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Impact of transposable elements on plant population evolution: insight from the model grass species brachypodium distachyon

English title Impact of transposable elements on plant population evolution: insight from the model grass species brachypodium distachyon
Applicant Roulin Anne
Number 182785
Funding scheme Project funding (Div. I-III)
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Genetics
Start/End 01.10.2019 - 30.09.2023
Approved amount 670'518.00
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All Disciplines (2)

Discipline
Genetics
Ecology

Keywords (6)

evolution; brachypodium distachyon; transposable elements; population genomics; grasses; local adaptation

Lay Summary (French)

Lead
Transposable elements constitute the main component of plant genomes. However, little is known about their impact on plant evolution in natural populations. The goal of the project is to make up for this lack and to investigate to what extent transposable elements may confer adaptive advantages in set of natural accessions of the grass Brachypodium distachyon.
Lay summary

Afin d'étudier le role des éléments transposables dans l'adaptation des plantes, je propose ici deux sujets complémentaires. Avec le projet 1, nous allons scanner le genome pour détecter des signaux de sélection positive et balancée et pour d'identifier des éléments transposables jouant un role adaptatif. Ses candidats seront validés au niveau moléculaire dans un second temps. Avec project 2, nous allons activer les éléments transposables in planta afin d'étudier directement leur impact sur le phénotype des plantes.

Direct link to Lay Summary Last update: 15.07.2019

Responsible applicant and co-applicants

Employees

Associated projects

Number Title Start Funding scheme
154724 Population genomics and local adaptation: genome wide analysis of transposable elements and natural population evolutionary trajectories. 01.03.2015 Ambizione

Abstract

Local adaptation constitutes the first step to biological diversification and speciation. Elucidating the genetic mechanisms underlying this evolutionary process remains thus a major question in biology. Even though transposable elements (TEs) constitute the main component of Eukaryotic genomes and a great source of genetic diversity and phenotypic variation, their role in local adaption has been poorly studied. The aim of my research is to unravel how TE activity may influence population evolution and adaptation in the grass Brachypodium distachyon. Established as a powerful system for research in grass genomics, the relatively small genome of B. distachyon (280Mb) is fully assembled into five chromosomes and harbors over 30% of transposable elements. In addition, the species is broadly distributed around the Mediterranean rim, providing access to natural populations from contrasting habitats for which hundreds of accessions have been collected. Eventually, a large collection of T-DNA lines is also available and CRISPR-Cas9 has been successfully established in this species, making it a prime system to investigate at the functional level the genetic basis of local adaptation in natural grass populations. Capitalizing on my former SNSF project, I propose here two complementary projects to specifically investigate the role of TEs in this process:Project 1: I plan to (i) use genome-wide scans of selection to detect in silico adaptive TEs under positive and balancing selection across a large number of populations and (ii) select a subset of adaptive insertions to functionally validate their impact on phenotypes. Project 2: I intend to assess in planta the link between environmental condition variation, TE activity and adaptation by (i) applying a combination of stresses across a subset of genetically divers B. distachyon accessions to create small bursts of transposition (ii) assess the impact of stress-induced neo-insertions on gene expression, phenotypic and fitness variation in the plants in which TEs were successfully activated. B. distachyon is a model for research on temperate grass species as it is closely related to major crop cereals and to some of the annual and perennial grasses used as biofuel crops. B. distachyon, however, has a far less complex genome than most crops with regard to ploidy level and TE content, which ease bioinformatics and comparative genomics analyses. The combined approaches proposed here will foster our understanding on the link between genome structural changes and population evolution, and open the way to further fundamental and applied research. It will also provide the community with unprecedented genomic data that will be valuable for allele mining and candidate gene validation through genome-wide association analyses.
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