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Background  Rapeseed ( Brassica napus  L.) and soybean ( Glycine max  L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism.    Results  An integrated omics analysis was performed in soybean, rapeseed,  Arabidopsis  ( Arabidopsis thaliana  L. Heynh), and sesame ( Sesamum indicum  L.), based on  Arabidopsis  acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the  PEPC  gene family, were found to be largely associated with the difference between the two species. First, three soybean genes ( Glyma.13G148600, Glyma.13G207900  and  Glyma.12G122900 ) co-expressed with  GmPEPC1  are specifically enriched during seed storage protein accumulation stages, while the expression of  BnPEPC1  is putatively inhibited by bna-miR169, and two genes  BnSTKA  and  BnCKII  are co-expressed with  BnPEPC1  and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits β-CT ( BnaC05g37990D ) and BCCP1 ( BnaA03g06000D ) of heterogeneous ACCase, which could interfere with synthesis rate, and  β-CT  is positively regulated by four transcription factors ( BnaA01g37250D, BnaA02g26190D, BnaC01g01040D  and  BnaC07g21470D ). In triglyceride synthesis,  GmLPAAT2  is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation.    Conclusions  The molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1542-8) contains supplementary material, which is available to authorized users.

bmc plant biology

An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus