AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS
Location: Genomics and Gene Discovery
Title: A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 27, 2009
Publication Date: October 27, 2009
Citation: Gu, Y.Q., Ma, Y., Huo, N., Vogel, J.P., You, F., Lazo, G.R., Nelson, W., Soderlund, C., Dvorak, J. 2009. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. Biomed Central (BMC) Genomics. 10:496
Interpretive Summary: Brachypodium distachyon is an emerging model species for cereal (Wheat and Barley) and bioenergy crops (Switchgrass) due to it possesses many desirable attributes. To develop genomic resource, a high-resolution physical map was developed based on fingerprinting profiles of genomic DNA fragments cloned in bacteria. This physical map was used to compare the genomes of other grass species such as rice and wheat to understand the evolution and function of cereal genomes. The resources generated in this study have been made available to the research community.
The wheat high molecular weight (HMW)-glutenins are important seed storage proteins that determine bread-making quality in hexaploid wheat (Triticum aestivum). In this study, detailed comparative sequence analyses of large orthologous HMW-glutenin genomic regions from eight grass species, representing a wide evolutionary history of grass genomes, reveal a number of lineage-specific sequence changes. These lineage-specific changes, which resulted in duplications, insertions, and deletions of genes, are the major forces disrupting gene colinearity among grass genomes. Our results indicate that the presence of the HMW-glutenin gene in Triticeae genomes was caused by lineage-specific duplication of a globulin gene. This tandem duplication event is shared by Brachypodium and Triticeae genomes, but is absent in rice, maize, and sorghum, suggesting the duplication occurred after Brachypodium and Triticeae genomes diverged from the other grasses ~35 million years ago (mya). Aside from their physical location in tandem, the sequence similarity, expression pattern, and conserved cis-acting elements responsible for endosperm specific expression further support the paralogous relationship between the HMW-glutenin and globulin genes. While the duplicated copy in Brachypodium has apparently become non-functional, the duplicated copy in wheat has evolved to become the HMW-glutenin gene by gaining a central prolamin repetitive domain.