Fig 2: EC genes are essential for flowering in rice. (A) Flowering time for elf3-1, elf3-2, and lux in rice from the emergence of the second leaf. Plants were grown under ND conditions (12-h day, 12-h night). Nonflowering genotypes are marked with “NF”. P values are for two-tailed unpaired t test with n = 10. (B) Adult lux plants (line 120T7, 2 nucleotide insertion) at 6 and 12 mo growth in SD (10-h day, 14-h night). (Yellow scale bars represent 10 cm.) (C–E) lux (line 69S4b, insertion of one nucleotide in one allele and deletion of four nucleotides in the other allele) showing decreased distance between internodes. (White scale bars represent 1 cm.) P values are for two-tailed unpaired t test.

Fig 3: ELF3-1 directly binds and represses the expression of LD responsive genes in rice. (A) 21.4% of the genes in cluster 7 and 6.5% of genes in cluster 3 are directly repressed by ELF3-1 at ZT14. Values for log2(TPM ratio) > 2 or < −2 are transformed to the range of ± 2. (B) Representative views showing ELF3-1 binding peaks at key circadian and floral regulators.

Fig 4: The EC integrates photoperiod information in rice. ELF3 activity increases during darkness, enabling the EC to reduce expression of key floral repressors such as PRR37 and Ghd7 in SD conditions. Activation of PhyB under LD conditions enables repression of ELF3-1, resulting in the enhanced expression of the transcriptional regulators that, in concert with Hd1, repress florigen genes Hd3a and RFT, therefore delaying flowering.

Fig 5: EC activity is essential for the SD transcriptome. (A) Clustering of gene expression under SD (10-h day, 14-h night) and LD (14-h day, 10-h night) reveals groups of genes that are activated (e.g., clusters 4 and 2) and repressed (e.g., clusters 7, 6, and 3) by SD photoperiods. These clusters become largely daylength neutral in the elf3-1 elf3-2 background (line 246U1.6a2: 1 nucleotide insertion in ELF3-1 locus: two nucleotide deletion in ELF3-2 locus). Values for log2(TPM ratio) > 2 or < −2 are transformed to the range of ± 2. (B) Examples of circadian and flowering time genes that lose their photoperiod responsiveness in elf3-1 elf3-2 and lux (line 120T7, two nucleotide insertion). Blue and red ribbons denote the overall behavior of the relevant cluster in SD and LD, respectively.