Bulked-segregant analysis is a time- and cost-saving strategy for identifying major quantitative trait loci (QTL) in a mapping population. Bulked-segregant analysis combined with whole-genome sequencing (BSA-seq) was performed to rapidly identify QTL for heading date, plant height, and panicle length in a large F₂ population derived from two landraces: Chuan 7 (C7) and Haoboka (HBK). Twenty plants with extremely low or high phenotypic values for the target traits were selected from an F₂ population of 940 plants to construct low- and high-value bulks. Three pairs of bulks for the three traits were constructed, resulting in six DNA pools. BSA-seq revealed nine QTL: four for heading date, three for plant height, and two for panicle length. These QTL were validated in a random F₂ population or BC₄F₂ populations. The major novel plant height QTL, qPH8, acting additively with an effect equivalent to that of semi-dwarf 1 (sd1), is potentially valuable for hybrid rice breeding. qPH8 controls mainly the elongation of basal internodes. The C7 allele of qPH8 reduces plant height and increases lodging resistance without yield penalty, suggesting a potential role for qPH8 in improving rice plant architecture.

Seed dormancy of cultivated rice was largely weakened during the progress of domestication. Correct timing and uniformity of seed germination are important for rapid seedling establishment and high-yield production. In the present study, we found that the heading-date gene Ghd7 acted as a negative regulator of germination. A mutant of ghd7 showed low sensitivity to exogenous ABA treatment during seed germination. Further investigation revealed reduced accumulation of ABA in mature ghd7 seeds as a consequence of dampened expression of OsNCED genes. Moreover, elevated GA₃ level was detected in seeds of ghd7 mutant during imbibition course, which was attributed to the induction of genes responsible for the synthesis pathways of bioactive GAs. Thus, Ghd7 inhibits seed germination by increasing the ABA/GA₃ ratio. Besides revealing pleiotropic effects of Ghd7, our results indicate its role in linking seed germination to growth-phase transition in rice, which would enrich the theoretical basis for future breeding practices.