Leveraging the Oryza telomere-to-telomere genome and wild-rice substitution lines for rice-quality improvement

With the growing demand for enhanced eating and the nutritional quality of rice, improving grain quality has become a central objective in modern breeding.¹ However, translating reported quality-related loci, particularly favorable alleles from wild rice, into practical breeding programs remains challenging.² This difficulty stems from the insufficient haplotype resolution in elite hybrid parental backgrounds and the absence of trackable, modular resources for effectively deploying introgressed segments. Here, we report the first telomere-to-telomere (T2T) gap-free genome assembly of high-quality Oryza sativa ssp. indica variety Youzhan 8 (Y8) with a size of 395.90 Mb and further reveal its abundant structural variation and the unique integration of Oryza sativa ssp. japonica haplotypes. Using a set of chromosome segment substitution lines (CSSLs) developed from a cross between Y8 and wild rice (Oryza rufipogon) and quantitative trait loci (QTL) mapping within this population, we identified a major locus for grain quality. We prioritized LOC_Os08g02094, a gene encoding a GDSL-like lipase involved in lipid metabolism, which supports its role as a regulator of both grain appearance and lipid content. Furthermore, a modular analysis of introgressed wild-rice segments indicated that a specific segment on chromosome 8, spanning the OsSSIIIa gene (bbbab), is associated with the relatively high taste value and a favorable grain morphology. Overall, our study delivers a foundational genomic resource and a clear molecular roadmap to support the design and breeding of rice varieties with improved agronomic performance and nutritional quality.