Simplified 3D genome and gap-less CC group Oryza genome reveal genetic dynamics of rice triploid lines from distant hybridization

Intergeneric hybridization and domestication breeding is an efficient means for utilizing wild rice germplasm resources. In this study, we constructed gap-less genome assemblies for two CC, two BBCC and one CCDD wild rices to explore the role of the C subgenome in rice diversification. Furthermore, we assembled the genome of a cultivated rice (AA) and further developed A/C hybrids with enhanced resistance to BPH using an efficient hybrid embryo rescue system. To facilitate the tracking of chromosomes in backcross and selfed progeny of these hybrids, we developed a streamlined 3D genome method, enabling an ultra-rapid and low-cost Hi-C library construction process (sHi-C). By integrating these resources with whole-genome resequencing and genome assembly, we effectively tracked chromosomal dynamics in A/C hybrids and their progeny with cultivated rice. For the first time, we characterized the gamete segregation features and preferences in the progeny of distant hybrid lines and redrew the subgenome dynamics. We revealed that the progeny of A/C hybrids tend to exist predominantly as multiple types of euploid triploids, but also exhibit coexistence of triploids and diploids. Furthermore, we identified chromosomal exchanges between A and C subgenomes in selfed progeny, which may key for fertile offspring development. Preliminary gene identification also highlighted the activity of the C subgenome in progeny and its contribution to insect resistance. Our findings provide a robust framework for harnessing beneficial alleles from CC wild rice through distant hybrid breeding and open new opportunities for rice improvement.