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Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps


Fischer, Martin C; Rellstab, Christian; Tedder, Andrew; Zoller, Stefan; Gugerli, Felix; Shimizu, Kentaro K; Holderegger, Rolf; Widmer, Alex (2013). Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. Molecular Ecology, 22(22):5594-5607.

Abstract

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here we examine genome- wide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST–based analyses. We tested only the most strongly differentiated SNPs for associations with a non-redundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genome-wide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here we examine genome- wide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST–based analyses. We tested only the most strongly differentiated SNPs for associations with a non-redundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genome-wide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 University Research Priority Programs > Systems Biology / Functional Genomics
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
580 Plants (Botany)
Language:English
Date:2013
Deposited On:19 Sep 2013 09:20
Last Modified:05 Apr 2016 16:59
Publisher:Wiley-Blackwell
ISSN:0962-1083
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1111/mec.12521
Official URL:http://onlinelibrary.wiley.com/doi/10.1111/mec.12521/abstract
Permanent URL: https://doi.org/10.5167/uzh-81031

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