Splicing variation at a FLOWERING LOCUS C homeolog is associated with flowering time variation in the tetraploid Capsella bursa-pastoris.
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.
Slotte
Tanja
T
Department of Evolution, Genomics and Systematics, Uppsala University, SE-752 36 Uppsala, Sweden. t.slotte@utoronto.ca
Huang
Hui-Run
HR
Holm
Karl
K
Ceplitis
Alf
A
Onge
Kate St
KS
Chen
Jun
J
Lagercrantz
Ulf
U
Lascoux
Martin
M
D017398:Alternative Splicing / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D029687:Capsella / Q000235:genetics* / Q000254:growth & development; D056931:Cryptochromes / Q000235:genetics; D035264:Flowers / Q000235:genetics* / Q000254:growth & development*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation / Q000502:physiology; D005843:Geography; D026161:MADS Domain Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D011123:Polyploidy; D017385:Sequence Homology; D013997:Time Factors
D029681:Arabidopsis Proteins; C538962:CRY1 protein, Arabidopsis; D056931:Cryptochromes; C418902:At5g10140 protein, Arabidopsis; D026161:MADS Domain Proteins