ArticleGenetics2007
SFP genotyping from affymetrix arrays is robust but largely detects cis-acting expression regulators.
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Development of Genome-Wide SNP Markers for Barley via Reference- Based RNA-Seq Analysis.Frontiers in plant science · 2019Article
- Quantitative trait loci from identification to exploitation for crop improvement.Plant cell reports · 2017Review
- The E-MS Algorithm: Model Selection with Incomplete Data.Journal of the American Statistical Association · 2015Article
- Conserved synteny-based anchoring of the barley genome physical map.Functional & integrative genomics · 2013Article
- Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference.Journal of experimental botany · 2013Article
- Prospects for advancing defense to cereal rusts through genetical genomics.Frontiers in plant science · 2013Article
- An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays.Molecular ecology resources · 2012Article
- Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).BMC genomics · 2012Article
- Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping.BMC bioinformatics · 2011Article
- Combining genetical genomics and bulked segregant analysis-based differential expression: an approach to gene localization.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus.BMC genomics · 2011Article
- Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley.BMC genomics · 2010Article
- A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.BMC genomics · 2010Article
- High-throughput marker discovery in melon using a self-designed oligo microarray.BMC genomics · 2010Article
- An empirical method for establishing positional confidence intervals tailored for composite interval mapping of QTL.PloS one · 2010Article
- Article
- Significance test and genome selection in bayesian shrinkage analysis.International journal of plant genomics · 2010Article
- Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding.BMC genomics · 2009Article
- Article
- Comparative transcriptomics in the Triticeae.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent development of Affymetrix chips designed from assembled EST sequences has spawned considerable interest in identifying single-feature polymorphisms (SFPs) from transcriptome data. SFPs are valuable genetic markers that potentially offer a physical link to the structural genes themselves. However, most current SFP prediction methodologies were developed for sequenced species although SFPs are particularly valuable for species with complex and unsequenced genomes. To establish the sensitivity and specificity of prediction, we explored four methods for identifying SFPs from experiments involving two tissues in two commercial barleys and their doubled-haploid progeny. The methods were compared in terms of numbers of SFPs predicted and their ability to identify known sequence polymorphisms in the features, to confirm existing SNP genotypes and to match existing maps and individual haplotypes. We identified >4000 separate SFPs that accurately predicted the SNP genotype of >98% of the doubled-haploid (DH) lines. They were highly enriched for features containing sequence polymorphisms but all methods uniformly identified a majority of SFPs ( approximately 64%) in features for which there was no sequence polymorphism while 5% mapped to different locations, indicating that "SFPs" mainly represent polymorphism in cis-acting regulators. All methods are efficient and robust at predicting markers for gene mapping.
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