Studying the function and regulation of grass genes through comparative genomics

The grasses (Poaceae) are one of the key plant clades responsible for feeding the seven-billion people who now live on this planet and, as a result, the genomes of more grass species have been sequenced to date than any other plant family. This abundance of “model” systems, many important crops species in their own right, is a challenge, however it also creates the potential for new and powerful forms of analysis. Normally, determining the function of individual promoter sequences is accomplished through promoter bashing. This approach can take years, and are particularly troublesome in the grasses were transformation efficiencies tend to be lower than eudicot systems. By comparing syntenic orthologous genes in distantly related grasses – for example rice and sorghum -- it is possible to identify functionally constrained noncoding sequences. To assign function to these elements we take advantage of a whole genome duplication in maize which occurred after the divergence of the maize and sorghum lineages. While duplicate maize genes initially had much the same complement of regulatory elements as their shared sorghum co-ortholog, the large amount of sequence deletion following whole genome duplication sometimes removed a conserved noncoding element from one of the two gene copies, creating a natural promoter bashing experiment. By comparing the relative expression of these duplicate genes in a wide range of RNA-seq experiments, it becomes possible to develop testable hypotheses about the specific function of regulatory sequences.