Fig. 1. Genomic comparison, transcriptome analysis, and genetic analysis of OsARF13 in callus formation. A, Expression levels of OsARF13 were quantified by qRT-PCR in 7-day-old callus induced from the scutellum of three japonica [Nipponbare (NIP), Zhonghua 11 (ZH11), Kitaake] and three indica [9311, Minghui 63 (MH63), Zhenshan 97 (ZS97)] rice varieties. Data are mean ± SD (n = 3). Y-axis values represent relative transcript abundance normalized to the internal reference gene OsUBQ5. Lowercase letters above bars indicate statistically significant differences among varieties based on one-way ANOVA followed by Tukey’s HSD test (P < 0.05). B, Sequence variation analysis of OsARF13 promoter among six varieties. Three polymorphic regions (I-III) containing cis-element variations are shown in detail. Red boxes highlight auxin-responsive elements (AuxRE). The lower panel presents the alignment of nucleotide polymorphisms across the -3 253 bp to ATG region, with variable bases highlighted in different colors. C, Frequency of two major promoter haplotypes in 2 322 rice accessions, including 1 615 indica and 707 japonica subspecies. The proportions of each haplotype are indicated as percentages within the respective subspecies. D‒G, Phenotypes of callus induction from mature seeds of NIP and osarf13 mutants cultured for 21 d on N6 medium supplemented with 10 μmol/L (D) or 5 μmol/L (F) 2,4-D and their corresponding callus fresh weights were quantificated (E and G). Representative plates are shown for each genotype. Scale bars, 1 cm. Data are mean ± SD of three biological replicates. Asterisks indicate significant differences compared with NIP (**, P < 0.01; ***, P < 0.001; t-test).