To assess the variation in nutrient homeostasis in oilseed rape and to identify genes responsible for this variation we determined foliar anion levels in a diversity panel of Brassica napus accessions, 84 of which had been genotyped previously using mRNA sequencing. We applied Associative Transcriptomics (AT) to identify sequence polymorphisms linked to variation in nitrate, phosphate, or sulfate in these accessions. The analysis identified several hundred significant associations for each anion. Using functional annotation of Arabidopsis homologues and available microarray data we identified 60 candidate genes for controlling variation in the anion contents. To verify that these genes function in control of nutrient homeostasis we obtained Arabidopsis T-DNA insertion lines for these candidates and tested them for accumulation of nitrate, phosphate, and sulfate. Fourteen lines differed significantly in levels of the corresponding anions. Several of these genes have been shown previously to affect accumulation of the corresponding anions in Arabidopsis mutants. These results thus confirm the power of AT in dissection of the genetic control of complex traits and present a set of candidate genes for use in improvement of efficiency of B. napus mineral nutrition.