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Genetic differentiation, clinal variation and phenotypic associations with growth cessation across the Populus tremula Photoperiodic Pathway
Program in Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University.
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. (Evolutionary Ecology)
Program in Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0002-7906-6891
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2010 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 186, 1033-1044 p.Article in journal (Refereed) Published
Abstract [en]

Perennial plants monitor seasonal changes through changes inenvironmental conditions such as the quantity and quality oflight. To ensure a correct initiation of critical developmentalprocesses, such as the initiation and cessation of growth, plantshave adapted to a spatially variable light regime and genesin the photoperiodic pathway have been implicated as likelysources for these adaptations. Here we examine genetic variationin genes from the photoperiodic pathway in Populus tremula (Salicaceae)for signatures diversifying selection in response to varyinglight regimes across a latitudinal gradient. We fail to identifyany loci with unusually high levels of genetic differentiationamong populations despite identifying four SNPs that show significantallele frequency clines with latitude. We do, however, observelarge covariance in allelic effects across populations for growthcessation, a highly adaptive trait in P. tremula. High covariancein allelic effects is a signature compatible with diversifyingselection along an environmental gradient. We also observe significantlyhigher heterogeneity in genetic differentiation among SNPs fromthe photoperiod genes than among SNPs from randomly chosen genes.This suggests that spatially variable selection could be affectinggenes from the photoperiod pathway even if selection is notstrong enough to cause individual loci to be identified as outliers.SNPs from three genes in the photoperiod pathway (PHYB2, LHY1,and LHY2) show significant associations with natural variationin growth cessation. Collectively these SNPs explain 10–15%of the phenotypic variation in growth cessation. Covariancesin allelic effects across populations help explain an additional5–7% of the phenotypic variation in growth cessation.

Place, publisher, year, edition, pages
2010. Vol. 186, 1033-1044 p.
Keyword [en]
association study, genetic diversity, populus, bud set
National Category
Genetics Ecology
URN: urn:nbn:se:umu:diva-30358DOI: 10.1534/genetics.110.120873ISI: 000283996100021OAI: diva2:281857
Available from: 2009-12-17 Created: 2009-12-17 Last updated: 2016-06-20Bibliographically approved
In thesis
1. Tracing selection and adaptation along an environmental gradient in Populus tremula
Open this publication in new window or tab >>Tracing selection and adaptation along an environmental gradient in Populus tremula
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The distribution of the expressed genotype is moved around in the population over time byevolution. Natural selection is one of the forces that act on the phenotype to change the patterns ofnucleotide variation underlying those distributions. How the phenotype changes over aheterogeneous environment describes the type of evolutionary force acting on this trait and thisshould be reflected in the variation at loci underlying this trait. While the variation in phenotypesand at the nucleotide level in a population indicates the same evolutionary force, it does notnecessarily mean that they are connected. In natural populations the continuous shifting of geneticmaterial through recombination events break down possible associations between loci facilitates theexamination of possible causal loci to single base pair differences in DNA-sequences. Connecting thegenotype and the phenotype thus provides an important step in the understanding the geneticarchitecture of complex traits and the forces that shape the observed patterns.This thesis examines the European aspen, Populus tremula, sampled from subpopulations overan extensive latitudinal gradient covering most of Sweden. Results show a clear geneticdifferentiation in the timing of bud set, a measure of the autumnal cessation of growth, betweendifferent parts of Sweden pointing at local adaptation. In the search for candidate genes thatunderlie the local adaptation found, most genes (25) in the photoperiodic gene network wereexamined for signals of selection. Genes in the photoperiodic network show an increase in theheterogeneity of differentiation between sampled subpopulations in Sweden. Almost half (12) of theexamined genes are under some form of selection. Eight of these genes show positive directionalselection on protein evolution and the gene that code for a photoreceptor, responsible for mediatingchanging light conditions to downstream targets in the network, has the hallmarks of a selectivesweep. The negative correlation between positive directional selection and synonymous diversityindicates that the majority of the photoperiod gene network has undergone recurrent selectivesweeps. A phenomenon that likely has occurred when P. tremula has readapted to the northern lightregimes during population expansion following retracting ice between periods of glaciations. Two ofthe genes under selection also have single nucleotide polymorphisms (SNP) that associate with budset, two in the PHYB2 gene and one in the LHY2 gene. Furthermore, there is an additional SNP inLHY1 that explain part of the variation in timing of bud set, despite the lack of a signal of selection atthe LHY1 gene. Together these SNPs explain 10-15% of the variation in the timing of bud set and 20-30% more if accounting for the positive co-variances between SNPs. There is thus rather extensiveevidence that genes in the photoperiod gene network control the timing of bud set, and reflect localadaptation in this trait.

Place, publisher, year, edition, pages
Umeå: Institutionen för Ekologi, miljö och geovetenskap, Umeå universitet, 2009. 42 p.
Local adaptation, Selection, genetic differentiation, QST, FST, Association study, frequency spectra, recurrent hitchhiking, selective sweep, Tree, Populus, natural selection, quantitative genetics
National Category
Research subject
Population Biology; Genetics
urn:nbn:se:umu:diva-30123 (URN)978-91-7264-907-1 (ISBN)
Public defence
2010-01-16, Stora Hörsalen KBC, KB3B1, Umeå Universitet, KBC, Linnaeus väg 6, Umeå, 10:00 (English)
Available from: 2009-12-17 Created: 2009-12-07 Last updated: 2010-02-01Bibliographically approved

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Hall, DavidJansson, StefanIngvarsson, Pär K
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Department of Ecology and Environmental SciencesDepartment of Plant PhysiologyUmeå Plant Science Centre (UPSC)
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