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The genetic basis for evolution of environmental adaptation is a central question in biology. Arabidopsis thaliana is an annual long-day plant and displays an extensive diversity in flowering response to various environmental factors, including photoperiods and temperature. The genetic pathways that regulate plant’s response to these factors have been studied extensively, however, our knowledge in the genetic basis for flowering time variation in nature is limited.
 We examined genetic diversity of CONSTANS (CO), a central mediator in the photoperiod pathway. By sequencing 25 European accessions, we identified an allelic variation in the copy number of a 7-nt cis-regulatory element in the CO promoter. The cis-element is known as the binding motif of CDF1, a member of a plant-specific Dof transcription factor family, that is regulated by GIGANTEA and FKF1 and plays an essential role in generating the diurnal CO mRNA peak1, 2. Among the 271 accessions genotyped, most of the accessions carry 4 or 5 copies of the cis-element (59% and 41%, respectively), while only Cvi-0 carries 3 copies. The haplotype carrying 5 copies exhibits features that suggest recent positive selection, including no polymorphisms within the haplotype and an extended low genetic diversity across the genomic region nearby the CO locus. Transgenic approaches were used to examine the effect of the copy number variation of the cis-element in the CO transcriptional regulation and the CO function. Plants expressing luciferase under the control of the CO promoter carrying 5 copies of the cis-element showed higher level of the luciferase signal than other copy number variants. In addition, transgenic plants expressing the CO coding region under the control of the CO promoter carrying 5 copies flowered earlier than 4 copies. Moreover, our genome-wide association study showed a significant association between the polymorphisms in the CO locus and flowering time.
We extended our focus to 52 well-characterized flowering genes in the photoperiod, vernalization, gibberellin, and integration pathways with the aim of clarifying how the flowering gene networks evolved. Our analysis suggests that a large number of polymorphisms in the flowering genes affect natural flowering time variation, and that heterogeneous selection has acted on the flowering gene networks.

References:
1. J. Imaizumi et al., (2005) Science. 309, 293-297.
2. M. Sawa et al., (2007) Science. 318, 261-265.