Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus (QTL) mapping and candidate gene analysis using wholegenome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 (OsPRR37; hereafter PRR37) is responsible for the Early heading7-2 (EH7-2)/Heading date2 (Hd2) QTL which was identified from a cross of late-heading rice ‘Milyang23 (M23)’ and early-heading rice ‘H143’. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT (CONSTANS, CO-like, and TOC1) domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day conditions, and are adapted to the northernmost regions of rice cultivation, up to 53° N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and Ghd7/Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions

The timing of flowering, which is of crucial importance for plant growth and survival, is controlled by intricate pathways. To identify heading date-QTL, we constructed high resolution map on chromosome 3 using heterogeneous inbred family-near isogenic lines (H-NILs) derived from F7 RILs generated by the cross of early-heading japonica rice ‘H143’ and middle-late-heading indica-japonica hybrid cultivar ‘Milyang23’. QTL and subsequent sequence analysis using H-NILs revealed that the gene underlining QTL EH3, which is detected in the region of Hd16, is EL1 encoding casein kinase I (CKI). Two types of single amino acid substitutions in Ser/Thr kinase domain of EL1 were found in various cultivars, among which H-NIL(eh3) caused loss of function in EL1 demonstrated by altered heading date and GA response. Moreover, the phosphorylation of EL1 appears to involve in EL1 activity to regulate heading date. Transcriptional analysis clearly indicated that H-NIL(EH3) suppresses heading under LD conditions by down-regulating Ehd1, there by Hd3a and RFT1 expressions were not induced, suggesting that EL1 is photoperiod-sensitive and functions as a LD-specific suppressor of heading. Further characterization suggested that EL1 is likely to involve in anther development and seed settings by regulating GAMYB expression. Our study demonstrated that the genetic basis of natural variation occurred in ‘H143’ was revealed by QTL analysis using H-NILs, and EH3/EL1 function is crucial for heading and development in rice. The genetic natural variation of H-NIL(eh3) may have contributed to adaptation of rice cultivation to the higher regions by regulating the expression of rice flowering activator genes and GA signaling.

In field conditions, the zebra2 (z2) mutant in rice (Oryza sativa) produces leaves with transverse pale-green/yellow stripes. It was recently reported that ZEBRA2 encodes carotenoid isomerase (CRTISO) and that low levels of lutein, an essential carotenoid for non-photochemical quenching, cause leaf variegation in z2 mutants. However, we found that the z2 mutant phenotype was completely suppressed by growth under continuous light (CL; permissive) conditions, with concentrations of chlorophyll, carotenoids and chloroplast proteins at normal levels in z2 mutants under CL. In addition, three types of reactive oxygen species (ROS; superoxide [O2-], hydrogen peroxide [H2O2], and singlet oxygen [1O2]) accumulated to high levels in z2 mutants grown under short-day conditions (SD; alternate 10-h light/14-h dark; restrictive), but do not accumulate under CL conditions. However, the levels of lutein and zeaxanthin in z2 leaves were much lower than normal in both permissive CL and restrictive SD growth conditions, indicating that deficiency of these two carotenoids is not responsible for the leaf variegation phenotype. We found that the CRTISO substrate tetra-cis-lycopene accumulated during the dark periods under SD, but not under CL conditions. Its accumulation was also positively correlated with 1O2 levels generated during the light period, which consequently altered the expression of 1O2-responsive and cell death-related genes in the variegated z2 leaves. Taking these results together, we propose that the z2 leaf variegation can be largely attributed to photoperiodic accumulation of tetra-cis-lycopene and generation of excessive 1O2 under natural day-night conditions.