*2.4. QTL Detection and Analysis Using the BILs and BILF1 Population*

To elucidate the genetic mechanism underlying heterosis of yield traits, we primarily focused on the days to heading (DTH), plant height (PH), panicle number (PN), grain number per panicle (GNPP), setting rate (SR), and 1000-grain weight (TGW). A molecular linkage map with 3652 bins was constructed based on sequence variations in Sasanishiki and Habataki and those among the BILs using Highmaps software. In the BIL population, 10 QTLs for all of the traits were mapped independently to rice chromosomes 1, 4, 5, 7, 9, 10, and 12 (Figure 4). To detect QTLs for heterosis that was associated with the effects of the heterozygous on the genetic background of Sasanishiki, we used the BILF1 to conduct QTL analysis. Eight loci for the respective phenotypes were detected on chromosomes 1, 3, 6, 7, 9, and 10. Among the eight QTLs, four of these loci overlapped with QTLs detected in the BIL population, and four QTLs were detected independently in the BILF1 population. These results presented a mode of dominance or super-dominance in the heterozygote. Among the QTLs detected in both BILs and BILF1S, the cluster at the short arm of chromosome 10 corresponded to the days to heading in BILF1s and the grain number per panicle in both BILs and BILF1s. In addition, a cluster at chromosome 7 was related to days to heading in both BILs and BILF1s. As heterosis was mainly observed in the grain number per panicle, we subsequently summarized the grain number per panicle of each genotype for the four QTLs detected in the BIL and BILF1s (Figure 5). The results showed that in the *Gn1* and *Ghd7* loci, the heterozygous genotype and the homozygous Habataki genotype plants had significant advantage in grain number per panicle compared with the homozygous Sasanishiki genotype plants. In the *GNNP3* locus, the homozygous Sasanishiki and homozygous Habataki genotype plants had similar grain number per panicle but significantly fewer than the heterozygous genotype plants. In the *Gn3* locus, the heterozygous genotype plants showed a significant increase of grain number per panicle compared with homozygous Habataki genotype plants, whereas the homozygous Habataki genotype plants had a significantly higher grain number per panicle than the homozygous Sasanishiki genotype plants.

**Figure 4.** The position of quantitative trait locuses (QTLs) for yield-related traits and heterosis QTLs in BILs and BILF1s. Different colors represent the QTLs detected in BILs and BILF1s.

**Figure 5.** Grain number per panicle of each genotype for the four QTLs detected in BIL and BILF1s. The number inside the column represents the number of plants for each genotype. All data are given as mean ± s.e.m.,different letters indicate the significant differences at the 5% level.
