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Scots pine (Pinus sylvestris L.) has high ecological and economic importance in Latvia. Induced resistance can protect trees from pathogen attack, and has potential for sustainable pest management. The effect of methyl jasmonate (MeJA) on the gene expression profile of Scots pine was determined in order to assess its potential to induce resistance. Two year old Scots pine ramets were treated with 10 mM MeJA and needle samples were collected two weeks after treatment. RNA was isolated from samples and transcription profiling was performed using the Ion Torrent PGM platform, and RT-PCR was used to confirm expression profiles for selected genes. Gene expression profiles results were summarized by a gene network analysis using gene functionality annotations. Results revealed that MeJA treatment diverts metabolic functions from growth and development to defensive pathways. Analysis of the transcriptome indicated that the MeJA treated Scots pine clone had an altered gene expression profile two weeks after the treatment, suggesting that the induction of defence mechanisms was still active at this time. The organism is in an induced state at least two weeks after the treatment, which confirms the potential of the MeJA use to induce resistance responses in Scots pine trees. [ABSTRACT FROM AUTHOR]