Spatial analysis of lipid metabolites and expressed genes reveals tissue‐specific heterogeneity of lipid metabolism in high‐ and low‐oil <i>Brassica napus</i> L. seeds

<jats:title>Summary</jats:title><jats:p>Despite the importance of oilseeds to worldwide human nutrition, and more recently to the production of bio‐based diesel fuels, the detailed mechanisms regulating seed oil biosynthesis remain only partly understood, especially from a tissue‐specific perspective. Here, we investigated the spatial distributions of lipid metabolites and transcripts involved in oil biosynthesis from seeds of two low‐erucic acid genotypes of <jats:italic>Brassica napus</jats:italic> with high and low seed‐oil content. Integrated results from matrix‐assisted laser desorption/ionization‐mass spectrometry imaging (<jats:styled-content style="fixed-case">MALDI</jats:styled-content>‐<jats:styled-content style="fixed-case">MSI</jats:styled-content>) of lipids <jats:italic>in situ</jats:italic>, lipidome profiling of extracts from seed tissues, and tissue‐specific transcriptome analysis revealed complex spatial distribution patterns of lipids and transcripts. In general, it appeared that many triacylglycerol and phosphatidylcholine species distributed heterogeneously throughout the embryos. Tissue‐specific transcriptome analysis identified key genes involved in <jats:italic>de novo</jats:italic> fatty acid biosynthesis in plastid, triacylglycerols assembly and lipid droplet packaging in the endoplasmic reticulum (<jats:styled-content style="fixed-case">ER</jats:styled-content>) that may contribute to the high or low oil phenotype and heterogeneity of lipid distribution. Our results imply that transcriptional regulation represents an important means of impacting lipid compartmentalization in oil seeds. While much information remains to be learned about the intricacies of seed oil accumulation and distribution, these studies highlight the advances that come from evaluating lipid metabolism within a spatial context and with multiple omics level datasets.</jats:p>