QTL-seq identifies NAL1 and OsOFP19 as additive regulators of tiller number in rice (Oryza sativa L.)

Abstract

Background: Tiller number is a critical component of rice yield, as it directly influences overall productivity. While upland rice varieties are well adapted to lowland environments and prove resilient to fluctuating water availability, their typically low tillering capacity limits their performance in lowland ecosystems where conditions are more conducive to achieving higher yields. Results: To facilitate the marker-assisted selection (MAS) breeding of upland rice cultivars suitable for lowland conditions, we performed QTL-seq analysis using populations derived from a cross between a high-tillering lowland indica parent (PTT1) and a low-tillering upland tropical japonica line (NDCMP49). Two major QTLs associated with tiller number were identified on chromosomes 4 and 5 and designated as qTN4 and qTN5, respectively. Candidate gene analysis revealed NAL1 and OsOFP19 as putative genes underlying these loci. Functional validation of NAL1 using CRISPR-Cas9 knockout mutants confirmed its role as a negative regulator of tillering, as two independent alleles of nal1 mutant plants exhibited significantly increased tiller numbers compared with the wild type. Marker–trait association analysis further supported the additive effect of qTN4 (NAL1) and qTN5 (OsOFP19), indicating their potential for pyramiding in breeding programs. Functional KASP markers of NAL1 and OsOFP19 were developed and successfully validated in segregating populations, demonstrating their applicability for marker-assisted selection. Conclusions: Collectively, these findings advance our understanding of the genetic regulation of tillering in rice and provide molecular tools for improving plant architecture and yield in upland rice varieties cultivated under lowland conditions. © The Author(s) 2025.