Comparative Analysis of Gene Expression Regulation Among Diploid and Polyploid Wheat Genomes

Allopolyploidization substantially shaped the genome structure of the genus Triticum L., including one of the agricultural most important crops hexaploid bread wheat. Hybridization among species constitutes a "genomic schock", which often is accompanied by severe changes in cellular and molecular architecture including alterations of the genome structure as well as gene expression regulation. However, in absence of a suitable reference genome sequence, a comprehensive molecular understanding of the regulatory changes among di-, tetra- and hexaploid wheat species so far has been hampered. We utilized novel genome information generated for hexaploid bread wheat and applied RNA-seq analysis across multiple plant organs to gain novel insights the transcriptomes of hexaploid Triticum aestivum (AABBDD) and related diploid [Triticum urartu (AA) and Aegilops tauschii (DD)] and tetraploid [Triticum turgidum (AABB)] wheats. Comparative analysis of transcript abundance within genome lineages reveals substantial differences in the contribution of genes to the transcriptomes of diploid and polyploidy wheat, which could be associated with particular chromosomal domains. Variations in the expression ratios between the extant parental genomes and polyploidy successors indicate interacting cis- and trans-regulatory factors shaping the transcriptional landscape of hexaploid wheat. Superimposition of the observed expression patterns with a transcriptional network of hexaploid wheat suggests conservation and imparted regulatory mechanisms in the genus Triticum. This might contribute to autonomous orchestration of particular as well as homoeologous gene expression bias and genome asymmetry.