Change search
ReferencesLink to record
Permanent link

Direct link
Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European aspen (Populus tremula, Salicaceae).
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
Show others and affiliations
2008 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 178, no 4, 2217-26 p.Article in journal (Refereed) Published
Abstract [en]

We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the "hinge region," close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

Place, publisher, year, edition, pages
Pittsburgh, Pennsylvania, USA: the Genetics Society of America , 2008. Vol. 178, no 4, 2217-26 p.
URN: urn:nbn:se:umu:diva-9659DOI: 10.1534/genetics.107.082354PubMedID: 18245834OAI: diva2:149330
Available from: 2008-05-09 Created: 2008-05-09 Last updated: 2015-04-29Bibliographically 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

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Ingvarsson, PärGarcia, MaribelHall, DavidJansson, Stefan
By organisation
Department of Ecology and Environmental SciencesUmeå Plant Science Centre (UPSC)Department of Plant Physiology
In the same journal

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 75 hits
ReferencesLink to record
Permanent link

Direct link