Mexico is a megadiverse country, with a highh quantity of unique plant species; with different uses and applications, such as bactericidal, fungicidal, insecticidal, and recently nutrimental. The content of phytochemicals and the impact of them in the animal and human health, has been make them a target for biotechnological improvement. At the región Bajio in Mexico, have been identified several plants associated with ecological, medical and industrial potential, but also asocciated to the traditions of the population whit no real utility. The work in this Project includes the development of systems for the culture for production of secondary metabolites (in vitro root tissue culture) and the miRNA expresión analysis in order to find the molecules asocciated to metabolites production. In this study we include two plants: marigold (Tagetes erecta), which the genes associated to lutein production had been identified in flower development, systems for cell culture and plant transfromation has been developed, but no systems for in vitro root culture. To now there are not studies related to miRNA expresión and association to these molecules to secondary metabolites. In Heliopsis longipes, several metodologies had been developed for the isolation of afinin and its uses in agriculture, medicine and recently as analgesic activities in some other metabolites. First, a root tissue culture was established for both of the plants (marigold and Heliopsis), using a combination of auxins (2,4-D, IAA, IBA) in a cinetical assay, as the base for manipulation; differences in the root architecture were determined mainly in the time of production and root architecture. In the molecular analysis four miRNAs were found differentially expressed and associated to secondary metabolites production (miR146, miR164, miR168, miR171). The reordering of miRNAs synthesis and the targets was analysed and is associated to the secondary metabolites production in order to establish a system for the in vitro induction of metabolites.