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Genomics of adaptation in the context of a rapid plant radiation

English title Genomics of adaptation in the context of a rapid plant radiation
Applicant Widmer Alexander
Number 160123
Funding scheme Project funding
Research institution Institute of Integrative Biology Environmental Systems Science ETH Zurich
Institution of higher education ETH Zurich - ETHZ
Main discipline Botany
Start/End 01.06.2015 - 30.09.2018
Approved amount 600'000.00
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All Disciplines (2)

Discipline
Botany
Ecology

Keywords (5)

natural selection; adaptation; hybridization; standing genetic variation; genomics

Lay Summary (German)

Lead
Pflanzen passen sich auf vielfältige Weise an ihren Lebensraum an. Anhand von Alpenpflanzen lassen sich solche Anpassungsprozesse besonders gut untersuchen, da sich die Umweltbedingungen in den Alpen oft über geringe Distanzen dramatisch verändern. Dieses Projekt untersucht die genetische Grundlage der Höhenanpassung bei einheimischen Nelkenarten (Dianthus spp.) mittels einer Kombination aus Genomanalysen und ökologischen Experimenten.
Lay summary

Unser Verständnis der genetischen Grundlagen der Anpassung von Pflanzen an ihre belebte und unbelebte Umwelt ist heute noch sehr lückenhaft und weitgehend beschränkt auf relativ wenige Gene, die insbesondere in Modellorganismen im Detail untersucht worden sind. Bei der überwiegenden Mehrzahl einheimischer Pflanzen wissen wir jedoch nicht, ob Anpassung durch einige wenige Gene oder durch eine Vielzahl von Genen beeinflusst ist. Sobald wir diese Gene kennen, können wir untersuchen, ob die genetischen Variation, die mit Anpassungsunterschieden assoziiert ist, erst kürzlich entstand oder seit Jahrtausenden im Genpool dieser Arten vorhanden ist. Ebenso können wir anhand von ökologischen Experimenten testen, wie stark Pflanzen, die zum Beispiel in eine wärmere Umwelt verpflanzt werden - indem sie aus einer Hochlage in eine tiefere Lage versetzt werden - unter diesen veränderten Umweltbedingungen leiden und wir können herausfinden, welche genetischen Unterschiede es Pflanzen aus wärmeren Lagen erlauben, unter diesen Bedingungen zu überleben.

Dieses Projekt befasst sich mit Grundlagenforschung. Es hat das Ziel, zu einem besseren Verständis der Anpassung von Pflanzen an ihre Umwelt beizutragen. Das Studium von Modellorganismen wie z.B. Arabidopsis thaliana ist dazu sehr wichtig, jedoch nicht ausreichend. Eine bessere Kenntnis der genetischen Grundlage der Anpassung ist unabdingbar für eine Abschätzung, ob und wie rasch sich Pflanzen an eine sich verändernde Umwelt anpassen können.

Direct link to Lay Summary Last update: 28.05.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
Genomic imprinting mediates dosage compensation in a young plant XY system
Muyle Aline, Zemp Niklaus, Fruchard Cécile, Cegan Radim, Vrana Jan, Deschamps Clothilde, Tavares Raquel, Hobza Roman, Picard Franck, Widmer Alex, Marais Gabriel A. B. (2018), Genomic imprinting mediates dosage compensation in a young plant XY system, in Nature Plants, 4(9), 677-680.
Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia ?
Zemp Niklaus, Widmer Alex, Charlesworth Deborah (2018), Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia ?, in Proceedings of the Royal Society B: Biological Sciences, 285(1883), 20172824-20172824.
Trait differentiation and adaptation of plants along elevation gradients
Halbritter Aud H., Fior Simone, Keller Irene, Billeter Regula, Edwards Peter J., Holderegger Rolf, Karrenberg Sophie, Pluess Andrea R., Widmer Alex, Alexander Jake M. (2018), Trait differentiation and adaptation of plants along elevation gradients, in JOURNAL OF EVOLUTIONARY BIOLOGY, 31(6), 784-800.
Evolution of sex-biased gene expression in a dioecious plant
Zemp Niklaus, Tavares Raquel, Muyle Aline, Charlesworth Deborah, Marais Gabriel A. B., Widmer Alex (2016), Evolution of sex-biased gene expression in a dioecious plant, in Nature Plants, 2, 1-7.
Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia
Zemp Niklaus, Tavares Raquel, Widmer Alex (2015), Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia, in PLOS Genetics, 1-17.

Collaboration

Group / person Country
Types of collaboration
Prof. Dr. Gabriel AB Marais, University of Lyon France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Dr. Stefan Zoller, Genetic Diversity Centre ETHZ Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Prof. Dr. Daniel Wegmann Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Seminar series Individual talk Ecological genetics and genomics of altitudinal adaptation in wild carnation 18.06.2018 Vienna, Austria Widmer Alexander;
Seminar series Individual talk Adaptation from long-standing genetic variation in an alpine plant 14.03.2018 Bern, Switzerland Widmer Alexander;
Seminar series Individual talk Adaptation from long-standing genetic variation in an alpine plant 15.11.2017 Geneva, Switzerland Widmer Alexander;
Seminar series Individual talk Ecological adaptation and evolutionary divergence in Silene 01.12.2016 Basel, Switzerland Widmer Alexander;
Symposium of the Zuri -Basel Plant Science Center Talk given at a conference Genetic diversity and adaptation in natural populations 03.12.2015 Zurich, Switzerland Widmer Alexander;


Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions Genomik der Anpassung bei Alpenpflanzen German-speaking Switzerland 2018

Associated projects

Number Title Start Funding scheme
182675 Ecological Genomics of Plant Adaptation 01.10.2018 Project funding
141260 Genomic divergence in plants: exploring the consequences of ecological adaptation for plant divergence and speciation 01.05.2012 Project funding

Abstract

Developing a better understanding of plant adaptation to the environment is an important goal in modern plant sciences because adaptation is essential for the continued existence of viable plant populations and communities and for future crop production. Studying plant adaptation requires a multidisciplinary approach that focuses not only on the genes or genetic variants underlying adaptation, but also investigates the ecological effects and molecular functions of adaptive variation, and its evolutionary origins. The goal of this project is to contribute to the understanding of adaptation by continuing ongoing studies on altitudinal adaptation and ecological divergence in natural populations of wild carnation (Dianthus) using a combination of approaches from population genomics, evolutionary ecology and molecular plant biology. A major resource for this project is the assembly of draft genomes for D. sylvestris and D. carthusianorum, which facilitates the identification of highly differentiated genes and genomic regions associated with altitudinal adaptation and ecotype formation in both species. Interestingly, adaptive divergence between altitudinal ecotypes in both species is largely located in different genomic regions, indicating limited parallel adaptation to altitude in these species. In this project we plan to dissect and validate the genomic basis of altitudinal adaptation and divergence in Dianthus, and to explore the contribution of ancient polymorphisms versus novel mutations to adaptive genetic variation in Dianthus. The specific aims and objectives of this project are 1) to further characterize genomic divergence between altitudinal ecotypes in D. sylvestris and D. carthusianorum, 2) to experimentally validate the fitness effects and molecular functions of candidate genes and genomic regions, 3) to identify genes associated with phenotypic divergence between ecotypes using a genome-wide association approach, and 4) to quantify the genomic distribution and age of ancient polymorphisms versus novel mutations.Results from this project will hopefully reveal causal genes for altitudinal adaptation in Dianthus, unravel the genomic context of these genes - for example, whether they are located in inversions or other regions with reduced recombination rates, and whether they are arranged in tight linkage with other 'adaptation' genes - reveal the origins of shared ancestral polymorphisms in adaptive alleles and shed light on the long-standing question whether adaptation evolves from novel mutations or standing genetic variation.
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