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Background  Flax ( Linum usitatissimum  L.) is a crop plant used for fiber and oil production. Although potentially high-yielding flax varieties have been developed, environmental stresses markedly decrease flax production. Among biotic stresses,  Fusarium oxysporum  f. sp.  lini  is recognized as one of the most devastating flax pathogens. It causes wilt disease that is one of the major limiting factors for flax production worldwide. Breeding and cultivation of flax varieties resistant to  F. oxysporum  is the most effective method for controlling wilt disease. Although the mechanisms of flax response to  Fusarium  have been actively studied, data on the plant response to infection and resistance gene candidates are currently very limited.    Results  The transcriptomes of two resistant and two susceptible flax cultivars with respect to Fusarium wilt, as well as two resistant BC 2 F 5  populations, which were grown under control conditions or inoculated with  F. oxysporum , were sequenced using the Illumina platform. Genes showing changes in expression under  F. oxysporum  infection were identified in both resistant and susceptible flax genotypes. We observed the predominant overexpression of numerous genes that are involved in defense response. This was more pronounced in resistant cultivars. In susceptible cultivars, significant downregulation of genes involved in cell wall organization or biogenesis was observed in response to  F. oxysporum . In the resistant genotypes, upregulation of genes related to NAD(P)H oxidase activity was detected. Upregulation of a number of genes, including that encoding beta-1,3-glucanase, was significantly greater in the cultivars and BC 2 F 5  populations resistant to Fusarium wilt than in susceptible cultivars in response to  F. oxysporum  infection.    Conclusions  Using high-throughput sequencing, we identified genes involved in the early defense response of  L. usitatissimum  against the fungus  F. oxysporum . In response to  F. oxysporum  infection, we detected changes in the expression of pathogenesis-related protein-encoding genes and genes involved in ROS production or related to cell wall biogenesis. Furthermore, we identified genes that were upregulated specifically in flax genotypes resistant to Fusarium wilt. We suggest that the identified genes in resistant cultivars and BC 2 F 5  populations showing induced expression in response to  F. oxysporum  infection are the most promising resistance gene candidates.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1192-2) contains supplementary material, which is available to authorized users.

Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.)