Figure 3

Patterns of the pedigree haplotype blocks of Koshihikari and its related cultivars. Only haplotype blocks longer than 500-kb of Koshihikari (No. 61 in additional file 3) and consensus haplotype blocks among three progeny cultivars, Hitomebore (117), Akitakomachi (100), and Hinohikari (113) are shown. The black bars at the top indicate the range of the blocks in the 12 rice chromosomes. Vertical gray lines represent the borders between chromosomes. The numbers at the right indicate the proportion of the Koshihikari genome accounted for by the haplotype blocks. (A) Patterns of haplotype blocks in 12 parental cultivars in the pedigree chart of Koshihikari. Five warm colors (the red component of the 24-bit RGB color equaled 255 for all colors) indicate that the haplotype blocks were derived from the paternal parent, Norin1 (No. 39). Seven cool colors (the red component of the 24-bit RGB color equaled 0 for all colors) indicate that the haplotype blocks were derived from the maternal parent, Norin22 (47). Gray indicates unidentified haplotype blocks that may have been derived from either parent. The three yellow arrows indicate pedigree haplotypes that inherited more than 2 Mb of their length with a density of more than 1 SNP/100 kb. (B) The haplotype blocks of Koshihikari in three progeny cultivars, Hitomebore (117), Akitakomachi (100), and Hinohikari (113). (C) Consensus haplotype blocks between Koshihikari and the three progeny cultivars. Only blocks derived from the six ancestral cultivars of Koshihikari (purple and red names) are indicated. Red horizontal bars represent consensus haplotype blocks longer than 1 Mb and the names of the ancestral landraces.