The genetic architecture of the network underlying flowering time variation inArabidopsis thaliana

ABSTRACT Flowering time is a key adaptive trait in plants and is tightly controlled by a complex regulatory network that responds to seasonal signals. In a rapidly changing climate, understanding the genetic basis of flowering time variation is important for both agriculture and ecology. Genetic mapping has revealed many genetic variants affecting flowering time, but the effects on the gene regulatory networks in population-scale are still largely unknown. We dissected flowering time networks using multi-layered Swedish population data from Arabidopsis thaliana , consisting of flowering time and transcriptome collected under constant 10°C growth temperature in addition to full genome sequence data. Our analysis identified multiple alleles of the key flowering time gene FLOWERING LOCUS C ( FLC ) as the primary determinant of the network underlying flowering time variation under our condition. Genetic variation of FLC affects multiple-pathways through known flowering-time genes including FLOWERING LOCUS T ( FT ), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 ( SOC1 ). We demonstrated that an extremely simple single-locus model of FLC involving allelic variation and expression explains almost a half of flowering time variation, with 60% of the effect being mediated through FLC expression. Furthermore, the accuracy of the model fitted at 10°C is almost unchanged at 16°C.