A chromosome‐level genome assembly of an elite indica breeding line resolves the genomic architecture of drought‐yield QTLs qDTY 2.2 and qDTY 4.1 in rice

Drought‐yield quantitative trait loci (QTLs) qDTY 2.2 and qDTY 4.1 improve grain yield under reproductive‐stage drought in rice ( Oryza sativa L.), yet their genomic architecture remains poorly resolved in elite indica breeding backgrounds. We generated a chromosome‐level assembly of IR87707‐446‐B‐B‐B (IR64‐qDTY 2.2 + qDTY 4.1 ), which carries both QTLs in the IR64 background, and delineated donor‐derived introgressions using informative parental single‐nucleotide polymorphisms (SNPs). The 395.5‐Mb assembly comprised 12 chromosomes, showed 99.2% BUSCO completeness, and contained 40,189 predicted protein‐coding genes. Informative‐SNP analysis, supported by read‐depth assessment of low‐information regions, resolved qDTY 2.2 and qDTY 4.1 as continuous donor‐derived introgressions containing 194 and 97 genes, respectively. Comparative genome analysis showed that qDTY 2.2 was largely macrostructurally collinear with IRGSP‐1.0, whereas qDTY 4.1 showed pronounced structural divergence and contained a 15.6‐kb inversion relative to IR64sj. Comparative gene‐content analysis further showed that 37.1% and 55.7% of genes in qDTY 2.2 and qDTY 4.1 , respectively, lacked collinear orthologs in IRGSP‐1.0. Multi‐accession allele analysis revealed contrasting candidate‐gene profiles between the two loci. Six of eight qDTY 2.2 candidates had coding sequences identical to IR64sj, whereas all four qDTY 4.1 candidates showed coding differences from IR64sj. Coordinate‐based SNP markers were also developed for donor‐haplotype tracking across both QTL intervals. These results provide a genome‐resolved framework for characterizing drought‐yield QTLs and developing breeding‐background‐specific markers for recombination‐aware rice breeding.