Wheat is the world's most extensively cultivated crop covering over 215 million hectares annually. However, breeders are challenged to increasing production by approximately 60% within the next four decades to satisfy the needs of a growing global population. As part of the 10+ Wheat Genomes Project, genomes from 15 wheat cultivars were recently sequenced and assembled to enhance our understanding of genetic diversity and selection within the wheat pan-genome.

Our study contributes a wheat pan-transcriptome, featuring de novo annotation and differential expression analysis for nine of these cultivars across various tissues and whole seedlings sampled at dusk/dawn. Leveraging these de novo annotations, we uncovered genes absent from the Chinese Spring reference, identified cultivar-specific genes, and calculated the core and dispensable genomes.

Moreover, our expression analysis revealed conservation in the expression of a substantial core set of homeologous genes, alongside notable alterations in subgenome homeolog expression bias among cultivars. Co-expression network analysis elucidated the impact of sub-genome homeolog expression divergence and unveiled tissue-associated cultivar-specific expression profiles.

This comprehensive work not only provides a vital resource for the broader wheat community but also sheds light on the diversity in gene content and expression patterns among global wheat cultivars.