GENOMICS-ENABLED IMPROVEMENT OF ANDROPOGONEAE GRASSES AS FEEDSTOCKS FOR ENHANCED BIOFUEL PRODUCTION

Principal Investigator: Stephen Moose, U of Illinois
Co-PIs: Matt Hudson and Ray Ming, U of Illinois, and Dan Rokhsar, UC Berkeley
Postdocs: Magdy Alabady, Cuixia Chen, Megan Hall, Kankshita Swaminathan
Research Associates: Jayanand Boddu, Brandon Smith
Graduate Students: Adam Barling, Brandon James, Liang Xie, Won Byon Chae, Dedeepya Vaka
Undergraduate Students: Sharon Lee, Ornella Ngamboma, Arthur Rudolph
Subcontractor: Hawaiian Agricultural Research Center

Four related plant species are leading biomass candidates due to their efficiencies in photosynthesis, nitrogen economy, and water use – sugarcane, Miscanthus, switchgrass and sorghum. Through genetic sequencing and bioinformatics, investigations into gene structure and function will seek ways to improve crop yield, quality and sustainability.

2009 Project Update:
The primary goal of the EBI Feedstock Genomics Program is to employ the latest tools of genomic science to rapidly advance our biological understanding of Miscanthus and Saccharum, closely related perennial grasses with high biomass yields. Progress during the past year has been accelerated by the dramatic increases in sequencing throughput provided by new short-read and high-depth technologies, as well as the recent release of the whole-genome sequence for Sorghum, which is also closely related to both Miscanthus and Saccharum. Much of the effort in 2009 has focused on genome sequencing of representatives from each of the most important Miscanthus and Saccharum species to development of commercial feedstock cultivars. For Miscanthus, results from a number of pilot studies identified an appropriate strategy for producing a high-quality draft genome sequence of the highly productive hybrid species Miscanthus x giganteus (Mxg), which we anticipate will be completed by the Joint Genome Institute in 2010.

We also conducted sequencing surveys of gene-enriched fractions from the genomes of M. sinensis and M. sacchariflorus, the progenitor species to Mxg, and the three main Saccharum species used as germplasm sources in commercial sugarcane and energy cane cultivars. Analysis of these genome sequence datasets has led to the identification of nearly the entire complement of expressed genes in Miscanthus, including those producing small RNAs that play key roles in regulating gene expression. In addition, thousands of molecular markers have been generated for ongoing studies of genetic diversity and genetic mapping in Miscanthus and Saccharum. Furthermore, experiments were initiated to profile changes in Mxg gene expression in developing stems during the period of active biomass accumulation, upon the transition to flowering, and when nutrient recycling from vegetative tissue to rhizomes occurs in late fall. Web-based tools were created for visualization and analysis of genomics datasets that enable other EBI users to access and analyze the genomic information generated by this program.