Graphical genotype of the short arm of chromosome 3 in Nipponbare, N-CSSLs, Nipponbare substitution lines, Koshihikari, K-CSSLs and Koshihikari substitution lines. Positions of the SSR markers, the low-temperature germinability gene qLTG3-1, and the pre-harvest sprouting resistance QTL Sdr1 in the rice genome sequence (Build 4.0 Pseudomolecules of the Rice Genome; IRGSP 2005) are oriented from the short arm (left) to the long arm (right). Black and white bars indicate homozygous for the Nipponbare and Koshihikari alleles, respectively. ** and *** indicate germination percentages in pre-harvest sprouting test (30°C) and low-temperature germinability test (11°C) between CSSLs or substitution lines and their recurrent parents are significantly different at P < 0.01 and P < 0.001, respectively