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Originally published as Genetics Published Articles Ahead of Print on July 6, 2009.
Genetics, Vol. 183, 337-345, September 2009, Copyright © 2009
doi:10.1534/genetics.109.103705
Splicing Variation at a FLOWERING LOCUS C Homeolog Is Associated With Flowering Time Variation in the Tetraploid Capsella bursa-pastoris
Tanja Slotte*,1,
Hui-Run Huang*,
,
Karl Holm*,
Alf Ceplitis*,
,
Kate St. Onge*,
Jun Chen*,
Ulf Lagercrantz* and
Martin Lascoux*
* Department of Evolution, Genomics and Systematics, Uppsala University, SE-752 36 Uppsala, Sweden, South China Botanical Garden, Chinese Academy of Sciences, Leyiju, Guangzhou 510650, Guangdong, China and Department of Cell and Organism Biology (Genetics), Lund University, SE-223 62 Lund, Sweden
1 Corresponding author: Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M5S3B2, Canada.
E-mail: t.slotte{at}utoronto.ca
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.
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