Transcriptomic and metabolomic landscape of quinoa during seed germination

BACKGROUND: Quinoa (Chenopodium quinoa), a dicotyledonous species native to Andean region, is an emerging crop worldwide nowadays due to its high nutritional value and resistance to extreme abiotic stresses. Although it is well known that seed germination is an important and multiple physiological process, the network regulation of quinoa seed germination is largely unknown. RESULTS: Here, we performed transcriptomic study in five stages during transition from quinoa dry seed to seedling. Together with the GC–MS based metabolome analysis, we found that seed metabolism is reprogrammed with significant alteration of multiple phytohormones (especially abscisic acid) and other nutrients during the elongation of radicels. Cell-wall remodeling is another main active process happening in the early period of quinoa seed germination. Photosynthesis was fully activated at the final stage, promoting the biosynthesis of amino acids and protein to allow seedling growth. The multi-omics analysis revealed global changes in metabolic pathways and phenotype during quinoa seed germination. CONCLUSION: The transcriptomic and metabolomic landscape depicted here pave ways for further gene function elucidation and quinoa development in the future. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03621-w.