A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale
Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geograp...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.00967/full |
| _version_ | 1819028033863942144 |
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| author | Léa Frachon Léa Frachon Léa Frachon Claudia Bartoli Sébastien Carrère Olivier Bouchez Adeline Chaubet Mathieu Gautier Dominique Roby Fabrice Roux |
| author_facet | Léa Frachon Léa Frachon Léa Frachon Claudia Bartoli Sébastien Carrère Olivier Bouchez Adeline Chaubet Mathieu Gautier Dominique Roby Fabrice Roux |
| author_sort | Léa Frachon |
| collection | DOAJ |
| description | Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome–environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances. |
| first_indexed | 2024-12-21T05:51:56Z |
| format | Article |
| id | doaj.art-68e81135dd364571a7e967b73d8fcbb0 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T05:51:56Z |
| publishDate | 2018-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-68e81135dd364571a7e967b73d8fcbb02022-12-21T19:13:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-07-01910.3389/fpls.2018.00967375588A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic ScaleLéa Frachon0Léa Frachon1Léa Frachon2Claudia Bartoli3Sébastien Carrère4Olivier Bouchez5Adeline Chaubet6Mathieu Gautier7Dominique Roby8Fabrice Roux9Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, FranceDipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, ItalyDepartment of Systematic and Evolutionary Botany, University of Zurich, Zürich, SwitzerlandLaboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, FranceLaboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, FranceInstitut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, FranceInstitut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, FranceCentre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut de Recherche pour le Développement, Montpellier SupAgro, Université de Montpellier, Montpellier, FranceLaboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, FranceLaboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, FranceUnderstanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome–environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.https://www.frontiersin.org/article/10.3389/fpls.2018.00967/fullArabidopsis thalianaBayesian hierarchical modelclimate changegenome–environment association analysislocal adaptationPool-Seq |
| spellingShingle | Léa Frachon Léa Frachon Léa Frachon Claudia Bartoli Sébastien Carrère Olivier Bouchez Adeline Chaubet Mathieu Gautier Dominique Roby Fabrice Roux A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale Frontiers in Plant Science Arabidopsis thaliana Bayesian hierarchical model climate change genome–environment association analysis local adaptation Pool-Seq |
| title | A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale |
| title_full | A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale |
| title_fullStr | A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale |
| title_full_unstemmed | A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale |
| title_short | A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale |
| title_sort | genomic map of climate adaptation in arabidopsis thaliana at a micro geographic scale |
| topic | Arabidopsis thaliana Bayesian hierarchical model climate change genome–environment association analysis local adaptation Pool-Seq |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.00967/full |
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