Lodging continues to be a major cause of yield loss in important crop species such as Brassica napus. Understanding the genetic regulation of lodging resistance is therefore of key interest to breeders worldwide. Current strategies aimed at minimising lodging risk involve the incorporation of dwarfing genes or the application of plant growth regulators. However, despite these efforts, lodging continues to be a persistent problem and it is therefore of high interest that novel, complimentary strategies for lodging control are implemented. One approach would be to focus on understanding the genetic properties underlying stem mechanical strength. With this in mind, we screened a training genetic diversity panel of Brassica napus accession for variation in stem mechanical strength and related traits. Using Associative Transcriptomics we identified molecular markers for a suite of valuable traits. Using an independent test genetic diversity panel we show that the methods employed are robust for identification of predictive markers. Furthermore based on conserved synteny with Arabidopsis thaliana we are able to provide a biological context to the marker associations detected and provide evidence for a role in pectin methylesterification in contributing to stem mechanical strength in Brassicaceae.