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Y900 is one of the top hybrid rice (Oryza sativa) varieties, with its yield exceeding 15 t·hm−2. To dissect the mechanism of heterosis, we sequenced the male parent line R900 and female parent line Y58S using long-read and Hi-C technology. High-quality reference genomes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 single-nucleotide polymorphisms, 299,149 insertions/deletions, and 4,757 structural variations. The level of variation between Y58S and R900 was the lowest among the comparisons of Y58S with other rice genomes. More than 75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the portion of Geng/japonica (GJ)-type genetic components from different male parents increased with yield increasing in their corresponding hybrids. Transcriptome analysis revealed that the partial dominance effect was the main genetic effect that constituted the heterosis of Y900. In the hybrid, both alleles from the two parents were expressed, and their expression patterns were dynamically regulated in different tissues. The cis-regulation was dominant for young panicle tissues, while trans-regulation was more common in leaf tissues. Overdominance was surprisingly prevalent in stems and more likely regulated by the trans-regulation mechanism. Additionally, R900 contained many excellent GJ haplotypes, such as NARROW LEAF1, Oryza sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13, and Grain number, plant height, and heading date8, making it a good complement to Y58S. The fine-tuned mechanism of heterosis involves genome-wide variation, GJ introgression, key functional genes, and dynamic gene/allele expression and regulation pattern changes in different tissues and growth stages.

Y900 is one of the top hybrid rice varieties with a yield exceeding 15 t/hm2. To dissect the mechanism of heterosis, the male parent line R900 and female parent line Y58S were sequenced using long-read and Hi-C technology. High-quality reference genomes of sizes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 SNPs and 299,149 Indels. No megabase level structural variations exist. >75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the Geng/japonica-type genetic components from different male parents showed an increasing trend from phase 2-4 super-hybrid rice; Transcriptome analysis revealed that additive and dominance effects are the main genetic effects that constitute the heterosis of Y900. Allele-specific expression patterns and expression regulation patterns are quite dynamic in different tissues. For young panicle tissues, cis-regulation is dominant, while trans-regulation is more popular in leaf issues. Overdominance is more likely regulated by the trans-regulation mechanism. The differential gene expression and regulation pattern are closely related to Geng/japonica introgression. Additionally, R900 contained several excellent japonica haplotypes, such as NAL1, OsSPL13, Ghd8, OsBRI1, and DTH2, which make a good complement to Y58S. The fine tune mechanism through dynamic expression or regulation pattern change, especially on some key functional genes, is the base for heterosis.

The enhancement of rice production numbers can be achieved by using quality rice cultivars and fertilizers. The double rice cropping model has given rise to an important rice production system in southern China. Exploring the possibility of whether hybrid vigor could make a substantial contribution to early and late season rice production, and how the heterosis expression of hybrid rice functions under different levels of fertilizer application is of great significance. The objective of this study was to evaluate the grain yield and associated plant traits of popular hybrid and inbred rice varieties with large–scale promotion under conditions of customary (high) and combined (low) fertilization in the early and late seasons of 2017–18 in Changsha County, Hunan Province, China. We found that hybrid rice varieties displayed their respective advantages in the early and late rice seasons, but the advantages in their relative yield traits varied. The leading advantages of early season rice were effective panicle number per hill (EPN), 1000–grain weight (KGW), harvest index (HI), yield, and nitrogen use efficiency (NUE), whereas in late season rice, the foremost advantages were grain number per panicle (GNP), HI, yield, and NUE. The EPN was the prime advantage of early season hybrid rice with a short growth period, and the GNP was the main advantage of late season hybrid rice with a long growth period. Notably, the main yield advantage of hybrid rice was stronger under combined (low) fertilization than under customary (high) fertilization. Hence, high yield can be achieved by selecting the best hybrid rice varieties supported by combined fertilization (lower fertilizer use with higher efficiency).