The genomic characterization of sugarcane plants has been achieved by suppressing key genes of the phenylpropanoid pathway; as a result, a new function of phenolic metabolites has been characterized during micropropagation in TIBs. Genes related to cell metabolism and development (10), plant defenses (9), phenylpropanoids (7), methyl jasmonate response (5), ethylene (5), oxidative burst (3) and, auxins (3) pathways, among others (8) were found to be induced in sugarcane plants micropropagating in TIBs with phenolic metabolites, supporting that phenylpropanoids might act as elicitor molecules of others biochemical pathways. During adaptation to natural conditions, plants micropropagated in TIBs with highest levels of phenolics displayed an increased number of functional roots, a high growth rate and, an early ability to be colonized by the natural sugarcane endophytic Gluconacetobacter diazotrophicus. (c) 2008 Elsevier Ireland Ltd. All rights reserved.