Genome-wide identification and expression analysis of the WOX gene family in quinoa ( Chenopodium quinoa Willd.)

Chenopodium quinoa exhibits broad-spectrum tolerance to abiotic stresses. However, its limited regenerative capacity hinders systematic functional characterization and the application of gene editing. WOX transcription factors play pivotal roles in meristem maintenance, organogenesis and regeneration. Here, we identified 11 CqWOX family members from the quinoa genome and conducted phylogenetic, structural, promoter, and expression analyses. The CqWOX proteins showed marked variation in length and physicochemical properties and were predicted to localize to the nucleus. Expression profiling revealed strong tissue- and stage-specific expression, and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) during callus induction showed non-significant but consistent trends between cotyledonary nodes and hypocotyls. CqWOX1 , CqWOX7 and CqWOX10 showed high expression during seed germination and seedling stages, implying roles in embryonic development and organ differentiation. CqWOX6 and CqWOX8 were enriched in meristems, potentially maintaining stem cell zone homeostasis. In 14-day callus, qRT-PCR showed that cotyledonary nodes tended to increase CqWOX3/4/5/11 , whereas in hypocotyls CqWOX3 and CqWOX11 tended to increase and CqWOX4 and CqWOX5 to decrease. Abiotic stress assays demonstrated differential responses. CqWOX8 was significantly upregulated under salt, combined salt-alkali, and low-temperature stresses, suggesting its mediation of broad-spectrum stress signaling integration. CqWOX3 and CqWOX10 specifically responded to alkali stress, potentially linking to ion/osmotic homeostasis, whereas CqWOX2 and CqWOX9 were suppressed under multiple stresses. Protein interaction predictions indicated that CqWOX4 may crosstalk with the CLV3/CLE-ARR signaling module to coordinate hormonal and developmental pathways, and collaborate with the BBM-GIF-LEC2 regeneration network to establish a stem cell homeostasis-hormone response-organ regeneration regulatory cascade. Collectively, this study provides a resource for WOX evolution and candidate genes for improving quinoa regeneration and stress resilience.