Temporal transcriptome analysis reveals the two-phase action of florigens in rice flowering

Renwei Sun, Yifeng Ding, Manaki Mimura, Noriko Nishide & Takeshi Izawa

Theoretical and Applied Genetics; April 12 2025; vol. 138; article 100

Two florigen genes, Hd3a and RFT1, are essential for the floral transition in rice. To elucidate the early steps of the transcriptional dynamics during rice floral induction, we compared a set of temporal transcriptome data of SAM (shoot apical meristem)—region samples between the wild-type and a non-flowering line of the hd3a rft1 double mutant during a short-day (SD) treatment after growing under long-day conditions for 42 days, and identified 6,978 DEGs (differentially expressed genes). As expected, FUL-like MADS-box genes were induced just after 4 days SD treatment; meanwhile, SEP-type and AGL-type MADS-box genes were induced after 9 days of SD treatment. We here newly revealed that majority of rhythmic genes including major circadian clock genes were not affected by the florigen genes, implying normal circadian clock phasing at the SAM regions regardless of floral transitions. We found that around two thousands of genes were repressed by Hd3a and RFT1 genes at the SAM regions before the SD treatments and become derepressed and similar to WT expression levels in the double mutants according to the SD treatments. These clearly imply two distinct actions of florigen genes: one for repression of some developmental key genes during vegetative growth possibly by very low level of florigen expression and the other for floral induction by relatively high florigen expressions upon short-day inductions. This repression by low levels of florigens may serve as a maintenance system for vegetative growth before floral induction, which implies a novel role for florigen genes in rice.

See https://link.springer.com/article/10.1007/s00122-025-04869-0

Figure 1

The double mutants of rice florigen genes exhibited non-flowering and did not respond to photoperiods. A The 45 bp and 18 bp deletions at the first exon of Hd3a and RFT1, respectively, in the original double mutant line. B Flowering time of the wild-type and the florigen double mutants. The plants were grown for 42 days under the long-day conditions and then subjected to SD treatments. n = 18. On flowering-time of WT: p < 0.0001 by Student’s t test (two-tailed). C Time schedules for SAM sampling. The wild-type and mutant samples were sampled as indicated. The sampling started at 42 days after sowing. Sampling timings are illustrated by orange arrows. White and dark bars denote the light and dark periods, respectively. Sampling was conducted six times over a day, with intervals of four hours. D Phenotypic changes of wild-type and the double mutant plants at SD4. Stem elongation started in the wild-type plants, but no elongation in the double mutant plants. Bars represent 2 mm. The location of the SAM is marked with a white box. Red arrows indicate the node positions. Photographs of SAM regions after removal of surrounding leaves are also shown