Characterization and fine-mapping of qHd2-1, a minor quantitative locus that affects heading date under long-day conditions in rice (Oryza sativa L.)

Heading date, a complex quantitative trait, determines regional adaptability and is associated with grain yield and quality in rice. In this study, we characterized qHd2-1, a minor-effect quantitative locus (QTL) for promoting heading date (by 3–4 days) under long-day (LD) conditions, but not short-day (SD) conditions. The qHd2-1 locus was detected in single segment substitution line (SSSL) N22-1, which was developed using indica 9311 as the donor and japonica Nipponbare (NP) as the recipient. A set of substitution lines were developed from a segregating population derived from a cross between N22-1 and NP. Based on the genotypic identification and phenotypic evaluation of the target substitution lines, qHd2-1 was narrowed down to a 105-kb region between STS2-20 and STS2-22 on the short arm of chromosome 2. Furthermore, qHd2-1 was found to function by upregulating the florigen genes Hd3a and RFT1 during floral induction under LD conditions. Field tests showed that qHd2-1 promotion of heading date affects grain yield‑related agronomic traits, such as plant height, panicle number per plant, and flag leaf size, as well as thousand-grain weight and grain width. Taken together, these findings establish a foundation for cloning this minor-effect QTL involved in heading date, and qHd2-1 could be of great significance in rice breeding to allow the fine-tuning of heading date in rice cultivars.