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Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Chinese Acad Sci, Key Lab Stress Physiol & Ecol Cold & Arid Reg, Lanzhou, Peoples R China..
Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy..
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2016 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 7, 1979-1989 p.Article in journal (Refereed) PublishedText
Abstract [en]

The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.

Place, publisher, year, edition, pages
2016. Vol. 6, no 7, 1979-1989 p.
Keyword [en]
pooled sequencing, F-ST, allele frequencies, local adaptation
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URN: urn:nbn:se:uu:diva-300546DOI: 10.1534/g3.116.028753ISI: 000379590200018PubMedID: 27172202OAI: oai:DiVA.org:uu-300546DiVA: diva2:951708
EU, European Research CouncilSwedish Research Council Formas
Available from: 2016-08-10 Created: 2016-08-09 Last updated: 2016-08-10Bibliographically approved

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Chen, JunKällman, ThomasLascoux, Martin
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Plant Ecology and EvolutionDepartment of Medical Biochemistry and Microbiology
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