This work presents a pipeline for optimizing semi-hydroponic growth conditions and analyzes the impact on the growth and metabolism in three Mentha species (M. arvensis, M. x piperita, or M. spicata) and three Ocimum basilicum genotypes (́Chládek červená́, ́Litrá, or ́Máneś). The plant growth and the content- of nitrogen-containing compounds, phenolics, and terpenoids were determined under different nitrate concentrations and salt stress. Different responses were observed among genotypes for both species. ́Chládek červená́ had the best growth under low nitrate, with lower histamine and higher flavonoid levels. Mentha x piperita was the best mint species performing under low nitrate and salt stress. Altogether, we demonstrate that a combination of phenomics and metabolomics is ideal to identify the optimal growth conditions for these plants and the chemical markers associated with these conditions. Besides, we showed that both primary and secondary metabolites can be good markers for classifying both species.

Centre of Region Haná for Biotechnological and Agricultural Research Czech Advanced Technology and Research Institute Palacky University Šlechtitelů 27 78371 Olomouc Czech Republic

Centre of Region Haná for Biotechnological and Agricultural Research Czech Advanced Technology and Research Institute Palacky University Šlechtitelů 27 78371 Olomouc Czech Republic; Centre of the Region Haná for Biotechnological and Agricultural Research Department of Genetic Resources for Vegetables Medicinal and Special Plants Crop Research Institute Šlechtitelů 29 78371 Olomouc Czech Republic

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