Chen, H., Seguin, P., Jabaji, S. and Liu, W. 2011. Spatial distribution of isoflavones and isoflavone-related gene expression in high and low isoflavone soybean cultivars. Can. J. Plant Sci. 91: 697–705. Soybean contains high concentrations of isoflavones that have putative health-beneficial effects. A study was conducted to document the spatial distribution of isoflavones and the expression of 14 key genes and gene homologs encoding enzymes involved in isoflavone synthesis using quantitative reverse transcription (QRT)-PCR. Genes studied included phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), chalcone reductase (CHR), and isoflavone synthase (IFS). Two cultivars were used, AC Proteina and AC Orford, high- and low-isoflavone cultivars, respectively. Plants were harvested at the seed filling stage (R5) and were separated into leaf, stem, root, flower, pod, and seed parts. The present study revealed that at the R5 stage the expression of 14 key genes and gene homologs involved in isoflavone synthesis is observed in all plant parts, being, however, minimal in pods and seeds and greatest in leaves and roots. Gene expression data parallel isoflavone concentrations, which are also minimal in pods and seeds. In most cases, expression of all homologs of a given gene family was comparable in specific parts, the expression of homologs not being part-specific. Finally, gene expression differences between cultivars also paralleled differences observed in their isoflavone concentrations.