The evening complex integrates photoperiod signals to control flowering in rice

Abstract

Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the long- and short-day flowering pathways are integrated, and the mechanism of photoperiod perception is not understood. While many of the signaling components controlling photoperiod-activated flowering are conserved between Arabidopsis and rice, flowering in these two systems is activated by opposite photoperiods. Here we establish that photoperiodism in rice is controlled by the evening complex (EC). We show that mutants in the EC genes LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) paralogs abolish rice flowering. We also show that the EC directly binds and suppresses the expression of flowering repressors, including PRR37 and Ghd7. We further demonstrate that light acts via phyB to cause a rapid and sustained posttranslational modification of ELF3-1. Our results suggest a mechanism by which the EC is able to control both long- and short-day flowering pathways.

Keywords: ELF3; Evening Complex; LUX; flowering; rice.

Fig. 1.

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. 2.

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.

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.

ELF3-1 protein stability responds to light. (A) Anti-ELF3 specifically recognizes ELF3-1, which occurs in two bands during darkness. During light periods, only the higher (H) band is present. During SD (10-h day, 14-h night) the low (L) band is able to accumulate during the long night. (B) In the phyb background ELF3-1 loses photoperiod responsiveness, and both H and L bands are present in both light and dark periods. (C) The reduction in ELF3-1 levels in response to light is rapid, with only 15 min of NB being sufficient.

Fig. 5.

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.