Identification of the Dof Gene Family in Quinoa and Its Potential Role in Regulating Flavonoid Synthesis Under Different Stress Conditions

Quinoa (<i>Chenopodium quinoa</i> Willd.), often referred to as the "golden grain", is a highly nutritious crop that has garnered significant global attention due to its exceptional nutritional profile and health benefits. Flavonoids present in quinoa have been shown to possess antioxidant, anti-inflammatory, antiviral, anticancer, and antidepressant properties. The DNA binding with one finger (Dof) transcription factor is crucial for regulating growth, development, and stress responses. However, the identification of the Dof family using the latest quinoa genomic data and its function in abiotic stress response have not been fully elucidated. Here, 36 <i>CqDof</i> genes were identified from the quinoa genome and classified into ten subfamilies through phylogenetic analysis. Physicochemical property analysis predicted that <i>CqDofs</i> predominantly encode basic, hydrophilic, and unstable nuclear proteins. <i>CqDofs</i> were distributed across 15 chromosomes, with segmental duplication being the primary driver of their expansion. Subsequently, basic information on <i>CqDofs</i> was systematically analyzed, including conserved motifs, gene structure, cis-acting elements, and expression patterns. Notably, the promoter regions of all <i>CqDof</i> genes were enriched with cis-acting elements related to light responsiveness. Further analysis revealed that red and blue light significantly affected <i>CqDof</i> expression and flavonoid accumulation (epigallocatechin, rutin, naringenin, morin, pinocembrin, quercetin-7-O-rutinoside, quercetin-3-O-glucoside, and naringenin), in which 5 <i>CqDofs</i> exhibited a pronounced response to both light conditions and showed a significant correlation with flavonoid levels. Finally, RT-PCR analysis indicated that the expression levels of <i>CqDofs</i> (except <i>CqDof21</i>) were significantly upregulated under drought, salt, and saline-alkali stresses. These findings lay the groundwork for future studies on how <i>CqDofs</i> regulate flavonoid biosynthesis under different light qualities and function in abiotic stress.