The maize B chromosome shapes the transcriptome throughout the entire plant life cycle.

Maize (Zea mays) is one of the world's most important crops and a recognized model for biological research, with some individuals having supernumerary B chromosomes. This B chromosome has been studied for decades, yet its gene expression across different plant tissues has not been thoroughly described. Here, we present a comprehensive transcriptomic atlas of the maize plant with and without the B chromosome. By analysing 11 tissues/organs, we found that genes encoded by the B chromosome contribute to the transcriptome throughout plant growth, with the highest activity observed in reproductive organs. Co-expression analysis revealed a cluster of 30 genes expressed specifically in tassels and indicated that Shortage in chiasmata 1 is a promising candidate for regulation of crossover frequency mediated by the B chromosome. In addition to its own transcriptional activity, our results also demonstrated that the B chromosome influences the expression of genes located on the A chromosome in all the tissues that we analysed. As well as providing new insights into the expression and regulatory effects of the B chromosome, our study has also generated fundamental information that will provide a basis for exploring its wider biological role.