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Proc Natl Acad Sci U S A. 2018 May 8;115(19):5028-5033. doi: 10.1073/pnas.1719998115. Epub 2018 Apr 23.

Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana.

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Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523;
Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523.
Department of Biology, Pennsylvania State University, University Park, PA 16802.
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907.
Center for Plant Biology, Purdue University, West Lafayette, IN 47907.
Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden.
Department of Genetics, Rutgers University, Piscataway, NJ 08854.


Evidence for adaptation to different climates in the model species Arabidopsis thaliana is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish A. thaliana populations [Ågren J, et al. (2013) Proc Natl Acad Sci USA 110:21077-21082]. We find that genomic regions enriched in high FST SNPs colocalize with GT QTL peaks. Many of these high FST regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high FST SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation.


FST; divergent selection; ecotype; selective sweep; tradeoff

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