Transcriptional reprogramming under drought reveals divergent adaptive strategies in Quinoa

Quinoa (Chenopodium quinoa Willd.) is known for its resilience to drought, yet the organ-specific transcriptional mechanisms underlying this trait remain insufficiently characterized. To address this, we investigated long-term drought responses in two contrasting cultivars, a sensitive (F15) and a tolerant (F16) genotype, by analyzing gene expression in leaves and seeds across three key reproductive stages: early (milky), thick, and mature seed development. This study complements previous physiological and biochemical investigations in the same genotypes, offering a deeper understanding of the molecular basis of drought tolerance.

Transcriptomic profiling has revealed distinct drought responses based on cultivar and organ. The sensitive cultivar F15 exhibited rapid changes in gene expression, with significant downregulation of photosynthesis- and ribosome-related genes, suggesting growth arrest. In contrast, F16 showed more stable expression patterns and maintained essential metabolic functions longer under stress. Regulation of genes involved in sugar metabolism, raffinose oligosaccharides, phenylpropanoids, and fatty acids varied between the two genotypes and tissues. Hormonal profiling indicated that F16 leaves had reduced jasmonate levels and increased cytokinin accumulation, indicating sustained growth potential. In F15 leaves, salicylic acid (SA) levels increased during the early stages. Additionally, mature F16 seeds showed reduced jasmonoyl-isoleucine levels, reflecting organ-specific and genotype-dependent hormonal changes.

These results suggest that drought tolerance in quinoa involves a finely regulated, genotype-specific coordination of gene networks and hormonal pathways that control development, metabolism, and stress responses in an organ-dependent manner. The tolerant cultivar F16 exhibited a more controlled transcriptional and hormonal response under drought, maintaining photosynthetic and metabolic stability while activating protective mechanisms related to sugar and osmolyte metabolism, including raffinose and stachyose biosynthesis, as well as cytokinin-mediated regulation of senescence. This study identifies molecular targets for future breeding efforts to improve quinoa drought tolerance for cultivation in water-limited environments.