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Background  The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress ( Lepidium campestre ) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services.  Lepidium  is closely related to  Arabidopsis  and display significant proportions of syntenic regions in their genomes.  Arabidopsis  genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of  Lepidium-Arabidopsis  would facilitate the identification of  Lepidium  candidate genes regulating various desirable traits.    Results  Homologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in  Arabidopsis  were identified and partially characterized in  Lepidium . Alignments of sequences representing field cress and two of its closely related perennial relatives:  L. heterophyllum  and  L. hirtum  revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine non-synonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to  L. heterophyllum  than to  L. hirtum .    Conclusions  There is significant variation within and among  Lepidium  species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the  Lepidium  species revealed in this study does not only shed some light on  Lepidium  genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different  Lepidium  species as part of the domestication efforts.    Electronic supplementary material  The online version of this article (10.1186/s12863-018-0624-9) contains supplementary material, which is available to authorized users.

Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop