Projekt

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Functional genomics of adaptive introgression: experimental transfer of zinc resistance between Arabidopsis halleri and A. lyrata.

Gesuchsteller/in Arrigo Nils
Nummer 148224
Förderungsinstrument Ambizione
Forschungseinrichtung Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Botanik
Beginn/Ende 01.10.2014 - 30.09.2017
Bewilligter Betrag 600'000.00
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Alle Disziplinen (2)

Disziplin
Botanik
Genetik

Keywords (5)

Gene flow; Systems biology; Heavy-metal resistance; Adaptive introgression; Admixture

Lay Summary (Französisch)

Lead
Une large fraction de la biodiversité des plantes voit son origine attribuée aux processus d'adaptation à l’environnement. Ce phénomène repose sur la présence de variabilité au sein des populations, de sorte que la sélection naturelle puisse « repérer » les individus les plus aptes dans un environnement donné. Dans ce contexte, l'hybridation (le croisement d’espèces distinctes) fournit une contribution significative en permettant le transfert d'adaptations environnementales d'une espèce à l'autre (un processus nommé “introgression adaptative”). Peu d’études ont cependant abordé la génomique de l'introgression adaptative. Ainsi, l'influence de nombreux paramètres liés à l'architecture génétique (tels que le nombre de gènes impliqués, leur position physique au sein du génome ainsi que leur contribution fonctionnelle au trait considéré) sur le potentiel d'introgression restent peu clairs.
Lay summary

Nous visons ici à combler ces lacunes par un suivi détaillé du phénomène, reproduit en conditions expérimentales et analysé au moyen de la génétique des populations, la génomique fonctionnelle et la bioinformatique. Nous nous basons sur un modèle bien connu; la résistance aux métaux lourd exprimée par Arabidopsis halleri, que l'on introgressera au sein de A. lyrata, une espèce cousine intolérante à ce même stress. Nous suivrons alors, sur un total de six générations, l'introgression des 40 gènes contribuant à cette adaptation par séquençage ADN haut-débit.

Notre projet porte un regard inédit sur la façon dont les liens fonctionnels entre génome et phénotype influencent l'introgression adaptative. Cette question fondamentale trouve de nombreuses applications, car le transfert d'adaptations entre espèces, via hybridation, est au centre de nombreux programmes d’amélioration des espèces cultivées.

Direktlink auf Lay Summary Letzte Aktualisierung: 17.07.2014

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution
Baniaga Anthony E, Arrigo Nils, Barker Michael S (2016), The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution, in Genome Biology and Evolution, 8(5), 1516-1525.
Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub
Mastretta-Yanes Alicia, Zamudio Sergio, Jorgensen Tove H., Arrigo Nils, Alvarez Nadir, Piñero Daniel, Emerson Brent C. (2014), Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub, in Genome biology and evolution, 6(10), 2611-2624.
Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis
Pajkovic Mila, Lappe Sylvain, Barman Rachel, Parisod Christian, Neuenschwander Samuel, Goudet Jerome, Alvarez Nadir, Guadagnuolo Roberto, Felber Francois, Arrigo Nils (2014), Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis, in MOLECULAR ECOLOGY, 23(20), 5089-5101.
Hybridization as a threat in climate relict Nuphar pumila (Nymphaceae)
Arrigo N, Bétrisey S, Graff L, Bilat J, Gerber E, Kozlowski G, Hybridization as a threat in climate relict Nuphar pumila (Nymphaceae), in Biodiversoty and Conservation, 25, 1863.
Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on museum collection specimens
Suchan T, Pitteloud C, Gerasimova N, Kostikova A, Arrigo N, Pajkovic M, Ronikier M, Alvarez N, Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on museum collection specimens, in Plos one, 11(3), e0151651.
Is hybridization driving the evolution of climatic niche in Alyssum montanum (Brassicaceae)?
Arrigo N, de la Harpe M, Litsios G, Zozomová-Lihová J, Španiel S, Marhold K, Barker MS, Alvarez N, Is hybridization driving the evolution of climatic niche in Alyssum montanum (Brassicaceae)?, in American Journal of Botany, 103(7), 1348-1357.
On the relative abundance of autopolyploids and allopolyploids
Barker Michael S., Arrigo Nils, Baniaga Anthony E., Li Z, Levin Donald A., On the relative abundance of autopolyploids and allopolyploids, in New Phytologist.
Parallel declines in species and genetic diversity driven by anthropogenic disturbance: a multi-species approach in a French Atlantic dune system
Frey D, Arrigo N, Granereau G, Sarr A, Kozlowski G, Parallel declines in species and genetic diversity driven by anthropogenic disturbance: a multi-species approach in a French Atlantic dune system, in Evolutionary Applications, 9(3), 479-488.
Repeated whole-genome duplication, karyotype reshuffling and biased retention of stress-responding genes in Buckler Mustards
Geiser C, Mandáková T, Arrigo N, Lysak MA, Parisod C, Repeated whole-genome duplication, karyotype reshuffling and biased retention of stress-responding genes in Buckler Mustards, in The Plant Cell, TPC2015-0.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Levi Yant, John Ines Center Grossbritannien und Nordirland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Annaliese Mason, Institut für Pflanzenbau und Pflanzenfüchtung, Uni. Giessen Deutschland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Isobel Parkin, Agriculture & Agri-food Canada, Saskatoon Kanada (Nordamerika)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Daniel Winkler, Dpt Ecology & Evolution, UC Davis Vereinigte Staaten von Amerika (Nordamerika)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
S. Buerki, NHM, London,UK Grossbritannien und Nordirland (Europa)
- Forschungsinfrastrukturen
Charles Davis, Dpt of organismic and Evolutionary Biology, Harvard Vereinigte Staaten von Amerika (Nordamerika)
- Publikation

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
OPTIMA 2016 Vortrag im Rahmen einer Tagung Hybridization in the Triticum­Aegilops species complex 11.06.2016 Montpellier, Frankreich Arrigo Nils;
International Conference on Polyploidy, Hybridization and Biodiversity 2016 Vortrag im Rahmen einer Tagung Is hybridization driving the evolution of climatic niche in Alyssum montanum (Brassicaceae)? 11.05.2016 Rovinj, Kroatien Arrigo Nils;
International Conference on Polyploidy, Hybridization and Biodiversity 2016 Poster Is hybridization impacting the diversification rates of land plant polyploids ? 11.05.2016 Rovinj, Kroatien Arrigo Nils;
Congress of the European Society for Evolutionary Biology 2015 (ESEB) Poster Is hybridization impacting the diversification rates of land plant polyploids ? 10.08.2015 Lausanne, Schweiz Arrigo Nils;


Kommunikation mit der Öffentlichkeit

Kommunikation Titel Medien Ort Jahr
Weitere Aktivitäten Société Neuchâteloise des Sciences Naturelles Westschweiz 2016

Abstract

A large fraction of land plant biodiversity is assumed to have arisen through adaptive processes, where the ecological and morphological features of species reflect adaptations to the environment. Such adaptations arise via the natural selection of individuals that have the largest reproductive success in a given environment. This process requires that some degree of genetic variation exists within a species, so that selection forces can operate. Hybridization (the interbreeding of different species) contributes significantly to adaptive processes by enabling genetic exchanges among species (a process termed “introgression”). Such exchanges have been shown to facilitate the transfer of ecological and morphological adaptations between species (e.g. involving key functions such as photosynthesis, mating system, flower morphology, or environmental stress tolerance). This process, termed "adaptive introgression", is highly significant from an evolutionary standpoint because it facilitates and accelerates the adaptation to new environments for the recipient species.Using whole genome sequencing, several studies have shown that the probability of introgression varies from one gene to another, thus producing so-called “porous species boundaries” where some genes flow readily among species while others remain trapped in their original genome. Few studies, however, have investigated this pattern in the context of adaptive introgression. Indeed, how parameters related to the genetic architecture of an adaptive trait (e.g. the number of involved genes, their chromosomal location or their functional contribution to the focal trait) affect its introgressive potential remains unclear. Here, I aim to bridge this gap by combining experimental biology, population genetics and functional genomics to survey the introgression of an adaptive trait, and that of its corresponding genes, from one species into another. In particular, I will address the following questions: i) of all the genes that are involved in an adaptive trait, which ones can readily be transferred across species boundaries? ii) How is the introgression probability of a gene related to functional parameters, such as qualitative and quantitative contribution to the focal trait, physical position on chromosomes and interactions (including conflicts) with the recipient genome? I will focus on a well-studied model by experimentally introgressing the heavy-metal resistance expressed by Arabidopsis halleri into the closely related and metal-sensitive Arabidopsis lyrata. The introgression process will be conducted in a selective environment (exposure to zinc soil contamination) and surveyed during at least six generations by collecting detailed phenotype and genetic data. To this end, the introgression of nearly 40 genes contributing to A. halleri heavy-metal resistance will be tracked in several experimental populations of A. lyrata, with the goal of providing a detailed and functional monitoring of adaptive introgression. The data will be generated using gene-targeted sequencing and genotyping-by-sequencing approaches. The obtained results will be investigated by combining the latest advances in population genomics (i.e. population simulations and Bayesian modelling of introgression) with genomic resources available for the Arabidopsis species.The project will show how the functional links between genome and phenotype influence adaptive introgression. This question bridges fundamental and applied sciences because understanding how adaptive traits are transferred among species is paramount for evolutionary biologists and crop breeders. The question is also important for assessing the risks associated with the spread of crop (trans)genes into related wild species. The proposed project is thus an essential contribution and will establish the foundations of this innovative research area in Switzerland.
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