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Switchgrass ESTs and SNPs

As part of our project, “Developing Association Mapping in Polyploid Perennial Biofuel Grasses” (DOE-USDA Plant Feedstock Genomics for Bioenergy Program grant DE-A102-07ER64454)*, two SNP discovery initiatives were carried out. The earlier one (2009) was an approach based on EST sequences. The latest initiative (2011-12) adopted a more powerful approach, based on GBS (Genotyping by Sequencing). We believe that the SNP markers identified in these studies will greatly enhance breeding efforts that target the improvement of key biofuel traits and the development of new switchgrass cultivars.

To enable genome-wide association study (GWAS) and genomic selection (GS) in switchgrass, we genotyped a full-sib population (n =130), a half-sib population (n =168) and association populations (66 pops, n =540). The parents of the linkage populations are upland tetraploids. The association populations are primarily of the upland ecotype, both tetraploid and octoploid, with a few lowland tetraploids as well. A total of 350 GB of sequence was generated from 840 individuals using GBS. Over 1.2 million putative SNPs were discovered with the UNEAK pipeline. In addition, ultra-high density paternal and maternal linkage maps, of 41K and 46K SNPs, respectively, were also constructed based on the conserved synteny between switchgrass and foxtail millet.

The data associated with this study are listed here:

  • Genotype calls from the full-sib population [65 MB]
  • Genotype calls from the half-sib population [80 MB]
  • Genotype calls from the association populations [164 MB]
  • Paternal and maternal linkage maps of the full-sib population [8 MB]

Dataset Info

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Buckler Lab for Maize Genetics and Diversity
Product Type
Cornell University
Contact Name
Romay, Cinta
Contact Email
Public Access Level
Primary Article

Lu, F., Lipka, A., Glaubitz, J., Elshire, R., Cherney, J., & Casler, M. et al. (2013). Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol. Plos Genetics, 9(1), e1003215.

Related Content
Funding Source(s)
Agricultural Research Service
U.S. Department of Energy
National Science Foundation
Program Code
005:037 - Department of Agriculture - Research and Education
Bureau Code
005:18 - Agricultural Research Service
Modified Date
Release Date
Ag Data Commons Keywords: 
  • Genomics & Genetics
  • Bioenergy
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