*2.6. Data Analysis and QTL Comparison*

We analyzed basic marker statistics, such as major allele frequency (MAF), heterozygosity, and polymorphism information content (PIC) of SNP markers using PowerMarker V3.25 [32]. PowerMarker V3.25 was used to calculate the genetic distance, based on CS Chord [33] and the constructed un-weighted pair group methods with the arithmetic mean algorithm (UPGMA) dendrogram, which was visualized in Molecular Evolutionary Genetics Analysis version 7.0; MEGA7 [34].

We extracted QTL information from the Q-TARO database at 25th August 2017. The physical position in Q-TARO is based on IRGSP build 4 of the Nipponbare genome, while IRGSP 1.0 of the Nipponbare genome was used in this study. Thus, the physical position of the start and end of each QTLs in Q-TARO were converted into the physical positions of IRGSP 1.0. Then, the QTLs overlapped on common *japonica*-originated regions of eight HYVs were selected. After checking if all the selected QTLs were unique or redundant, the redundant QTLs were discarded and only the unique QTLs were left remained. After the filtering step for the QTLs, they were classified into seven categories. The category classification was conducted by checking the characters and the trait names manually.
