Comparative transcriptome analysis reveals key genes and regulatory networks regulating flowering in rice varieties with different photoperiod sensitivity

BACKGROUND: Rice is a short-day plant whose flowering is critically regulated by photoperiod. Through long-term domestication and selective breeding, rice cultivation has adapted to photoperiod variations across different latitudes, resulting in varieties with broad photoperiod sensitivity (PS). PS is essential for rice to adapt to different geographical regions and a wide range of cultivation environments. RESULTS: This study compared the panicle differentiation phenotypes of four rice materials with different photoperiod sensitivities under long-day (LD) and short-day (SD) conditions. Results showed that highly photoperiod-sensitive varieties exhibit a stronger response to photoperiod shifts, leading to accelerated young panicle differentiation and earlier heading under SD conditions. For example, the highly photoperiod-sensitive material H26 headed 56 days earlier under SD than under LD conditions. Correspondingly, under SD conditions, the expression of key flowering genes Hd3a and RFT1 was significantly upregulated in H20, H17, and H26. Transcriptome analysis of leaves treated on day 10 revealed that SD conditions significantly upregulated the expression of key flowering genes such as RFT1, Hd3a, and Se5, while downregulating flowering repressor genes such as Ghd7 and Ghd8, thereby promoting photoperiod-induced early heading. Functional enrichment analysis indicated that these DEGs were primarily associated with starch and sucrose metabolism, plant hormone signal transduction, and circadian rhythm-plant pathway. Furthermore, we identified 125 upregulated and 56 downregulated genes that were uniquely co-expressed across all three photoperiod-sensitive materials. Additionally, five uniquely expressed DEGs related to flowering were identified in the highly photoperiod-sensitive material H26. CONCLUSIONS: Our study identified DEGs specifically associated with photoperiod-sensitive materials. These genes represent promising candidates for further investigation into the molecular mechanisms underlying photoperiod responsiveness in rice. Our research helps clarify how rice responds to changes in photoperiod, elucidates the expression pattern of photoperiod-induced genes, and provides valuable insights for breeding rice varieties that are better adapted to changing climatic conditions.