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G3 (Bethesda). 2016 Jul 7;6(7):1979-89. doi: 10.1534/g3.116.028753.

Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.

Author information

1
Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Sweden.
2
Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100 Italy.

Abstract

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 FST 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 FST 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.

KEYWORDS:

FST; allele frequencies; local adaptation; pooled sequencing

PMID:
27172202
PMCID:
PMC4938651
DOI:
10.1534/g3.116.028753
[Indexed for MEDLINE]
Free PMC Article

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