*Article* **Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF1 Lines Uncover Multiple Heterosis-related Loci**

**Yahui Yu 1,2,3,**†**, Mengmeng Zhu 1,**†**, Yue Cui 1,**†**, Yu Liu 2,**†**, Zhenyu Li 2, Nan Jiang 4, Zhengjin Xu 1, Quan Xu 1,\* and Guomin Sui 3,\***


Received: 5 December 2019; Accepted: 23 January 2020; Published: 25 January 2020

**Abstract:** Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice (*Oryza sativa* L.) consists of two subspecies, *indica* and *japonica*, and hybrid rice is the predominant form of *indica* rice in China. However, the molecular mechanism underlying heterosis in *japonica* remains unclear. The present study determined the genome sequence and conducted quantitative trait locus (QTL) analysis using backcross recombinant inbred lines (BILs) and BILF1 lines to uncover the heterosis-related loci for rice yield increase under a *japonica* genetic background. The BIL population was derived from an admixture variety Habataki and *japonica* variety Sasanishiki cross to improve the genetic diversity but maintain the genetic background close to *japonica*. The results showed that heterosis in F1 mainly involved grain number per panicle. The BILF1s 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 BILF1s; four QTLs were detected exclusively in the BILF1 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 *Grains Height Date 7* (*Ghd7*) was correlated in days to heading in both BILs and BILF1s. 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 *japonica* rice production.

**Keywords:** rice; heterosis; yield components; high-throughput sequence
