BSA-seq-based identification of a major additive plant height QTL with an effect equivalent to that of Semi-dwarf 1 in a large rice F₂ population

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.