Drought disrupts quinoa seed germination and seedling establishment via sugar metabolism and hormonal perturbations

Drought stress inhibits quinoa (Chenopodium quinoa Willd.) seed germination and seedlings growth, significantly affecting yield and quality. Nevertheless, the molecular mechanisms underlying quinoa's drought stress response are not yet fully elucidated. Therefore, a multi-omics analysis of the response to drought stress was conducted using two drought-resistant quinoa varieties (LL1 and LQ18) subjected to normal (CK) and severe (DS2, 20% PEG-6000) drought conditions. Drought stress exerted no statistically significant impact on germination rate, germinative force, and germination index for LQ18, but DS2 treatment reduced these germination indicators for LL1. Concomitantly, DS2 treatment notably decreased seedlings height, hypocotyl length, radicle length, dry and fresh weight, especially for LL1. Multi-omics analyses revealed that DS2 treatment markedly downregulated genes related with starch and sucrose metabolism and galactose metabolism during the radicle emergence stage, whereas these pathways were subsequently upregulated at the cotyledon expansion stage. Thus, the starch and sucrose content increased at the two stages, while glucose content decreased at radicle emergence stage but increased at cotyledon expansion stage. The low glucose concentration at radicle emergence stage likely suppressed abscisic acid (ABA) biosynthesis, resulting in no significant change in the abundance of the differentially accumulated metabolites (DAM) of ABA. The hormonal balance was significantly altered, with the gibberellins (GAs)/ABA ratio being significantly lower in LL1 under DS2, while it was slightly up-regulated in LQ18. In addition, DS2 treatment induced genes expression of antioxidant systems, in which soluble sugars, proline, and malondialdehyde content accumulated, and raffinose, stachyose, trehalose, glutathione, kaempferol, and quercetin abundance increased, especially for LQ18. Collectively, the findings of this study contribute to a deeper understanding of the drought tolerance mechanisms of quinoa, thereby providing a theoretical foundation for future research on quinoa's drought resistance.