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

Modern rice breeding faces the critical challenge of simultaneously improving yield, grain quality, and stress tolerance to meet sustainable production demands. This study systematically investigated the molecular mechanisms underlying high yield, superior quality, and heat tolerance in the thermo-sensitive genic male sterile line Gong 887 S, its restorer lines (Yuenongsimiao, Jingguizhan and YR592), and their hybrid combinations through an integrated approach combining whole-genome sequencing, functional gene analysis, and phenotypic characterization. The high-quality Gong 887 S genome assembly (LAI = 26.52, BUSCO = 98%) revealed 40,564 protein-coding genes and a remarkable 6.38% japonica introgression, substantially exceeding the < 3% typically found in indica varieties. Functional analysis identified key regulatory genes (OsLG3, Gn1a, TT3.1) on Chrs (chromosomes) 1, 3, and 7 that coordinately enhance panicle architecture, grain morphology, and thermotolerance. Hybrid combinations accumulated 56-83 favorable alleles (including LAX1, GS3, TT1, and Chalk5), demonstrating significant yield advantages (9,714-9,841 kg/ha, + 2.6-8.1%) across multiple locations. Notably, these hybrids maintained robust performance under heat stress, with seed-setting rates of 56.80-66.01% under controlled 40 °C conditions and > 85% in field trials. Grain quality analysis revealed premium characteristics: head rice rate (68.7-72.0%), chalkiness (1.0-1.9%), and amylose content (15-17%). Structural variations (chromosome inversion and chromosome 11 deletion) were found to regulate OsAAP6 and Chalk5 expression, simultaneously increasing protein content (+ 8.3%) and reducing chalkiness (-42.9%). By elucidating the genetic networks of Gong 887 S 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.

The online version contains supplementary material available at 10.1007/s11032-026-01699-w.