Single-feature polymorphism discovery in the barley transcriptome.
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.
Rostoks
Nils
N
Scottish Crop Research Institute, Genome Dynamics, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
Borevitz
Justin O
JO
Hedley
Peter E
PE
Russell
Joanne
J
Mudie
Sharon
S
Morris
Jenny
J
Cardle
Linda
L
Marshall
David F
DF
Waugh
Robbie
R
D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000235:genetics; D001467:Hordeum / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic / Q000235:genetics*
D018749:RNA, Plant