The Genus Brachypodium as a Tool to Study Polyploidy

Polyploid genomes are characteristic of grasses being developed as biomass crops and many grain crops. Therefore, a deeper understanding of gene regulation and genome evolution in polyploid genomes would be useful for developing improved crop varieties for both food and fuel. Unfortunately, biomass and grain crops are difficult experimental subjects because of their large, complex genomes, outbreeding nature and/or their large physical size. Thus, a simple model system to study polyploid genome regulation and evolutions would be very useful. The diploid Brachypodium distachyon has emerged as a powerful model to study various aspects of grass biology and numerous experimental resources and tools have been developed. Another member of the genus, B. hybridum, is an allotetraploid with subgenomes derived from ancestors similar or identical to the diploid species B. distachyon and B. stacei. All three species have very compact genomes, have small stature and are easily grown and manipulated in the laboratory. We have sequenced and assembled the genomes of B. hybridum and B. stacei and are conducting extensive comparative RNA-Seq experiments among the three species to understand the evolution of gene regulation in the subgenomes of B. hybridum. In addition, we have crossed B. distachyon and B. stacei to create a synthetic B. hybridum. Exceptional quality of the B. distachyon, B. stacei, and B. hybridum genomes and the genetic tractability of the species make a powerful system to explore many questions about polyploid genome regulation and evolution. This system may have great utility in defining functional gene regulatory elements that can be translated into crop grass species for applied applications.