*2.5. The Indica*/*Japonica Pedigree Analysis of Sasanishiki and Habataki*

Breeding history indicates that Habataki is an admixture line between *indica* and *japonica*. Thus we conducted an analysis of the *indica*/*japonica* pedigree of Sasanishiki and Habataki. The *indica*/*japonica* pedigree was defined using the subspecies-specific SNPs. The subspecies-specific SNPs were those of the same type in all *japonica*, but not in *indica*, which is based on the divergence of the 517 rice landraces [14]. In total, 100,529 subspecies-specific SNPs were selected. We matched the 1,947,668 SNPs between Sasanishiki and Habataki to 100,529 subspecies-specific SNPs, and 81,690 SNPs were merged. The 81,690 SNPs were then used to analyze the *indica*/*japonica* pedigree of Sasanishiki and Habataki. The results showed that there are 621 *japonica*-type SNPs in the genome of Habataki, which indicated that 0.76% of *japonica* genomic introgression involved Habataki. Meanwhile, there were only 81 *indica*-type SNPs in Sasanishiki, indicating that only 0.01% *indica* pedigree introgression occurred in the Sasanishiki genome. The distribution of subspecies-specific SNPs and *indica*/*japonica* genomic introgression is

shown in Figure 6. Agronomic-traits-related QTLs were located out of the *indica*/*japonica* genomic introgression, which confirmed that the heterosis QTL originated from the difference between *indica* and *japonica*.

**Figure 6.** Overview of the subspecies-specific SNPs and introgression in Sasanishiki and Habataki. Tracks from the outer to inner circles indicate the following. (**A**) The chromosome length. The loci of grain number per panicle are indicated on the inside of the circle. (**B**) The distribution of 81,690 subspecies-specific SNPs in the genome. (**C**) The introgression of *japonica*-type SNPs into the genome of Habataki. (**D**) The introgression of *indica*-type SNPs in the genome of Sasnishiki.
