.

Gentechnik im grünen Bereich?

Posted on November 20, 2018

Video from debate with Renate Künast read more

It's a (Wo)Man's World?

Posted on November 15, 2018

Detlef speaking at event on #WomenInSTEM read more

Public discussion on chances and opportunities for women in STEM professions. With Prof. Katharina Foerster, Dr. Brigit Buschmann, Prof. Corinna Salander and Detlef

November 28, 7 pm, Frauenprojektehaus Tübingen

Successful 2-day microbiome retreat

Posted on November 09, 2018

Intense brainstorming with Vorholt and Kemen labs read more

On November 6 and 7, we spent two days at Kloster Kirchberg to discuss the past, present and future of plant microbiome studies with the labs of Julia Vorholt at ETH and Eric Kemen at University of Tübingen. We generated lots of new ideas, and we are all looking forward to the next installment!

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