Comparative Transcriptomic Analysis Reveals Conserved and Nutrient-Specific Responses to Nutrient Deficiencies in Quinoa

Nutrient deficiency is a major constraint on crop productivity, yet the molecular mechanisms underlying adaptation to different essential nutrient deficiencies remain poorly understood in quinoa (Chenopodium quinoa Willd.). We performed the first comparative transcriptomic analysis of quinoa responses to deficiencies of twelve essential macro- and micronutrients across leaf and root tissues, generating 104 RNA-sequencing libraries analyzed using differential expression, multivariate, co-expression network, and pathway enrichment approaches. Nutrient deficiencies differed substantially in the magnitude and character of their transcriptional responses, with the number of differentially expressed genes ranging from 225 (boron) to 4367 (magnesium) across treatments, and leaves generally exhibiting greater transcriptional plasticity than roots, particularly under nitrogen, potassium, magnesium, and zinc deficiencies. Despite these differences, a conserved transcriptional response centered on protein turnover, ion transport, and nutrient recycling was triggered across nearly all nutrient deficiencies in roots, while suppression of photosynthesis-related genes recurred independently across several deficiencies in leaves; individual deficiencies also elicited distinct regulatory signatures reflecting their physiological functions. Macronutrient deficiencies primarily affected central metabolism, whereas micronutrient deficiencies predominantly altered metal homeostasis, redox balance, and specialized cofactor-dependent pathways. Together, these findings demonstrate that quinoa integrates conserved, tissue-specific stress responses with nutrient-specific regulatory mechanisms to cope with nutrient limitation. This work provides a comparative transcriptomic framework and candidate genes for improving nutrient use efficiency in quinoa and its adaptation to nutrient-limited environments.