Transcriptome evolution and whole genome duplication

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The genomes (total cellular DNA) of flowering plants, including all crop species, have undergone multiple rounds of whole genome duplication (WGD, polyploidy). The availability of duplicated genes, combined with extensive genome remodeling that follows WGD events, gives rise to a wide range of novel traits. It is clear that gene expression mediates many of these responses, and selection on gene dosage may drive gene family and network evolution. Yet surprisingly little is known about how genome duplication affects individual gene expression or the entire transcriptome (the combined expression of all genes in the genome in a given tissue). This project will use a suite of novel approaches to estimate whole transcriptome size and to assay expression changes of genes across the genome in response to WGD. Several synthetic and recently formed natural polyploids and their diploid progenitors will be studied in order to determine both the immediate and longer-term effects of genome duplication on gene expression. This project is of broad significance and impact because quantifying dosage responses on a genomic scale will clarify our understanding of how selection on gene dosage has shaped plant evolution, leading to important traits in species of agricultural importance, such as soybean, whose close relatives are the targets of this project. In addition, the project funds opportunities for undergraduates to participate in the research, and facilitates scientific collaboration between a major research university (Cornell) and an undergraduate-only institution (Reed College).