Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet

DNA Res. 2014 Feb;21(1):41-52. doi: 10.1093/dnares/dst039. Epub 2013 Oct 1.


Generating genomic resources in terms of molecular markers is imperative in molecular breeding for crop improvement. Though development and application of microsatellite markers in large-scale was reported in the model crop foxtail millet, no such large-scale study was conducted for intron-length polymorphic (ILP) markers. Considering this, we developed 5123 ILP markers, of which 4049 were physically mapped onto 9 chromosomes of foxtail millet. BLAST analysis of 5123 expressed sequence tags (ESTs) suggested the function for ∼71.5% ESTs and grouped them into 5 different functional categories. About 440 selected primer pairs representing the foxtail millet genome and the different functional groups showed high-level of cross-genera amplification at an average of ∼85% in eight millets and five non-millet species. The efficacy of the ILP markers for distinguishing the foxtail millet is demonstrated by observed heterozygosity (0.20) and Nei's average gene diversity (0.22). In silico comparative mapping of physically mapped ILP markers demonstrated substantial percentage of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (∼50%), maize (∼46%), rice (∼21%) and Brachypodium (∼21%) chromosomes. Hence, for the first time, we developed large-scale ILP markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

Keywords: comparative mapping; foxtail millet (Setaria italica L.); intron-length polymorphism (ILP); physical mapping; transferability.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Plant / genetics
  • Computer Simulation
  • Genetic Markers*
  • Genotyping Techniques
  • Introns*
  • Polymorphism, Genetic
  • Setaria Plant / genetics*
  • Synteny


  • Genetic Markers