Grain quality in wheat is determined by the combination of multiple factors at several levels: from macroscopic features including grain position, size and shape, through to more detailed features within the grain including internal tissue organisation (encompassing the maternal fruit tissues and filial embryo/endosperm) and the starch/protein profiles within these tissues, particularly the endosperm. We have found that examining grain variation at macro, micro and molecular levels across species, genera and families can provide both fundamental and more subtle insights into what makes a grain economically or agriculturally valuable. We have already found that a simple comparative approach using the undomesticated Brachypodium grain can provide insights into what defines the wheat grain’s nutritional importance. At the molecular level of comparison we focus on transcription factor genes: sequence, phylogeny, expression and function. Transcription factors control key processes in plant reproductive development, from organ identity to development of specialized tissues such as the grain and endosperm and specific metabolic and biochemical pathway components in these tissues. Using this approach we link fundamental approaches in evolutionary and developmental biology to tangible traits. We are currently undertaking comprehensive evolutionary and functional analysis of several transcriptional regulators involved in various aspects of development from organ patterning (early) to metabolic processes (late). I will focus on current analyses on genes from YABBY, AP2 and bZIP families.