W565 Differences between the subgenomes of ancient polyploids

Date: Saturday, January 14, 2012
Time: 4:10 PM
Room: Golden West
James C. Schnable , University of California-Berkeley, Berkeley, CA
Michael Freeling , University of California-Berkeley, Berkeley, CA
The genomes of all flowering plant species have been shaped by repeated rounds of whole genome duplication. Using comparative genomics and syntenic analysis it is possible to identify duplicate regions of modern genomes. However, in almost every case it is impossible to group these duplicate segments into parental subgenomes millions or tens of millions of years after the fact. We have demonstrated a link between genomic/genome dominance – the observation that genes from one parental subgenome tend to show higher levels of expression in recent and synthetic polyploids -- and the biased loss of genes following whole genome duplication in maize. This biased loss of genes makes it possible to divide even ancient polyploids into high- and low-gene loss subgenomes. Even in whole genome duplications as ancient as that shared by all grass species (estimated to be between 70 and 90 million years old), the more expressed copy of duplicate gene pairs remains more likely to be found on the low gene loss subgenome. While the initial cause of genome dominance remains unclear, biased expression in ancient polyploids could be the result result of the differential loss of conserved regulatory elements we observe between subgenomes following the pre-grass whole genome duplication.