Objective Plant height and tillering are key agronomic traits that directly influence rice lodging resistance and panicle number. Common wild rice in China represents a valuable reservoir of genetic diversity. Therefore, identifying novel dwarf and high-tillering genes from common wild rice can enrich the genetic resources for improving these traits in rice breeding programs.

Method In this study, we used 'Qiansui', a stable dwarf and high-tillering line derived from Gaozhou common wild rice, and the African cultivated rice 'Morobrecan' to construct segregating populations via reciprocal crosses. We employed agronomic trait evaluation, genetic analysis, BSA-seq, and candidate gene sequencing to identify the causal gene in 'Qiansui'.

Result Genetic analysis revealed that the dwarf and high-tillering traits in 'Qiansui' were controlled by a single recessive nuclear gene. BSA-seq initially mapped the locus to a 4.07 Mb physical interval on chromosome 4. Based on gene annotations within this region, we amplified and sequenced candidate genes. Sequence alignment identified two missense mutations in the HTD1 gene of 'Qiansui'. The first was a C→A transversion at nucleotide position 736, resulting in an amino acid substitution from alanine to aspartic acid. However, this mutation was also present in normal plant-type varieties 'Yuenongsimiao' and 'Mingyuesimiao', which ruled out its causal role in the 'Qiansui' phenotype. The second mutation was a G→A transition at position 2 084, causing premature termination of protein translation. This mutation was absent in 'Morobrecan', 'Yuenongsimiao', and 'Mingyuesimiao'. Subsequent sequencing of an expanded segregating population confirmed that all dwarf plants carried this G→A mutation, whereas all tall plants exhibited the wild-type sequence. We therefore hypothesize that this mutation disrupts the function of HTD1, which encodes carotenoid cleavage dioxygenase 7 (CCD7), leading to impaired strigolactones (SLs) biosynthesis and consequently the observed dwarf and high-tillering phenotype. Both genetic and molecular evidence indicate that the 'Qiansui' phenotype is controlled by a novel allele of HTD1, which we designated as htdq (high tillering dwarf Qiansui).

Conclusion In conclusion, the dwarf and high-tillering phenotype of 'Qiansui' is controlled by the htdq allele of HTD1. Our findings provide novel and valuable dwarf germplasm for elucidating the molecular mechanisms of SLs and for breeding rice with ideal plant architecture, thereby enhancing the genetic diversity for plant height in new rice varieties.