Natural variation in HD10.1 promoter causing delayed heading date in rice

Heading date is a critical agronomic trait in rice (Oryza sativa L.). Utilizing chromosome segment substitution lines (CSSLs) with the indica cultivar “Huanghuazhan” (HHZ) as the recipient parent and “Basmati Surkh 89–15” (BAS) as the donor parent, we identified a quantitative trait locus (QTL) regulating heading date, designated as HD10.1. In this study, we characterized a functionally defective allele of HD10.1^BAS, a novel allele of Ehd1. The divergence in the promoter region between HD10.1^BAS and HD10.1^HHZ results in reduced transcriptional expression of HD10.1^BAS in NIL-HD10.1^BAS, leading to a delay in heading by approximately 10 days compared to NIL-HD10.1^HHZ under long-day conditions. An insertion-deletion (InDel) within the HD10.1^BAS promoter may be a key factor contributing to its decreased transcriptional activity. Moreover, our findings suggest that the introgression of HD10.1^BAS into the HHZ cultivar exhibits potential for yield improvement. This study provides valuable genetic resources for molecular breeding strategies aimed at optimizing heading date while simultaneously enhancing yield in rice.