Graphical genotypes of the reciprocal chromosome segment substitution lines (CSSLs). We obtained 41 CSSLs in the Koshihikari genetic background (A) and 39 CSSLs in the Takanari genetic background (B). White regions denote homozygosity for Koshihikari; black regions denote homozygosity for Takanari; gray regions denote heterozygosity. The graphical genotypes shown here are based on the physical map distance in Os-Nipponbare-Reference-IRGSP-1.0 . Genotype classes of the 141 DNA markers in each CSSL are shown in Additional file 1: Figure S1.