Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice ( L.) consists of two subspecies, and , and hybrid rice is the predominant form of rice in China. However, the molecular mechanism underlying heterosis in remains unclear. The present study determined the genome sequence and conducted quantitative trait locus (QTL) analysis using backcross recombinant inbred lines (BILs) and BILF lines to uncover the heterosis-related loci for rice yield increase under a genetic background. The BIL population was derived from an admixture variety Habataki and variety Sasanishiki cross to improve the genetic diversity but maintain the genetic background close to . The results showed that heterosis in F mainly involved grain number per panicle. The BILFs showed an increase in grain number per panicle but a decrease in plant height compared with the BILs. Genetic analysis then identified eight QTLs for heterosis in the BILFs; four QTLs were detected exclusively in the BILF population only, presenting a mode of dominance or super-dominance in the heterozygotes. An additional four loci overlapped with QTLs detected in the BIL population, and we found that () was correlated in days to heading in both BILs and BILFs. The admixture genetic background of Habataki was also determined by subspecies-specific single nucleotide polymorphisms (SNPs). This investigation highlights the importance of high-throughput sequencing to elucidate the molecular mechanism of heterosis and provides useful germplasms for the application of heterosis in rice production.
