U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


New Analytical Tool Enables Switchgrass Improvement
Published: January 17, 2013
Posted: February 26, 2013

Switchgrass (Panicum virgatum L.) is a prime bioenergy feedstock candidate due to its high biomass yields, minimal input requirements, broad adaptability, and perenniality. However, its large genome size, complicated genetics, and lack of a reference genome make efforts to improve switchgrass extremely challenging. Some of these difficulties can be overcome with genotyping-by-sequencing (GBS), a relatively low-cost method that targets a fraction of the genome for sequencing. GBS has already been used in many plant species to find molecular markers called single nucleotide polymorphisms (SNPs). To be both accurate and economical, however, this strategy requires a fully sequenced and assembled reference genome. To respond to this challenge, researchers funded in part by the joint U.S. Department of Agriculture-U.S. Department of Energy Plant Feedstocks Genomics for Bioenergy Program used GBS to develop a SNP discovery platform that does not require a reference genome and that can be applied to any complex plant species. This pipeline, called the Universal Network-Enabled Analysis Kit (UNEAK), was validated with maize and then successfully tested on switchgrass. Over one million SNPs were discovered in the switchgrass collection and used to construct high-density linkage maps, providing insight into the genetic diversity, population structure, phylogeny, and evolution of this species. UNEAK is providing an invaluable resource for switchgrass improvement programs.

Reference: Lu, F., A. E. Lipka, J. Glaubitz, R. Elshire, J. H. Cherney, M. D. Casler, E. S. Buckler, and D. E. Costich. 2013. "Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol," PLoS Genetics 9(1), e1003215. DOI: 10.1371/journal.pgen.1003215. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Plant Systems and Feedstocks, Plant-Microbe Interactions
  • Research Area: Sustainable Biofuels and Bioproducts

Division: SC-23.2 Biological Systems Science Division, BER

 

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