uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Splicing variation at a FLOWERING LOCUS C homeolog is associated with flowering time variation in the tetraploid Capsella bursa-pastoris
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
Show others and affiliations
2009 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 183, no 1, 337-345 p.Article in journal (Refereed) Published
Abstract [en]

The long-term fates of duplicate genes are well studied both empirically and theoretically, but how the short-term evolution of duplicate genes contributes to phenotypic variation is less well known. Here, we have studied the genetic basis of flowering time variation in the disomic tetraploid Capsella bursa-pastoris. We sequenced four duplicate candidate genes for flowering time and 10 background loci in samples from western Eurasia and China. Using a mixed-model approach that accounts for population structure, we found that polymorphisms at one homeolog of two candidate genes, FLOWERING LOCUS C (FLC) and CRYPTOCHROME1 (CRY1), were associated with natural flowering time variation. No potentially causative polymorphisms were found in the coding region of CRY1; however, at FLC two splice site polymorphisms were associated with early flowering. Accessions harboring nonconsensus splice sites expressed an alternatively spliced transcript or did not express this FLC homeolog. Our results are consistent with the function of FLC as a major repressor of flowering in Arabidopsis thaliana and imply that nonfunctionalization of duplicate genes could provide an important source of phenotypic variation.

Place, publisher, year, edition, pages
2009. Vol. 183, no 1, 337-345 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-114084DOI: 10.1534/genetics.109.103705ISI: 000272067000030PubMedID: 19581451OAI: oai:DiVA.org:uu-114084DiVA: diva2:292799
Available from: 2010-02-09 Created: 2010-02-09 Last updated: 2017-12-12
In thesis
1. Demography and Polyploidy in Capsella
Open this publication in new window or tab >>Demography and Polyploidy in Capsella
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Studies of demography and population structure give insight into important evolutionary processes such as speciation and diversification. In the present work I perform such studies in the genus Capsella, which has three species: C. grandiflora, an outcrossing diploid, C. rubella a selfing diploid, and C. bursa-pastoris a selfing tetraploid. These three species make a good model system for evolutionary studies because they encompass two major plant evolutionary processes: mating system shifts and polyploidization. To conduct my studies I have gathered a large number of samples across the distributions of each species and scored them both phenotypically and genotypically: more specifically we measured flowering time and collected DNA sequence data.

In the tetraploid C. bursa-pastoris we applied an association mapping approach which takes population structure into account to search for genetic variation associated with variation in flowering time. Flowering time is an important and highly adaptive trait which is frequently subject to natural selection. We found evidence of association between flowering time and several single nucleotide polymorphisms (SNPs) within the flowering locus C (FLC) and cryptochrome 1 (CRY1). In the case of FLC these SNPs code for nonconsensus splice site variation in one of the two copies of the gene. The SNPs could potentially have functional consequences and our results imply that non-functionalization of duplicate genes could be an important source of phenotypic variation.

Using a novel coalescent based approach, we investigated the polyploid origin of C. bursa-pastoris and find evidence supporting a recent autopolyploid origin of this species. In the two diploid species, I use sequence data to investigate population structure and demographic history and to assess the effects of selfing on C. rubella. Observed patterns of population structure and genetic diversity in C. rubella can be explained by a combination of both demographic history and mating system. Observed patterns in C. grandiflora suggest that the investigated populations do not deviate strongly from the SNM, which has rarely been found in modern demographic studies.

Finally, we investigate the effect of sampling strategy on demographic inference. Extensive sampling both within and across our populations allow us to empirically test the effect of sampling strategy on demographic inference. We complement the empirical analysis with simulations and conclude that the effect of sampling strategy is in many cases weak compared with that of demographic events. Nevertheless, these effects are real and have the potential to lead to false inference and therefore sampling strategy should be carefully considered in demographic studies.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2010. 39 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 795
Keyword
Approximate Bayesian Computation, Mating system, Brassicaceae, flowering time, genetic diversity, Evolution
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-136696 (URN)978-91-554-7979-4 (ISBN)
Public defence
2011-02-04, Zootissalen, Evolutionary biology centre, Villavägen 9, Uppsala, 10:00 (English)
Opponent
Supervisors
Note
Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 725Available from: 2011-01-14 Created: 2010-12-14 Last updated: 2011-03-21Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Authority records BETA

Holm, KarlLagercrantz, Ulf

Search in DiVA

By author/editor
Holm, KarlLagercrantz, Ulf
By organisation
Evolutionary Functional Genomics
In the same journal
Genetics
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 492 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf