Genome-Wide Association Mapping of Seedling Development Traits and Gene Expression in Brassica napus

An optimal seedling development leads to a higher yield stability even under suboptimal growing conditions like reduced nutrient input or drought stress and has therefore a high importance in plant breeding. Up to now, the genetics of seedling development of Brassica napus is poorly understood. The objectives of our study were to examine (i) the expression levels of 15 candidate genes for seedling development and genes involved in main metabolic pathways in B. napus seedling leaves and (ii) to detect genome regions associated with seedling development traits and gene expression levels in a species-wide B. napus germplasm set of 509 inbreds. The seedling development traits of the B. napus germplasm set were analysed in greenhouse experiments. Across all 509 inbreds, the expression levels of 12 genes were significantly (α < 0.05) higher expressed in the modern germplasm types selected for seed yield than in the swede or vegetable types. The opposite trend was observed for two genes. In a genome-wide association analysis with 3733 SNPs, we observed 19 associations for the gene expression levels of the examined genes and 23 for the seedling development traits with a P-value < 0.0001. The identified loci explained individually up to ~14.5% of the phenotypic variance. Our data suggested for only two of the 15 genes, a cis regulation.