Latest News

Are gene technology and organic farming compatible?

Posted on September 09, 2018

Hear Detlef debate a prominent organic farmer read more

Deutschlandfunk radio: Detlef debates Felix Prinz zu Löwenstein, Chairman of the Board of the Organisation of Organic Farmers (Bund Ökologische Lebensmittelwirtschaft BÖLW). You can listen to the debate here.

(Or download the .mp file here.)

Rui's CRISPR/Cas9 vectors in Plant Methods

Posted on August 04, 2018

CRISPR vector toolbox for deletions – plasmids in Addgene read more

An efficient CRISPR vector toolbox for engineering large deletions in Arabidopsis thaliana

Rui Wu et al Plant Methods 14:65

Vectors available at Addgene

Our knowledge of natural genetic variation is increasing at an extremely rapid pace, affording an opportunity to come to a much richer understanding of how effects of specific genes are dependent on the genetic background. To achieve a systematic understanding of such GxG interactions, it is desirable to develop genome editing tools that can be rapidly deployed across many different genetic varieties. We present an efficient CRISPR/Cas9 toolbox of super module (SM) vectors. These vectors are based on a previously described fluorescence protein marker expressed in seeds allowing identification of transgene-free mutants. We have used this vector series to delete genomic regions ranging from 1.7 to 13 kb in different natural accessions of the wild plant Arabidopsis thaliana. Based on results from 53 pairs of sgRNAs targeting individual nucleotide binding site leucine-rich repeat (NLR) genes, we provide a comprehensive overview of obtaining heritable deletions. The SM series of CRISPR/Cas9 vectors enables the rapid generation of transgene-free, genome edited plants for a diversity of functional studies.

 

Moi's paper on flowering time under global change published

Posted on July 26, 2018

Fast flowering Northern genotypes will have an advantage read more

Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana

Exposito-Alonso et al., Evolution (2018)

The evolutionary response of organisms to global climate change is expected to be strongly conditioned by preexisting standing genetic variation. In addition, natural selection imposed by global climate change on fitness-related traits can be heterogeneous over time. We estimated selection of life-history traits of an entire genetic lineage of the plant Arabidopsis thaliana occurring in north-western Iberian Peninsula that were transplanted over multiple years into two environmentally contrasting field sites in southern Spain, as southern environments are expected to move progressively northwards with climate change in the Iberian Peninsula. The results indicated that natural selection on flowering time prevailed over that on recruitment. Selection favored early flowering in six of eight experiments and late flowering in the other two. Such heterogeneity of selection for flowering time might be a powerful mechanism for maintaining genetic diversity in the long run. We also found that north-western A. thaliana accessions from warmer environments exhibited higher fitness and higher phenotypic plasticity for flowering time in southern experimental facilities. Overall, our transplant experiments suggested that north-western Iberian A. thaliana has the means to cope with increasingly warmer environments in the region as predicted by trends in global climate change models.

Talia's paper on Pseudomonas population structure published

Posted on July 11, 2018

A single Pseudomonas lineage dominates local Arabidopsis populations read more

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales

Karaso. Almario, Friedemann et al.

Cell Host & Microbe, Volume 24, Issue 1, 11 July 2018, Pages 155-167.e5

Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.

Danelle's paper on transmission ratio distortion published

Posted on June 28, 2018

Over 500 segregating F2 populations analyzed read more

Transmission ratio distortion is frequent in Arabidopsis thaliana controlled crosses

Seymour et al., Heredity (2018), published online June 28

bioRxiv version with a slightly different title: The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana

The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. The preferential transmission of alleles or genotypes is termed transmission ratio distortion (TRD). Examples of TRD have been identified in many species, implying that they are universal, but the resolution of species-wide studies of TRD are limited. We have performed a species-wide screen for TRD in over 500 segregating F2 populations of Arabidopsis thaliana using pooled reduced-representation genome sequencing. TRD was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the biological basis of TRD in this species.

Pangenome analysis tool for Pseudomonas online

Posted on June 26, 2018

panX website for 1,524 Pseudomonas genomes read more

panX is a software package for comprehensive pan-genome analysis, web-based interactive visualization and dynamic exploration, developed by Wei Ding and Richard Neher. 

We have recently assembled the genomes of 1,524 Pseudomonas genomes collected from Arabidopsis thaliana around Tübingen. Our web tool allows exploration of these genomes, described in this paper.

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