A yield-reducing introgression linked to sd1 in rice.

The semi-dwarf (sd1) allele was central to the Green Revolution, but its widespread use in US tropical japonica rice (Oryza sativa L.) may have introduced unintended effects through linkage drag. This study examined the genomic region surrounding sd1 using genome-wide association and haplotype analyses in a multiparent population (MP6/8) evaluated across environments and in a biparental population (MP-D) for validation. Genomic and phenotypic evidence indicated that an indica-derived haplotype upstream of sd1 persists in US tropical japonica and global indica semi-dwarf germplasm and is associated with reduced grain yield. Genome-wide association analysis confirmed sd1 as the primary determinant of reduced plant height and identified a quantitative trait locus at 36.69 Mb upstream of sd1 that was consistently associated with reduced grain yield (0.6-0.9 t ha-1) across populations and environments. Haplotype analysis identified an indica-derived Presidio haplotype spanning this upstream region was associated with significant yield reductions in both populations. Pedigree analysis traced this unfavorable haplotype to the Taichung Native 1 donor lineage, representing one historically deployed sd1-linked introgression class. Although its frequency has declined in modern cultivars, its persistence highlights the long-term impact of linkage drag following major trait introgression. These findings emphasize the value of marker-assisted selection and targeted recombination to separate favorable dwarfing alleles from linked yield penalties and sustain yield gains in US rice improvement programs.