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PMID: 15960806 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Single-feature polymorphism discovery in the barley transcriptome.

Genome biology ·Vol. 6 ·No. 6 ·2005-00-00 ·Pages R54

Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R

Abstract

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.

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
Chemicals
RNA, Plant
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Rostoks Nils
Scottish Crop Research Institute, Genome Dynamics, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
Borevitz Justin O
Hedley Peter E
Russell Joanne
Mudie Sharon
Morris Jenny
Cardle Linda
Marshall David F
Waugh Robbie
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2005-6-6-r54
Published
2005-00-00
Epub
2005-00-11
Pages
R54
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1175974
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2005-6-6-r54 PMC Full Text View journal details
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