Fig. 3: Analysis of natural variations in OsSGR promoter.

a OsSGR transcript levels in the flag leaves of two japonica (JN, NP) and two indica (IR72, IR64) cultivars measured at seven time points with 1-week intervals from 1 to 7 weeks after heading. Data are means (± SE) of three biological repeats. b Haplotype analysis of the polymorphic OsSGR promoter region from 105 accessions. These accessions showed 21 polymorphic sites in the 2-kb promoter region, which split into eight haplotypes (Hap). Note that IR72 and IR64 (indica) belong to haplotype 1 and JN and NP (japonica) to haplotype 8. Genetic variations of 2 O. nivara and 2 O. rufipogon accessions were also noted at the bottom. c Average chlorophyll concentration of the flag leaves in each of the eight haplotype plants at 6 weeks after heading. Data are means ± SE for each haplotype. d Association analysis between the promoter polymorphisms and the chlorophyll levels among the 105 accessions. The accessions (rows) are shown with major subspecies to which they belong (middle panel) and are sorted in descending order of their chlorophyll contents (right panel). For each polymorphism in the promoter (column in the left panel), shown is the significance (upper left panel) of the difference in chlorophyll content between the accessions of which DNA base are the same (blue boxes) and different (white) from those of japonica. The 16 polymorphic sites noted in red and green (b, d) are associated with chlorophyll level. The polymorphic sites in red are same to those between indica and japonica. e Phylogenetic tree of the eight haplotypes (Hap) and the two progenitor subspecies, O. nivara and O. rufipogon. Promoter alleles of indica (Haplotype 1) and japonica (Haplotype 8) are grouped with those of O. nivara and O. rufipogon, respectively. The scale bar represents the number of nucleotide substitutions per nucleotide position. Source data of Fig. 3a and c are provided as a Source Data file.