Fig. 4

Functional variation, the haplotypes and origin of OsLG3. a Haplotype analysis of OsLG3. Gene structure and natural variation between alleles from SLG and Nipponbare (top). Natural variation in OsLG3 among 283 rice accessions of a mini-core collection compared with the NILs (bottom). b Cladogram of four haplotypes. c Grain lengths of accessions for the two classes in MCC1; raw data are provided in Additional file 32: Table S1; n, is the number of accessions. P values were generated by two-tailed t tests. Error bars, SEM. d Relative expressions of OsLG3 in two haplotypes (SLG-Hap, n = 17; Nip-Hap, n = 16). e Transient expression assays of the effect of the four consensus SNPs and one indel on gene expression. Relative firefly luciferase activities in Arabidopsis protoplasts, with data normalized to activity of co-transformed constitutively expressed Renilla luciferase. Data are shown as means ± SEM (n = 5 technical replicates). f Geographic origin of rice containing the SLG-type OsLG3. Hap1–4 are represented by red, green, purple, and blue circles, respectively. The indica and japonica cultivars are denoted by solid and dashed circles, respectively. g Nucleotide diversity analysis in OsLG3 and flanking regions (~400 kb). Representative samples included 99 indica accessions, 68 temperate japonica accessions, 27 tropical japonica accessions, and 10 wild rice accessions (Additional file 32: Table S1). Tej, temperate japonica; trj, tropical japonica. Y-axis, average π value; x-axis, Nipponbare TIGR v7.0 genome coordinate of chromosome 3. h Averaged nucleotide diversity of the 20 kb surrounding OsLG3. i A minimum-spanning tree for the OsLG3 region. Each haplotype group is represented by a circle, and circle size represents the number of lines within the haplotype, as in Fig. 4 f. Orange, brown, yellow, red, blue and pink represent O. rufipogon in China, O. rufipogon in Southeast Asia, indica, tropical japonica, temperate japonica, and template japonica with glutinous varieties from the Yunnan-Guizhou Plateau or mixtures with recently improved indica or tropical japonica. Grid corresponds to oslg3/oslg3