Genetic Dissection of Plant Height Variation Between the Parental Lines of the Elite Japonica Hybrid Rice ‘Shenyou 26’

Plant height is a key agronomic trait influencing both seed production and yield in hybrid rice. In the elite japonica hybrid 'Shenyou 26', optimal plant height differences between the restorer line ('Shenhui 26') and the male sterile line ('Shen 9A') are critical for efficient pollination. In this study, we dissected the genetic basis of plant height variation using a doubled haploid (DH) population derived from 'Shenyou 26'. Multi-environment phenotyping and QTL mapping identified seven QTLs associated with plant height, among which <i>qPH1.1</i> and <i>qPH9.1</i> were validated. <i>qPH1.1</i> co-localized with the semi-dwarf gene <i>SD1</i>, and 'Shen 9A' carries a rare <i>SD1-EQH</i> allele that potentially confers reduced height relative to the <i>SD1-EQ</i> allele in 'Shenhui 26'. <i>qPH9.1</i> also contributed significantly to plant height variation, with the Shenhui26 allele increasing plant height in backcross validation. These findings indicate that plant height variation in 'Shenyou 26' is controlled by multiple loci, including <i>SD1</i> allelic variants and other complementary QTLs, providing valuable resources for fine-tuning plant architecture in rice breeding.