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On bioRxiv: Genomics of climate change adaptation

Posted on May 14, 2018

Genomic & geographic maps of climate change-driven natural selection in A. thaliana read more

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

Exposito-Alonso, M., et al. doi: https://doi.org/10.1101/321133

Through the lens of evolution, climate change is a directional selection acting on populations, forcing them to change and adapt, or face extinction. We studied climate-driven selection at the genetic level by measuring fitness of 517 Arabidopsis thaliana lines grown in rainfall-manipulation experiments in Spain and Germany. Natural selection in the hot-dry Mediterranean location was the strongest, killing 63% of the lines and significantly changing the frequency of about 5% of all genome-wide variants. Rainfall treatment dictated the direction and magnitude of selection: variants that increased in frequency in a low-rainfall environment, decreased in frequency under high rainfall, and vice versa. A significant proportion of this selection was predictable from the annotation of variants and from the climate in the areas where different variants are found (R2=29-52%). Extrapolating our predictions to other areas of the species range suggested that selection driven by local climate would be strongest in the Mediterranean and Western Siberia -- the edge of the species' environmental limits -- and weakest in Central Europe. With rapidly increasing droughts and rising temperatures in Europe, we forecast a wave of directional selection moving North, consequently decimating and causing a genetic turnover of some native A. thaliana populations.

On bioRxiv: Link between ACD6 and NLR signaling

Posted on April 14, 2018

Modulation of ACD6 dependent hyperimmunity by natural alleles of an NLR resistance gene read more

Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene

Zhu, W., Zaidem, M., Van de Weyer, A.-L., Gutaker, R. M., Chae, E., Kim, S.-T., Bemm, F., Li, L., Schwab, R., Unger, F., Beha, M. J., Demar, M., and Weigel, D.

bioRxiv posted April 13, 2018

Plants defend themselves against pathogens by activating an array of immune responses. Unfortunately, immunity programs may also cause unintended collateral damage to the plant itself. The quantitative disease resistance gene ACCELERATED CELL DEATH 6 (ACD6) serves as a nexus for the trade-off between growth and pathogen resistance in wild populations of Arabidopsis thaliana. An autoimmune allele, ACD6-Est, first identified in the natural accession Est-1, is found in over 10% of wild strains, even though it causes a clear fitness penalty under optimal growth conditions. There is, however, extensive variation in the strength of the autoimmune phenotype expressed by strains with an ACD6-Est allele, indicative of genetic modifiers. Quantitative genetic analysis suggests that the population genetic basis of ACD6 modulation is complex, with different strains often carrying different large-effect modifiers. One modifier is SUPPRESSOR OF NPR1-1, CONSTITUTIVE 1 (SNC1), located in a highly polymorphic cluster of nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes, which are prototypes for qualitative disease resistance genes. Allelic variation at SNC1 correlates with ACD6-Est activity in multiple accessions, and a common structural variant affecting the NL linker sequence can explain differences in SNC1 activity. Taken together, we find that an NLR gene can mask the activity of an ACD6 autoimmune allele in natural A. thaliana populations, thereby linking different arms of the plant immune system.  

Detlef to receive the Barbara McClintock Prize 2019

Posted on March 25, 2018

The award is given annually for career accomplishments in plant genomics read more

On March 24, the Maize Genetics Executive Committee announced that Detlef will receive the Barbara McClintock Prize 2019 for Plant Genetics and Genome Studies. The announcement takes place at the 2018 Maize Genetics Conference in Saint-Malo. 

The prize, which recognizes scientific accomplishment over the course of a career, is awarded annually to the most creative minds and productive scientists in the study of plant genome structure, function, and evolution, including the analysis of gene regulation and epigenetics. It is named in honor of Barbara McClintock, a distinguished geneticist and winner of the 1983 Nobel Prize in Physiology or Medicine. The award and medal will be conferred during a ceremony in Saint Louis, MO, as part of the 61st Annual Maize Genetics Conference.

Regional GWAS of flowering adaptation

Posted on March 19, 2018

Collaborative work with Carlos Alonso-Blanco and Xavi Picó read more

Genome-wide signatures of flowering adaptation to climate temperature: regional analyses in a highly diverse native range of Arabidopsis thaliana

Tabas-Madrid et al.: Plant Cell Environ. published online Mar 8

Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavorable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse A. thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million SNPs provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome-wide associations (EGWA) supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome-wide associations (PGWA) provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of EGWA and PGWA genomic regions identified known (TSF, FRL1 and CKB1) and new (ESM1 and VDAC5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.

Live fast/die young or live slow/die old?

Posted on March 19, 2018

Within-species allometry variation informs on growth strategies read more

Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Are there biological constants unifying phenotypic diversity across scales? Metabolic scaling theory (MST) predicts mathematical regularity and constancy in the allometric scaling of growth rate with body size across species. Here we show that adaptation to climate in Arabidopsis thaliana is associated with local strains that substantially deviate from the values predicted by MST. This deviation can be linked to increased stress tolerance at the expense of seed production, and it occurs through selection on genes that are involved in the abiotic stress response and are geographically correlated with climatic conditions. This highlights the evolutionary role of allometric diversification and helps establish the physiological bases of plant adaptation to contrasting environments.

On bioRxiv: Incomplete epigenetic reprogramming during asexual reprodu...

Posted on February 20, 2018

Epigenetic reprogramming during regeneration depends on tissue type read more

Incomplete reprogramming of cell-specific epigenetic marks during asexual reproduction leads to heritable phenotypic variation in plants

Wibowo et al. bioRxiv 2018/02/19/267955

Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. However, it is not currently known if this developmental reprogramming is coupled to a global epigenomic resetting, or what impact it has on the phenotype of the clonal progeny. Here we show that plants asexually propagated via induction of a zygotic developmental program do not fully reset cell-specific epigenetic imprints. These imprints are instead inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the founder cell used. Our results demonstrate how novel phenotypic variation in plants can be unlocked through the incomplete reprogramming of cell-specific epigenetic marks during asexual propagation.

 

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Upcoming Events

May
29

EvE Seminar, University of Tübingen

Lecture Hall N12, Morgenstelle 28, 12 noon

Moises speaking about "Forecasting climate change-driven evolution"


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06

MiKo Talk Walter Salzburger


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15

Gordon Research Conference

June 10-15, 2018
Holderness, NH

Detlef speaking about "Genetics and Epigenetics of Environmental Adaptation in Real Time"