Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. To meet the demands of a growing global population, breeders face the challenge of increasing wheat production by around 60% within the next 40 years. The 10+Wheat Genomes Project recently sequenced and assembled 15 wheat cultivars to improve our understanding of genetic diversity and selection within the pan-genome of wheat (Walkowiak et al., 2020).

In this work, we present a wheat functional pan-transcriptome with full de novo gene predictions and differential expression analysis for 10 wheat cultivars over five different tissues and whole seedlings sampled at dusk/dawn. Analysis of de novo gene annotations, available in Ensembl Plants release52, facilitated the discovery of novel genes specific to particular cultivars, including genes absent from the existing Chinese Spring reference, and copy number variations including tandem arrays in high-resolution. Through our gene expression analysis, combined with the full de novo gene predictions of 10 wheat cultivars, we improve the definition of the core and shell genome of bread wheat, highlight tissue-specific genes, and reveal changes in bias of sub-genome homeolog expression between cultivars. In summary, this work provides both a novel resource for the wider wheat community and reveals several important findings about the core and dispensable genome and transcriptional diversity in wheat beyond a single reference genome.