Allele-informed QTL-seq identifies Hd18 as a minor modifier of heading date in elite rice cultivars

Fine-tuning heading date is critical for optimizing yield, grain quality, and local adaptation in rice (Oryza sativa L.). QTL-seq (where QTL is quantitative trait locus), which integrates bulked segregant analysis with whole-genome resequencing, provides a rapid and cost-effective approach for identifying QTLs underlying complex traits. Shinpyeong and Haedeul are elite Korean rice cultivars that carry identical alleles at four major heading date genes (Hd1, OsPRR37, Ghd7, and DTH8), yet differ by approximately 7 days in heading under natural long-day conditions. To elucidate the genetic basis of this difference, we applied allele-informed QTL-seq to an F₂ population derived from a cross between Shinpyeong and Haedeul. A single prominent QTL peak with the highest ΔSNP-index (where SNP is single nucleotide polymorphism) was consistently detected across both field and greenhouse environments and co-localized with Hd18, identifying it as the most likely causal gene. The underlying polymorphism was a previously reported missense A/G variant. Genotyping of the Hd18 A/G SNP using a dCAPS (derived cleaved amplified polymorphic sequence) marker revealed that F₂ plants homozygous for the A allele headed 4.1 days earlier in the field and 6.2 days earlier in the greenhouse than those homozygous for the G allele. Analysis of 290 Korean rice cultivars further demonstrated that the Hd18 A allele was associated with approximately 2 days earlier heading under a nonfunctional hd1 background. Evaluation of two recombinant inbred line populations showed that Hd18 had minimal effects on major agronomic traits, while exhibiting background-dependent effects on specific traits. These results establish Hd18 as a minor effect modifier of heading date with utility for fine-scale phenological adjustment in rice breeding.