Dissecting Agronomically Favorable Genotypes in Temperate Japonica Rice via Haplotype Analysis of a Japan-MAGIC Population

Crop breeding assembles genomic variants into cultivars via crossing and selection. Phenotypic selection has improved yield and lodging tolerance but has limited genetic insights. We show how specific genomic variants and their combinations underpin advances in modern rice breeding in Japan. Through genome-wide association study using a multi-parent advanced-generation intercross population derived from four temperate japonica cultivars, we identified 11 quantitative trait loci (QTLs) for key agronomic traits, including days to heading, shoot biomass, panicle length, and culm length under field conditions. GA20ox1, GA20ox2, and Hd1 were among the QTLs, and their natural variants were well conserved in temperate japonica cultivars bred in Japan, underscoring distinct selection pressures at these loci. By integrating genotype data with 5-year yield-performance-evaluation trials of elite cultivars, we found that cultivars carrying multiple-copy GA20ox1 and functional Hd1, together with non-functional ga20ox2, tended to have shorter culms and higher grain yield than cultivars with multiple-copy GA20ox1, functional Hd1, and GA20ox2. This yield advantage was consistent across latitudes in Japan. These results reveal favorable genotype combinations underlying modern japonica improvement and provide a genomic framework for breeding semi-dwarf, high-yielding cultivars adapted to temperate rice-growing regions in Asia. Overall design: Each of the first fully expanded leaf (from the top) of each JAM2 line was collected at 6 weeks after transplanting (1 July 2022 and 29 June 2023) from 9:00 to 11:00 am.