RNA-seq results at the SAM RNA-seq results at the SAM. A, Scatter plots of DE genes between the fd-2 mutant and pFD::GFP-FD fd-2 (control) at five time points before and during the transition to photoperiod-induced flowering. RNA-seq results at the SAM. A, Scatter plots of DE genes between the fd-2 mutant and pFD::GFP-FD fd-2 (control) at five time points before and during the transition to photoperiod-induced flowering. T0–T5 indicate day of sample collection before (T0) and 1, 2, 3, and 5 d after shifting plants to LD. Red dots indicate DE genes with an adjusted P value < 0.1. B, Venn diagrams showing the overlap between 572 unique FD target genes identified by ChIP-seq and DE genes found by RNA-seq at the SAM at five time points before (T0) and during (T1–T5) the transition to flowering. C, Venn diagram showing the overlap between 572 unique FD target genes identified by ChIP-seq at the SAM (two biological replicates) and genes found to be differentially expressed at the SAM by RNA-seq at least at one time point (T0, T1, T2, T3, and T5; three biological replicates per time point). A total of 135 genes were classified as putative direct targets of FD. Statistical significance was calculated using the Fisher’s exact test. *P = 1.03E-07. Silvio Collani et al. Plant Physiol. 2019;180:367-380 ©2019 by American Society of Plant Biologists