**1. Introduction**

Food security is a major global problem as the competition for arable land between food and energy crops, and population growth, continue to increase. Improving crop productivity has been the key focus of national and international efforts in breeding crops such as maize and rice. The vigor of *indica* rice hybrids often exhibits phenotypes that surpass their parents in terms of growth and fertility, which is also known as heterosis. In crop production, successful agronomic exploitation of yield

heterosis has been achieved in the past decades. Three major competing but non-mutually-exclusive hypotheses (dominance, overdominance, and epistasis) have been proposed to explain heterosis at the genetic level [1–6]. However, the progress in elucidating the molecular mechanism underlying crop heterosis has lagged.

In the past decades, heterosis has become a priority research target for both breeders and scientists based on its practical importance and scientific significance. Heterosis in crop breeding was first applied to hybrid maize in the 1930s, and the three-line method or cytoplasmic male sterility (CMS) system contributed to the commercialization of hybrid rice in the 1970s. Crop heterosis has been extensively applied to rice and maize production, significantly improving global yield compared with traditional inbred lines [7]. Currently, the planting area of hybrid rice accounts for 50–60% of the total rice planting area, and about 80% of *indica* rice is hybrid and is mainly planted in southern China. A study used recombinant inbred lines (RIL) derived from a cross between PA64s and 93-11, and RIL backcross F1 populations were analyzed to elucidate the molecular mechanism of heterosis among *indica* and *javanica* varieties [8]. A mega sequence project for 10,0742 F2 lines revealed the genomic architecture of heterosis for yield traits in rice using the cross combination of *Oryza sativa* subspecies (ssp.) *indica*–*indica* (three-line system), *indica*–*indica* (two-line system), and *O. sativa* ssp. *indica*–*O. sativa* ssp. *japonica* crosses [9]. Nevertheless, research on heterosis in *japonica* is limited. Almost all *japonica* varieties are conventional rice, and the hybrid *japonica* accounts for less than 3% among total *japonica*, which is mainly distributed in northern China and the middle range of China. The disappearance of hybrid *japonica* rice is due to the lack of genetic diversity among *japonica* cultivars.

In this study, we used a backcross RIL derived from the cross between Habataki (an admixture variety between the *indica* and *japonica* variety) and *japonica* variety Sasanishiki, and F1 plants were backcrossed to Sasanishiki once before inbreeding. The backcross improved genetic diversity through the introgression of the *indica* pedigree while maintaining the population under the *japonica* genetic background. After inbreeding for 10 generations, we obtained 85 lines of the backcross recombinant inbred line (BIL) population. Then, we crossed all of the 85 lines to Sasanishiki again to generate the BILF1 population. The present study used genome sequencing and quantitative trait locus (QTL) analysis of BILs and BILF1s to identify heterosis-related loci for yield increase.
