The Transcriptional Landscape of Bread Wheat

Allohexaploid bread wheat belongs to the most important crops worldwide accounting for approximately 20% of calories consumed by humans. To characterize the transcriptional landscape of bread wheat we applied RNA-seq analysis in different organs as well as in major endosperm cell types at three maturation stages reflecting the progress of starch and storage protein accumulation. The IWGSC bread wheat genome survey sequence and annotation facilitated assignment of the transcriptome sequence data to the three respective genomes A, B and D, which contribute about equally to the entire bread wheat transcriptome. Direct comparison of gene expression of homeologous gene triplets showed that genome-specific expression dominates over tissue-specific expression and suggests considerable autonomous regulation of the three genomes. Clustering of gene triplets revealed expression subdivision among wheat genomes for a high number of homeologs. Functional characterization of these modules suggests that biased expression towards only one genome is evident for various traits, which relate to different functions of the basal cellular machinery and major features of bread wheat grain development. Along all chromosomes we found expression levels to be oscillating and forming chromosomal domains, which are to a large extend similar among the A, B and D genome. Local occurrence of asynchronous genome expression potentially indicates epigenetic regulatory mechanisms that act differently on particular corresponding domains of homologous chromosomes. Thus interspecific hybridization and polyploidy potential impact the genetic and epigenetic regulatory mechanisms and eventually result in transcriptional asymmetry and favored expression of genes from individual genomes.