From germplasm diversity to genetic design: strategies for photoperiod adaptation in rice

Leina Zhou; Yinyin Liu; Salinda Sandamal; Yuhang Zhang; Asanka Tennakoon; Qian Qian; Xiaoming Zheng; Leina Zhou; Yinyin Liu; Salinda Sandamal; Yuhang Zhang; Asanka Tennakoon; Qian Qian; Xiaoming Zheng

doi:10.48130/seedbio-0025-0020

Figure 1.

From natural selection to artificial breeding: evolutionary adaptation and global expansion of rice. Rice has evolved from its wild progenitors (O. rufipogon and O. nivara) through successive breeding phases, including the Green Revolution (semi-dwarf, high yield), hybrid rice (heterosis utilization), super rice (yield and quality improvement), and molecular design breeding (trait-level precision). This evolutionary trajectory reflects a gradual reduction in photoperiod sensitivity and enhanced regional adaptability. The map illustrates current global rice-growing regions, including tropical and subtropical double-cropping, temperate single-cropping, high-altitude upland, and emerging areas, demonstrating rice's precise ecological adaptation to light, temperature, and water conditions.

Figure 2.

Integrated regulatory network linking light signaling, circadian rhythm, and photoperiodic flowering in rice. Photoreceptors (PHYA, OsPHYB, PHYC) entrain the circadian clock (the OsCCA1-OsPRR1 negative loop and the ELF3-ELF4-OsLUX evening complex), which routes signals into the OsGI-Hd1-Hd3a/RFT1 and Ghd7-Ehd1-Hd3a/RFT1 axes. Small SD/LD labels on edges indicate predominant effects under short-day (SD) or long-day (LD): Hd1 activates Hd3a/RFT1 in SD but represses in LD; Ghd7, OsPRR37/DTH7, and DTH8 predominantly repress Ehd1 in LD; DTH2 promotes Hd3a/RFT1 under LD; Ehd2/3/5 promote Ehd1. Protein-protein interactions are overlaid, including the florigen activation complex (FAC; Hd3a/RFT1-14-3-3-OsFD1) at the SAM. Protein post-translational modification control is indicated by Hd16/CKI-dependent phosphorylation that potentiates Ghd7 repression under LD. Chromatin badges mark H3K36me3⁺ (activation) at Hd3a/RFT1 and H4ac⁻ (deacetylation/raised repression threshold) at Ghd7. Green arrows denote promotion; magenta blunt lines denote repression. (Hd3a is SD-biased, whereas RFT1 is more LD-permissive).

Figure 3.

Region-specific adaptation of rice flowering driven by regulatory gene variation. Region-specific allelic variation underlies the adaptive differentiation of heading date across China. In southern regions, loss-of-function mutations in Hd1 and upregulation of RFT1 promote early flowering under long-day conditions. In central areas, inactivation of repressors (Ghd7, DTH8, OsPRR37, OsPHYB) relieves photoperiod sensitivity. In northern high-latitude zones, compensatory mechanisms involving DTH2 and Hd3a ensure timely flowering. Major mutation types include: a, promoter deletion; b, promoter insertion; c, premature stop; d, frameshift + stop; e, nonsynonymous mutation; f, dephosphorylation site loss. These variations form the molecular basis for latitudinal flowering adaptation.

Figure 4.

A strategic roadmap for smart and climate-resilient rice breeding. The roadmap highlights a transition from germplasm gatekeeper to strategic, technology-enabled breeding. Central components include the construction of a global adaptive resource network that links germplasm, genomic, and environmental data; multi-omics integration to decode signal-regulation-response pathways; AI-powered breeding platforms for predictive selection and field feedback; and synthetic biology approaches for programmable control of flowering traits. Together, these components support the development of intelligent, adaptive, and future-oriented rice breeding systems.