Mapping analysis of Epi-d1. (A) Gross morphology of Epi-d1 mutant (Center) and magnified view of its dwarf panicle and seed in dwarf tillers (Left) and normal panicle and seed in normal tillers (Right). Arrowheads indicate tillers (vegetative branch shoots), asterisks indicate panicles (inflorescences), and white circles indicate grains. (B) Epi-d1 shows varying phenotypes from completely dwarf to completely normal. (C) Chimeric phenotype in panicle. A panicle showing 2 separate rachises with either small round or normal grains (Left). A panicle showing small round and normal grains arranged alternately on the rachis (Center). A panicle showing a random distribution of the 2 grain phenotypes (Right). (D) Epi-d1 was mapped into 59 cM of chromosome 5, then narrowed down to a 33.5-kb region between 2 molecular markers, D1-1002 and D1-1005. In this region, there are 3 8.6-kb tandem repeats (red arrows) and 4 ORFs are predicted by RiceGAAS. There are 11 polymorphisms in this 33.5-kb region between Nipponbare and Epi-d1 mutant. The numbers indicate the positions of polymorphisms in this region. (E) Comparison of sequence of D1 gene between Epi-normal, Epi-dwarf, and Nipponbare. (F–H) The phenotypes of d1 loss-of-function mutant are shown. (I–K) The phenotypes of Epi-dwarf plant are shown. (L–N) The phenotypes of F1 plant derived from cross between Epi-dwarf and d1 are shown. The gross morphologies are shown in F, I, and L; panicles in G, J, and M, and seeds in H, K, and N. (O) Total RNAs were extracted from 4 independent chimeric plants by separating tissues with different phenotypes. RNA blots were hybridized with D1 probe. N and d indicate RNA extracted from normal and dwarf tillers, respectively. (P) Total RNAs were extracted from Epi-normal and Epi-dwarf plants and hybridized with D1 probe. (Q) Total RNAs were extracted from Epi-normal and Epi-dwarf plants and hybridized with probes of D1 and its neighbor genes. Hypothetical and DnaJ gene are located 7 kb downstream and 4 kb upstream of the D1 gene, respectively. N and d indicate RNA extracted from Epi-normal and Epi-dwarf, respectively. Actin1 is hybridized as a control (O–Q).