Parental genome assembly and transcriptome analysis of hybrid rice Y900

As an important manifestation of heterosis utilization, China's super-hybrid rice continues to set the world record for yield. Dissecting the mechanism of heterosis of superhigh-yielding key rice varieties is an important goal of molecular biologists and crop breeding and genetics experts. In this study, long-read sequencing and Hi-C technology were used for de novo assembly to obtain high-quality reference genomes of the parental strains (R900 and Y58S) of the two-line super-hybrid rice, Y900, with sizes of 396.41 Mb and 398.24 Mb, respectively. Then, a series of genome-wide variations of the parents were identified, especially the structural variations of large fragments, and the variations of some cloned functional genetic sites and their effects were verified. Transcriptome analysis of different spatiotemporal tissues revealed that additive and dominance effects are the main genetic effects that constitute the heterosis of Y900, and the role of allele-specific expression in the heterosis formation was also investigated. The <em>japonica</em>-type genetic components from the male parent in the phase 2-4 super-hybrid rice show an increasing trend; R900 contains several excellent <em>japonica</em> haplotypes, such as <em>NAL1</em>, <em>OsSPL13</em>, <em>Ghd8</em>, <em>OsBRI1</em>, and<em> DTH2</em>, which make a good complement to Y58S, and the overdominance effect at a few sites may be an important source of the difference in yield heterosis of the phase 3 super-hybrid rice. This study provides useful information on heterosis formation in rice as well as new sites as selection targets for improving the heading date and yield related traits of hybrid rice.