A major plant height QTL in foxtail millet exhibits developmental stage-dependent reversal of allelic effects and significant QTL-by-environment interaction

Highlights 1 A major locus, qPH9-1 , showed a striking stage‑specific reversal of allelic effects on plant height. The booting stage was identified as a critical window of heightened QEI, with a major contribution from qPH9-1 . Three high‑confidence candidate genes within the qPH9-1 interval were prioritized through integrated analysis. Plant height (PH) is a key determinant of yield potential and lodging resistance in foxtail millet and is under dynamic genetic control. To dissect this dynamic genetic architecture, we performed unconditional and conditional QTL mapping using a recombinant inbred line (RIL) population derived from a cross between Yugu 18 and Jigu 19. Phenotypic analysis showed that PH followed an approximately sigmoidal growth curve, with the most rapid elongation occurring between the jointing and booting stages (T2–T3). Genotype × environment interaction (G×E) effects were also most pronounced at T3. A total of 57 QTL were identified and integrated by meta-analysis into 23 consensus loci. Among these loci, qPH9-1 on chromosome 9 was consistently detected across multiple developmental stages. Notably, this locus exhibited a stage-specific reversal of allelic effects: the Yugu 18 allele increased PH before T3, whereas the Jigu 19 allele increased PH from T3 onward. QTL-by-environment interaction (QEI) analysis further identified T3 as a stage of heightened environmental sensitivity. At this stage, qPH9-1 showed a significant QEI effect, explaining up to 14.06% of the phenotypic variance. Within the qPH9-1 interval, integrated analysis of gene annotation, differential expression in elongating internodes, and haplotype variation prioritized Seita . 9G017500 , Seita . 9G018900 , and Seita . 9G019900 as high-confidence candidate genes. Collectively, these findings clarify the dynamic genetic architecture of PH in foxtail millet and provide a framework for targeted trait improvement and marker-assisted breeding.