Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula Academic Article uri icon

abstract

  • Eragrostis curvula (Schrad.) Nees is a forage grass native to the semiarid regions of Southern Africa, which reproduces mainly by pseudogamous diplosporous apomixis. A collection of ESTs was generated from four cDNA libraries, three of them obtained from panicles of near-isogenic lines with different ploidy levels and reproductive modes, and one obtained from 12 days-old plant leaves. A total of 12,295 high-quality ESTs were clustered and assembled, rendering 8,864 unigenes, including 1,490 contigs and 7,394 singletons, with a genome coverage of 22%. A total of 7,029 (79.11%) unigenes were functionally categorized by BLASTX analysis against sequences deposited in public databases, but only 37.80% could be classified according to Gene Ontology. Sequence comparison against the cereals genes indexes (GI) revealed 50% significant hits. A total of 254 EST-SSRs were detected from 219 singletons and 35 from contigs. Di- and tri- motifs were similarly represented with percentages of 38.95 and 40.16%, respectively. In addition, 190 SNPs and Indels were detected in 18 contigs generated from 3 to 4 libraries. The ESTs and the molecular markers obtained in this study will provide valuable resources for a wide range of applications including gene identification, genetic mapping, cultivar identification, analysis of genetic diversity, phenotype mapping and marker assisted selection.

authors

  • Cervigni, Gerardo DL
  • Paniego, Norma
  • Díaz, Marina
  • Selva, Juan P
  • Zappacosta, Diego
  • Zanazzi, Darío
  • Landerreche, Iñaki
  • Martelotto, Luciano
  • Felitti, Silvina
  • Pessino, Silvina
  • Spangenberg, Germán
  • Echenique, Viviana

publication date

  • May 2008