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Background  Accumulation of storage compounds during seed development plays an important role in the life cycle of oilseed plants; these compounds provide carbon and energy resources to support the establishment of seedlings.    Results  In this study, we show that  BnCIPK9  has a broad expression pattern in  Brassica napus  L. tissues and that wounding stress strongly induces its expression. The overexpression of  BnCIPK9  during seed development reduced oil synthesis in transgenic  B. napus  compared to that observed in wild-type (WT) plants. Functional analysis revealed that seed oil content (OC) of complementation lines was similar to that of WT plants, whereas OC in  Arabidopsis thaliana  (L.) Heynh.  Atcipk9  knockout mutants ( cipk9 ) was higher than that of WT plants. Seedling of  cipk9  mutants failed to establish roots on a sugar-free medium, but root establishment could be rescued by supplementation of sucrose or glucose. The phenotype of complementation transgenic lines was similar to that of WT plants when grown on sugar-free medium. Mutants,  cipk9 ,  cbl2 , and  cbl3  presented similar phenotypes, suggesting that CIPK9, CBL2, and CBL3 might work together and play similar roles in root establishment under sugar-free condition.    Conclusion  This study showed that  BnCIPK9  and  AtCIPK9  encode a protein kinase that is involved in sugar-related response and plays important roles in the regulation of energy reserves. Our results suggest that  AtCIPK9  negatively regulates lipid accumulation and has a significant effect on early seedling establishment in  A. thaliana . The functional characterization of  CIPK9  provides insights into the regulation of OC, and might be used for improving OC in  B. napus . We believe that our study makes a significant contribution to the literature because it provides information on how CIPKs coordinate stress regulation and energy signaling.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1122-z) contains supplementary material, which is available to authorized users.

CIPK9 is involved in seed oil regulation in Brassica napus L. and Arabidopsis thaliana (L.) Heynh.