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Background  Rapeseed ( Brassica napus, B. napus ) is an important oil seed crop in the world. Previous studies showed that seed germination vigor might be correlated with seed oil content in  B. napus , but the regulation mechanism for seed germination has not yet been explained clearly. Dissecting the regulation mechanism of seed germination and germination vigor is necessary.    Results  Here, proteomic and genomic approaches were used to analyze the germination process in  B. napus  seeds with different oil content. The identification of 165 differentially expressed proteins (DEPs) in the germinating seeds of  B. napus  with high and low oil content was accomplished by two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE). The comparative proteomic results revealed that seeds with high oil content had higher metabolic activity, especially for sulfur amino acid metabolism. Thirty-one unique genes were shown to be significantly changed during germination between the seeds with high and low oil content, and thirteen of these genes were located within the confidence interval of germination-related quantitative trait locus (QTLs), which might play an important role in regulating seed germination vigor.    Conclusions  The present results are of importance for the understanding of the regulation mechanism for seed germination vigor in  B. napus .    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1624-7) contains supplementary material, which is available to authorized users.

Integration of proteomic and genomic approaches to dissect seed germination vigor in Brassica napus seeds differing in oil content