Genome stability and carbon-nitrogen metabolic reprogramming are associated with regeneration competence in quinoa

Quinoa (Chenopodium quinoa Willd.) is a nutritionally valuable pseudocereal; however, its genetic improvement is severely constrained by the absence of an efficient regeneration system and mechanistic understanding of the regeneration process. Here, we established a high efficiency cluster bud regeneration system using N6 basal medium supplemented with 0.1 mg/L 6-benzylaminopurine (6-BA) and 1.0 mg/L naphthaleneacetic acid (NAA), achieving a 93.5% induction rate and a 1.95-fold proliferation coefficient. In contrast, the combination of 0.5 mg/L kinetin (KT) and 1.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) was associated with only non-regenerative callus that failed to produce plants. Flow cytometry indicated that regenerable cluster buds showed stable ploidy levels, whereas non-regenerative callus exhibited endoreduplication, polyploidization and possible aneuploidy, suggesting a close association between genome stability and regeneration competence. Transcriptomic analysis of cluster buds versus yellow callus indicated activation of starch and sucrose catabolism, while targeted metabolomics of regenerated seedlings, representing a later developmental stage, revealed increased levels of essential amino acids (including lysine, valine, and tryptophan) and key metabolic nodes (glutamate and aspartate), alongside reduced levels of stress-associated proline. Moreover, genes involved in defense responses and transcriptional regulation were significantly upregulated in cluster buds compared to recalcitrant calli, which may help safeguard genome fidelity during active proliferation. The study provide an efficient regeneration platform and identify ploidy stability and carbon-nitrogen metabolic reprogramming as features associated with regeneration in the tested quinoa genotype, offering a basis for future genetic improvement of this crop.