Single-feature polymorphism discovery in the barley transcriptome 英文参考文献.docVIP

Open Access M d 2005RostoksetV al.lumeetho6, Issue 6, Article R54 Single-feature polymorphism discovery in the barley transcriptome Nils Rostoks*, Justin O Borevitz?, Peter E Hedley*, Joanne Russell*, Sharon Mudie*, Jenny Morris*, Linda Cardle*, David F Marshall* and Robbie Waugh* Addresses: *Scottish Crop Research Institute, Genome Dynamics, Invergowrie, Dundee, DD2 5DA, Scotland, UK. ?University of Chicago, Department of Ecology and Evolution, Chicago, IL 60637, USA. Correspondence: Justin O Borevitz. E-mail: borevitz@. Robbie Waugh. E-mail: rwaugh@scri.sari.ac.uk Published: 11 May 2005 Received: 8 February 2005 Revised: 22 March 2005 Accepted: 14 April 2005 Genome Biology 2005, 6:R54 (doi:10.1186/gb-2005-6-6-r54) The electronic version of this article is the complete one and can be found online at /2005/6/6/R54 ? 2005 Rostoks et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Single-featureympoArpphriosmbeslbeevpolymorphismtewl meeondtewl ofobraarnldiscoveryeaylygseisnotfyGpineensthe,ewChibarleytihpagehnigtranscriptomeehexpressisensitivitny.dataThisismpresentedethod is awhichpplicabidentifiedle to all olmoreigonuthancleoti10,000de micrsingle-featureoarray data./pol-p 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. Background A nu