Genotypic variation and root traits associated with hypoxia tolerance in quinoa (Chenopodium quinoa Willd.)

Waterlogging-induced hypoxia is becoming an increasingly important constraint to crop production under climate change. Although quinoa ( Chenopodium quinoa Willd.) is recognized for its tolerance to drought and salinity, its response to hypoxia remains poorly understood. This study evaluated the effects of hypoxia on growth, root development, biomass accumulation, and individual seed yield in 28 quinoa genotypes. Hypoxia reduced plant height by 31%, leaf area by 47%, root length by 39%, and shoot dry weight by 37% (mean hypoxia tolerance index 0.69, 0.53, 0.61, and 0.63); shoot dry weight remained 44% lower after recovery, whereas root diameter increased by 28% under hypoxia. Correlation analysis revealed that root length and root surface area were positively associated with individual seed yield, whereas root diameter was negatively related to several growth traits, highlighting the importance of maintaining root development under hypoxia. Permutational multivariate analysis of variance across 19 traits attributed 37.1% of overall phenotypic variation to genotype, 30.0% to oxygen regime, and 18.8% to their interaction (each p = 0.001), and hierarchical clustering on hypoxia tolerance indices resolved three genotype groups with contrasting trait profiles. Under hypoxia, Amachuha and Isluga produced the highest individual yields, followed by EDK4 and Chadmo. Under genotype-level validation (leave-one-genotype-out, leave-one-cluster-out, and highland-versus-lowland cross-ecotype splits), no model predicted the individual yield of genotypes excluded from training better than the mean yield of the training genotypes under the same oxygen regime, so trait-based yield prediction does not transfer to unseen quinoa genotypes. These findings provide valuable insights into the mechanisms of hypoxia tolerance and identify promising genetic resources for breeding quinoa cultivars adapted to waterlogging-prone environments.