About Us | Help Videos | Contact Us | Subscriptions
 

Abstract

 

doi:10.3835/plantgenome2008.08.0003

Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

  1. Christian M. Tobias ,
  2. Gautam Sarath,
  3. Paul Twigg,
  4. Erika Lindquist,
  5. Jasmyn Pangilinan,
  6. Bryan W. Penning,
  7. Kerry Barry,
  8. Maureen C. McCann,
  9. Nicholas C. Carpita and
  10. Gerard R. Lazo
  1. C.M. Tobias and G.R. Lazo, USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Unit, 800 Buchanan St., Albany, CA; G. Sarath, USDA-ARS, Grain, Forage, and Bioenergy Research Unit, Keim Hall, East Campus, Univ. of Nebraska, Lincoln, NE, 68583; P. Twigg, Dep. of Biology, Univ. of Nebraska, 905 W. 25th St., Bruner Hall, Kearney, NE 68849; E. Lindquist, J. Pangilinan, and K. Barry, Lawrence Berkeley National Lab., 1 Cyclotron Rd., Mail Stop PGF, Berkeley, CA 94720; B.W. Penning and M.C. McCann, Dep. of Biological Sciences, Purdue Univ., West Lafayette, IN 47907; N.C. Carpita, Dep. of Botany & Plant Pathology, Purdue Univ., West Lafayette, IN 47907. Sequencing conducted at and supported through the Community Sequencing Program, DOE-Joint Genome Institute CSP-776898. All sequences have been submitted to the dbEST division of Genbank Accessions FE597478–FE659062.

Abstract

The development of genomic resources for switchgrass (Panicum virgatum L.), a perennial NAD+-malic enzyme type C4 grass, is required to enable molecular breeding and biotechnological approaches for improving its value as a forage and bioenergy crop. Expressed sequence tag (EST) sequencing is one method that can quickly sample gene inventories and produce data suitable for marker development or analysis of tissue-specific patterns of expression. Toward this goal, three cDNA libraries from callus, crown, and seedling tissues of ‘Kanlow’ switchgrass were end-sequenced to generate a total of 61,585 high-quality ESTs from 36,565 separate clones. Seventy-three percent of the assembled consensus sequences could be aligned with the sorghum [Sorghum bicolor (L.) Moench] genome at a E-value of <1 × 10−20, indicating a high degree of similarity. Sixty-five percent of the ESTs matched with gene ontology molecular terms, and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. The representation in the three libraries of gene families known to be associated with C4 photosynthesis, cellulose and β-glucan synthesis, phenylpropanoid biosynthesis, and peroxidase activity indicated likely roles for individual family members. Pairwise comparisons of synonymous codon substitutions were used to assess genome sequence diversity and indicated an overall similarity between the two genome copies present in the tetraploid. Identification of EST–simple sequence repeat markers and amplification on two individual parents of a mapping population yielded an average of 2.18 amplicons per individual, and 35% of the markers produced fragment length polymorphisms.

  Please view the pdf by using the Full Text (PDF) link under 'View' to the left.

Copyright © 2008. Copyright © 2008 Crop Science Society of America