Single-feature polymorphism discovery in the barley transcriptome

Genome Biol. 2005;6(6):R54. doi: 10.1186/gb-2005-6-6-r54. Epub 2005 May 11.


A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling
  • Genome, Plant / genetics
  • Hordeum / genetics*
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Single Nucleotide / genetics*
  • RNA, Plant / genetics
  • Sequence Analysis, DNA
  • Transcription, Genetic / genetics*


  • RNA, Plant