Molecular dissection of high-yield, high-quality, and heat-tolerance traits in Gong 887S and its hybrid rice combinations

Modern rice breeding urgently requires a paradigm shift from single-trait improvement to the integrated optimization of complex traits, including yield potential, grain quality, heat tolerance, and multi-resistance, aiming to establish a resource-efficient and environmentally sustainable production system. This study systematically investigated the molecular mechanisms underlying high yield, superior quality, and heat tolerance in the thermo-sensitive genic male sterile line Gong 887S, its restorer lines (Yuenongsimiao, Jingguizhan, YR592), and their hybrid combinations through an integrated approach combining whole-genome sequencing, functional gene analysis, and phenotypic characterization. High-quality genome assembly of Gong 887S demonstrated exceptional contiguity ( LAI  = 26.52) and completeness (BUSCO = 98%), with 40,564 annotated genes. Notably, a 6.38% japonica introgression was identified, significantly higher than conventional indica varieties. Critical genes (such as OsLG3, Gn1a, TT3.1 ) located on Chrs 1, 3, and 7 were found to coordinately regulate grain number per panicle, grain length, and thermotolerance. The hybrid combinations (Gongliangyou Yuenongsimiao, Gongliangyou Jingguizhan, and Gong 8 Liangyou 892) pyramided 56–83 favorable loci, including LAX1, GS3, TT1 , and Chalk5 . Multi-location trials showed that these hybrids achieved average yields of 9,714–9,841 kg/ha, representing a 2.6–8.1% increase over controls. Heat tolerance evaluations revealed sustained seed-setting rates of 56.80–66.01% under 40°C greenhouse stress and over 85% under field conditions, significantly outperforming controls. Grain quality parameters, including head rice rate (68.7–72.0%), chalkiness (1.0–1.9%), and amylose content (15–17%), all met premium standards. Genomic structural variation analysis identified a Chr7 inversion and Chr11 deletion in Gong 887S that modulate OsAAP6 and Chalk5 expression, enhancing protein content while reducing chalkiness. By elucidating the genetic networks of Gong 887S and its hybrids, this study highlights the substantial contributions of indica-japonica introgression, multi-gene synergy, and structural variations to trait improvement, providing a robust theoretical foundation for molecular design breeding in rice.