Genome-wide analyses of NPF and NRT2 reveal a potential role for a key gene, CqNRT2.2, in the quinoa response to nitrate

BACKGROUND: NO₃⁻ serves as the primary nitrogen source for plants and functions as a key signaling molecule in regulating growth and development. Despite its recognized importance, research on NO₃⁻ uptake and signaling in quinoa remains limited. RESULTS: In this study, a genome-wide analysis identified 114 CqNPF and 15 CqNRT2 genes in quinoa. Heterologous complementation assays in the NO₃⁻-transporter-deficient yeast mutant Δynt confirmed that 11 CqNPF and 3 CqNRT2 transporters possess NO₃⁻ uptake capacity. Under NO₃⁻-deficient conditions, CqNRT2.2 was highly expressed in the roots of the quinoa cultivar 'W32'. Using WGCNA and promoter binding site prediction, CqNLP2.1 is predicted to regulate CqNRT2.2 Further experiments showed that the transcription factor CqNLP2.1 binds to the CqNRT2.2 promoter. Overexpression of either CqNRT2.2 or CqNLP2.1 in Arabidopsis significantly promoted primary root elongation. Molecular docking predicted that both CqNLP2.1 and CqNLP2.2 may bind directly to NO₃⁻ ions, suggesting a potential but unconfirmed role in nitrate sensing. However, these are computational predictions only and do not demonstrate biological nitrate-sensing function, which requires experimental validation. Collectively, these findings indicate that CqNLP2.1 acts as a transcription factor in the quinoa NO₃⁻ signaling pathway, potentially regulating growth and development by modulating expression of the NO₃⁻-responsive gene CqNRT2.2. CONCLUSIONS: This study offers novel insights into the molecular mechanisms of NO₃⁻ signal transduction in quinoa and provides a theoretical framework for enhancing nitrogen use efficiency in quinoa cultivation.