Abstract
BACKGROUND: Phosphorus (P) deficiency is a major constraint on soybean (Glycine max (L.) Merr.) productivity, a key global source of edible oil and protein. Enhancing low-phosphorus (LP) tolerance through improved phosphorus-use efficiency is therefore crucial for sustainable soybean cultivation. RESULTS: This study elucidates the molecular mechanism by which GmAux/IAA16 regulates root morphogenesis and coordinates LP responses. Bioinformatics analysis showed that GmAux/IAA16 shares 92.43% sequence identity with its wild soybean (Glycine soja) ortholog, and subcellular localization confirmed its nuclear-specific accumulation. Stable overexpression of GmAux/IAA16 in tobacco via Agrobacterium-mediated transformation enhanced root development and maintained physiological stability under phosphate deprivation. Under LP stress, transgenic plants exhibited significant increases in key root enzyme activities: increased by 27.75% for indole‑3‑acetic acid oxidase (IAAO), 11.99% for superoxide dismutase (SOD), 42.59% for acid phosphatase (ACP), and 123.55% for catalase (CAT), alongside elevated ATP levels, reduced malondialdehyde (MDA) accumulation, and increased proline (Pro) content. Furthermore, endogenous levels of indole-3-acetic acid (IAA), jasmonic acid (JA), and salicylic acid (SA) were significantly higher in both leaves and roots, indicating a coordinated hormonal response that facilitates LP adaptation. Transcriptome analysis revealed that GmAux/IAA16 overexpression substantially reshapes the transcriptional landscape of tobacco roots under phosphorus stress. CONCLUSION: These findings demonstrate that GmAux/IAA16 positively regulates low-phosphorus tolerance, likely through cascading regulation of downstream phosphate-starvation response genes. This study provides novel insights into the role of the Aux/IAA gene family in soybean root development and phosphorus-use efficiency, and identifies GmAux/IAA16 as a promising genetic target for molecular breeding of phosphorus-efficient soybean cultivars. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08492-z.