Feedstock Development programs

Genomics-Enabled Improvement Of Andropogoneae Grasses As Feedstocks For Enhanced Biofuel Production

Using genetic sequencing and bioinformatics, investigators seek ways to improve crop yield, quality and sustainability of the four leading biomass candidates — sugarcane, Miscanthus, switchgrass and sorghum.

program Highlights

2014 Highlights

The Andropogoneae tribe of grasses includes the leading bioenergy crops sorghum, sugarcane, energy cane, Miscanthus, and maize. The EBI Feedstock Genomics program has applied recent advancements in genome science to build a draft assembly and functional annotation of the Miscanthus sinensis genome sequence, which serves as a stepping-stone for bridging information from the simple diploid genome of annual sorghum to the more complex polyploid genomes of the perennial sugarcane and energy cane. The Miscanthus genome sequence is being used to further characterize patterns of genetic diversity and gene expression variation associated with traits important to the sustainable production of bioenergy from perennial C4 grasses. These traits include changes in rhizome physiology and nutrient remobilization during the annual growth cycle of Miscanthus, and comparison of stem carbon partitioning between sugarcane and energy cane.

2013 Highlights

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.

2012 Highlights

The Andropogoneae tribe of grasses includes the leading bioenergy crops sorghum, sugarcane, energy cane, Miscanthus, and maize. Extensive resources for genomic studies are available for the annual species maize and sorghum, which are accelerating the genetic improvement of these crops. The long-term goal of the EBI Feedstock Genomics program is to use the latest tools of genome science to provide the foundation for rapid genetic improvements of the perennial bioenergy grasses Miscanthus and Saccharum (sugarcane and energy cane). In 2012, we reported the first complete genetic map for Miscanthus sinensis, which revealed that like its closest relatives in the Saccharum complex, Miscanthus arose through a recent whole genome duplication of a sorghum-like ancestor. We finished a detailed analysis of the actively expressed genes within the Miscanthus genome and discovered suites of genes associated with the emergence of new shoots from spring rhizomes and the deposition of biomass in stems. In addition, we produced an initial draft assembly of the Miscanthus sinensis genome sequence that effectively separates its two sub-genomes. This advance will not only be useful for molecular breeding of Miscanthus, but is 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. We are on track to produce a high-quality genome sequence from Miscanthus sinensis.

Publications

Published in 2014

Transcriptional Responses Indicate Maintenance of Photosynthetic Proteins as Key to the Exceptional Chilling Tolerance of C4 Photosynthesis in Miscanthus×giganteus, A. K. Spence, J. Boddu, D. Wang, B. T. James, S. P. Moose, S. P. Long, Journal of Experimental Botany, doi: 10.1093/jxb/eru209, June 22, 2014. 

 

Mapping the Genome of Miscanthus sinensis for Loci Associated with Biomass Productivity, J. M. Gifford, W. B. Chae, K. Swaminathan, S. P. Moose, J. A. Juvik, Global Change Biology -- Bioenergy, doi: 10.1111/gcbb.12201, June 19, 2014. 

Published in 2012

A Framework Genetic Map for Miscanthus sinensis from RNAseq-based Markers Shows Recent Tetraploidy, Kankshita Swaminathan, Won B Chae, Therese Mitros, Kranthi Varala, Liang Xie, Adam Barling, Katarzyna Glowacka, Megan Hall, Stanislaw Jezowski, Ray Ming, Matthew Hudson, John Juvik, Daniel Rokhsar, Stephen P. Moose, BMC Genomics, 13(142), doi: 10.1186/1471-2164-13-142, April 24, 2012.

Published in 2011

Development of Microsatellite Markers in Autopolyploid Sugarcane and Comparative Analysis of Conserved Microsatellites in Sorghum and Sugarcane, Brandon James, Cuixia Chen, Arthur Rudolph, Kankshita Swaminathan, Jan Murray, Jong-Kuk Na, Ashley Spence, Brandon Smith, Matthew Hudson, Stephen Moose, Ray Ming, Molecular Breeding, doi: 10.1007/s11032-011-9651-1, October 14, 2011.

Published in 2010

Microcollinearity Between Autopolyploid Sugarcane and Diploid Sorghum Genomes, Jianping Wang,  Bruce Roe, Simone Macmil, Qingyi Yu, Jan Murray, Haibao Tang, Cuixia Chen, Fares Najar, Graham Wiley, John Bowers, Marie-Ane Van Sluys, Daniel Rokhsar, Matthew Hudson, Stephen Moose, Andrew Paterson, Ray Ming, BMC Genomics, 11(261), April 23, 2010.

 

Genomic and Small RNA Sequencing of Miscanthus x Giganteus Shows the Utility of Sorghum as a Reference Genome Sequence for Andropogoneae Grasses, Kankshita Swaminathan, Magdy Alabady, Kranthi Varala, Emanuele De Paoli, Isaac Ho, Dan Rokhsar, Aru Arumuganathan, Ray Ming, Pamela Green, Blake Meyers, Stephen Moose, Matthew Hudson, Genome Biology, 11(2), Feb. 3, 2010.

 

Surveying and Characterizing Genomic Repeats and Small RNA Production in Miscanthus x giganteus, Matthew Hudson, Kankshita Swaminathan, Magdy Alabady, Kranthi Valara, Ray Ming, Cuixia Chen, Daniel Rokhsar, Stephen Moose, Plant and Animal Genomes XVIII, San Diego, January 2010.

 


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