Feedstock Development projects
Genomics-Enabled Improvement of Andropogoneae Fuelstock Grasses
Miscanthus and sugarcane are highly productive C4 grasses that are emerging biomass crops. Rokhsar’s project employs the latest tools of genomic science to advance understanding of Miscanthus and sugarcane biology, and to identify genes with utility in improving cellulosic biomass yields and quality. To achieve these goals they will conduct deep sequencing of genomes and transcriptomes using "next generation" technologies, assess genetic diversity, develop molecular markers for high density genetic mapping, and associate marker genotypes with phenotypes that contribute to biomass yield and composition in structured genetic populations. This information will be assembled into an integrated bioinformatics system to facilitate investigations of gene structure and function in these grasses.
The Andropogoneae tribe of grasses includes the leading bioenergy crops sorghum, sugarcane, energy cane, Miscanthus, and maize. Extensive genomics resources are accelerating the genetic improvement of the annual species maize and sorghum. The EBI Feedstock Genomics program uses the latest tools of genome science to enable genetic improvements of the perennial bioenergy grasses Miscanthus and Saccharum (sugarcane and energy cane). In 2013, we published the first comprehensive catalog of expressed genes in the Miscanthus genus, where we identified Miscanthus genes corresponding to nearly all known genes in its close relative sorghum, as well as genes apparently specific to Miscanthus. We also discovered changes in gene expression associated with rhizome physiology and perenniality, including spring rejuvenation, nutrient remobilization in fall, and winter dormancy. Another major breakthrough was the generation of the first gene-scale assembly of the Miscanthus sinensis genome, which effectively separates the two subgenomes that arose following genome duplication. This advance is not only useful for Miscanthus, but also as an important bridge to the highly complex genomes found throughout the entire Saccharum complex. The sequence information we have generated is being used to further characterize genetic diversity and gene functions that are associated with variation in traits important to the sustainable production of bioenergy from Miscanthus, sugarcane, and energy cane.
Published in 2013
A Detailed Gene Expression Study of the Miscanthus Genus Reveals Changes in the Transcriptome Associated with the Rejuvenation of Spring Rhizomes, Adam Barling, Kankshita Swaminathan, Therese Mitros, Brandon T. James, Juliette Morris, Ornella Ngamboma, Megan C. Hall, Jessica Kirkpatrick, Magdy Alabady, Ashley K. Spence, Matthew E. Hudson, Daniel S. Rokhsar, Stephen P. Moose, BMC Genomics, 14, pp. 864, doi: http://dx.doi.org/10.4236/jsbs.2013.34038, December 9, 2013.