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Background  An optimal seedling development of  Brassica napus  plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of  B. napus  and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in  B. napus  by genome-wide association mapping.    Results  The expression levels of the 15 candidate genes examined in the 509  B. napus  inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509  B. napus  inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes  GER1 ,  AILP1 ,  PECT , and  FBP  were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a  P -value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7.    Conclusion  A total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in  B. napus , the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the  B. napus  diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit ( RBC ) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor ( FBP ) on the chromosomes A9 and C8 are  cis -regulated.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0496-3) contains supplementary material, which is available to authorized users.

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping