Wheat is one of the major sources of food for much of the world. However, because bread wheat’s genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence.
The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world’s major crops. Here researchers from the John Innes Centre combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. They found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.
Seventy percent of triads (A, B, and D homoeologs) show balanced expression among homoeologs and are ubiquitously expressed (left), whereas ~30% show nonbalanced expression and are more tissue-specific (right; symbolized by three exemplar tissues). Variation in promoter elements and nonsynonymous substitution rates distinguish between individual triads with stable relative expression across tissues and triads with more inter-tissue variation (tissue-dynamic triads).