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Technological breakthroughs have enabled the bread wheat genome – for a long time considered intractable due to its size (more than 5x the size of the human genome) and high repeat content – to be assembled by a number of groups employing a variety of approaches. The availability of multiple assemblies of the same genome, each with their own strengths and weaknesses, presents a challenge for end users. The IWGSC RefSeq v1.0 genome assembly now provides a point of reference for deciphering the wheat genotype-phenotype interface in agriculture and to continue the process of adapting wheat to a changing agricultural environment. In this workshop we cover issues in genome assembly that are still outstanding, the interpretation of the transcriptome with special reference to tissue-specific expression of homoeologous genes, and presentations of case studies in wheat development.