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

Fischer MC, Rellstab C, Tedder A, Zoller S, Gugerli F, Shimizu KK, Holderegger R, Widmer A - Mol. Ecol. (2013)

Bottom Line: We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors.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 genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

View Article: PubMed Central - PubMed

Affiliation: ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland.

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Population genomic evidence for adaptation to environmental variation in A. halleri for candidate gene P-GLYCOPROTEIN 1 (AT2G36910). (a) Pairwise FST values from highly differentiated sliding windows (lines) and SNPs (open circles). The dashed line at 0.038 indicates the mean FST across all SNPs, and the dotted line at 0.47 represents the 99.9% quantile threshold for strongly differentiated sliding windows. (b) Correlation between pairwise population differences in FST and solar radiation. rPMT represents the correlation coefficient of the partial Mantel test. (c) Linear regression between major allele frequencies and solar radiation. Results for the remaining candidate genes are shown in Fig. S1 (Supporting information).
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fig04: Population genomic evidence for adaptation to environmental variation in A. halleri for candidate gene P-GLYCOPROTEIN 1 (AT2G36910). (a) Pairwise FST values from highly differentiated sliding windows (lines) and SNPs (open circles). The dashed line at 0.038 indicates the mean FST across all SNPs, and the dotted line at 0.47 represents the 99.9% quantile threshold for strongly differentiated sliding windows. (b) Correlation between pairwise population differences in FST and solar radiation. rPMT represents the correlation coefficient of the partial Mantel test. (c) Linear regression between major allele frequencies and solar radiation. Results for the remaining candidate genes are shown in Fig. S1 (Supporting information).

Mentions: Results of the FST and sliding-window analyses and environmental association plots are shown in Fig.4 for candidate gene PGP1 and for the three other top candidate genes in Fig. S1 (Supporting information). The strongly differentiated regions span distances of at least 1000 bp (Fig.4a and Fig. S1a–c; Supporting information), which is consistent with a footprint of selection. Amino acid differences caused by nonsynonymous substitutions were found between MACHs (Table2). Interestingly, two of the nonsynonymous substitutions in genes GPX3 and ATGLR 3.6 were among the highly differentiated SNPs that are associated with the corresponding environmental factors.


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

Fischer MC, Rellstab C, Tedder A, Zoller S, Gugerli F, Shimizu KK, Holderegger R, Widmer A - Mol. Ecol. (2013)

Population genomic evidence for adaptation to environmental variation in A. halleri for candidate gene P-GLYCOPROTEIN 1 (AT2G36910). (a) Pairwise FST values from highly differentiated sliding windows (lines) and SNPs (open circles). The dashed line at 0.038 indicates the mean FST across all SNPs, and the dotted line at 0.47 represents the 99.9% quantile threshold for strongly differentiated sliding windows. (b) Correlation between pairwise population differences in FST and solar radiation. rPMT represents the correlation coefficient of the partial Mantel test. (c) Linear regression between major allele frequencies and solar radiation. Results for the remaining candidate genes are shown in Fig. S1 (Supporting information).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4274019&req=5

fig04: Population genomic evidence for adaptation to environmental variation in A. halleri for candidate gene P-GLYCOPROTEIN 1 (AT2G36910). (a) Pairwise FST values from highly differentiated sliding windows (lines) and SNPs (open circles). The dashed line at 0.038 indicates the mean FST across all SNPs, and the dotted line at 0.47 represents the 99.9% quantile threshold for strongly differentiated sliding windows. (b) Correlation between pairwise population differences in FST and solar radiation. rPMT represents the correlation coefficient of the partial Mantel test. (c) Linear regression between major allele frequencies and solar radiation. Results for the remaining candidate genes are shown in Fig. S1 (Supporting information).
Mentions: Results of the FST and sliding-window analyses and environmental association plots are shown in Fig.4 for candidate gene PGP1 and for the three other top candidate genes in Fig. S1 (Supporting information). The strongly differentiated regions span distances of at least 1000 bp (Fig.4a and Fig. S1a–c; Supporting information), which is consistent with a footprint of selection. Amino acid differences caused by nonsynonymous substitutions were found between MACHs (Table2). Interestingly, two of the nonsynonymous substitutions in genes GPX3 and ATGLR 3.6 were among the highly differentiated SNPs that are associated with the corresponding environmental factors.

Bottom Line: We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors.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 genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

View Article: PubMed Central - PubMed

Affiliation: ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland.

Show MeSH
Related in: MedlinePlus