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Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (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 Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
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2012 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 191, no 3, 865-881 p.Article in journal (Refereed) Published
Abstract [en]

Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

Place, publisher, year, edition, pages
2012. Vol. 191, no 3, 865-881 p.
Keyword [en]
clinal variation, photoperiodic pathway, Norway spruce, FT genes
National Category
Evolutionary Biology Genetics
Identifiers
URN: urn:nbn:se:uu:diva-177467DOI: 10.1534/genetics.112.140749ISI: 000308999900015PubMedID: 22542968OAI: oai:DiVA.org:uu-177467DiVA: diva2:541003
Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2017-12-07Bibliographically approved
In thesis
1. Conifer Evolution, from Demography and Local Adaptation to Evolutionary Rates: Examples from the Picea genus
Open this publication in new window or tab >>Conifer Evolution, from Demography and Local Adaptation to Evolutionary Rates: Examples from the Picea genus
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Evolutionary process can be inferred at three different levels: the species level, the population level and the molecular level. In this thesis, I applied approaches at these three levels and aimed to get a comprehensive picture of conifer evolution, from speciation and demography to geographic variation and local adaptation, and then to the molecular evolution of proteins and small regulatory RNAs.

Spruce species have been observed to possess a large number of trans-species shared polymorphisms. Using an “Isolation with migration” model, we found that the large effective population size of spruce retained these shared polymorphisms, inheriting them from the common ancestor. Post-divergence gene flow only existed between Picea abies and P. glauca, and between P. wilsonii and P. schrenkiana. The combination of Tajima’s D and Fay & Wu’s H at most of loci suggested an ancient and severe bottleneck for most species except P. breweriana.

Furthermore, I investigated the effect of local selection in two parallel clines, which is one of the major forces that can cause divergence or even speciation. The timing of bud set and growth cessation was found correlated with latitude in populations of P. abies and P. obovata. Using allele frequency spectrum analyses we identified three genes under local selection in both species including two circadian-clock genes GI and PRR7, and one photoperiodic gene FTL2. This indicated that parallel evolution could occur through groups of genes within related pathways. Clinal variation at expression level provided stronger evidence of selection in FTL2, which has previously been associated with bud set in P. abies.

Finally we focused on the molecular evolution of mRNA and small regulatory RNAs in P. abies. With the help of Next-Generation sequencing, we have achieved in spruce the first de novel assembly of the needle transcriptome and a preliminary characterization of sRNA populations. Along with features common in plants, spruce also exhibited novelties in many aspects including lower substitution rate and protein evolutionary rate, dominance of 21-nt sRNA, and a large proportion of TIR-NBS-LRR genes as sRNA sources and targets.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 52 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 947
Keyword
Speciation, Demographics, clinal variation, convergent evolution, transcriptome, small regulatory RNA
National Category
Evolutionary Biology Genetics
Research subject
Biology with specialization in Evolutionary Functional Genomics; Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-177482 (URN)978-91-554-8411-8 (ISBN)
Public defence
2012-09-14, Lindahlsalen, EBC, Norbyvägen 18A, Uppsala, 10:00 (English)
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Available from: 2012-08-24 Created: 2012-07-13 Last updated: 2013-01-22Bibliographically approved

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Chen, JunKällman, ThomasMa, XiaofeiLagercrantz, UlfLascoux, Martin

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