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Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
INRA Nancy, 54280 Champenoux, France.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Dept. of Plant Biology and Forest Genetics, Swedish Agricultural University, Uppsala, Sweden.
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2014 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 9, no 5, e95306- p.Article in journal (Refereed) Published
Abstract [en]

The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce

Place, publisher, year, edition, pages
2014. Vol. 9, no 5, e95306- p.
National Category
Natural Sciences Genetics Biological Sciences
URN: urn:nbn:se:uu:diva-180367DOI: 10.1371/journal.pone.0095306ISI: 000338213300010OAI: diva2:549703
Available from: 2012-09-05 Created: 2012-09-05 Last updated: 2014-08-06Bibliographically approved
In thesis
1. Population Genetics and Genome Organization of Norway Spruce
Open this publication in new window or tab >>Population Genetics and Genome Organization of Norway Spruce
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the underlying genetic causes of adaptation to local conditions is one of the main goals of population genetics. A strong latitudinal cline in the phenotypic trait of bud set is observed in present day populations of Norway spruce (Picea abies (L.) Karst). The first step towards determining how this strong selection on adaptive traits translates at the loci underlying the trait was to use multilocus sequence data to gain information on the fundamental population genetic properties of Norway spruce. We determined that the level of LD was low and genetic diversity was in the low range. Coalescent simulations revealed a demographic scenario of a fairly old and severe bottleneck as consistent with the observed data. To examine the role of selection at genes putatively involved in the control of bud set we, again, used a multilocus data set to test for deviations from neutrality and demographic scenarios inferred from background loci. Different candidate genes were identified by using different approaches, highlighting the difficulty in predicting how local adaptation will manifest itself on different time scales and in rangewide samples. When examining properties important in the design of association studies, the inevitable next step in identifying genes involved in local adaptation, we found that previous estimates of a low level of LD were highly influenced by the joint analysis of several loci over a large distribution range and that estimates of LD was in fact heterogeneous across loci and increased within populations. In addition, we found that within species tests for deviations from neutral expectations were highly sensitive to sample size. Additional genomic sequence characterization in Norway spruce is necessary to provide more comprehensive sets of markers for association studies, also including gene promoters and non-genic regions of the genome. In the final paper we show that the HMPR method is effective in constructing libraries enriched for the single copy fraction of the genome when applied to the large and dominantly repetitive genome of Norway spruce.

In summary, the studies presented in this thesis together constitute a foundation for future studies on adaptive evolution in Norway spruce.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 44 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 969
Picea abies, demographic history, linkage disequilibrium, HMPR
National Category
Genetics Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Functional Genomics
urn:nbn:se:uu:diva-180370 (URN)978-91-554-8465-1 (ISBN)
Public defence
2012-10-19, Zootissalen, Evolutionsbiologiskt Centrum (EBC), Villavägen 9, Uppsala, 10:00 (English)
Available from: 2012-09-28 Created: 2012-09-05 Last updated: 2013-01-23Bibliographically approved

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