ArticleBMC genetics2009
Single-feature polymorphism discovery by computing probe affinity shape powers.
Article in BMC genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays.Plant cell reports · 2017Article
- Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions of Medicago truncatula.The Plant journal : for cell and molecular biology · 2014Article
- Transcriptomic characterization of two major Fusarium resistance quantitative trait loci (QTLs), Fhb1 and Qfhs.ifa-5A, identifies novel candidate genes.Molecular plant pathology · 2013Article
- The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses.Functional & integrative genomics · 2013Article
- Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).BMC genomics · 2012Article
- Quantitative trait loci conferring resistance to Fusarium head blight in barley respond differentially to Fusarium graminearum infection.Functional & integrative genomics · 2011Article
- Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement.BMC genomics · 2010Article
- Parallel multiplicity and error discovery rate (EDR) in microarray experiments.BMC bioinformatics · 2010Article
- An integrative approach to genomic introgression mapping.Plant physiology · 2010Article
- Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean.BMC plant biology · 2010Article
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8 authors.
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Abstract
backgroundSingle-feature polymorphism (SFP) discovery is a rapid and cost-effective approach to identify DNA polymorphisms. However, high false positive rates and/or low sensitivity are prevalent in previously described SFP detection methods. This work presents a new computing method for SFP discovery.
resultsThe probe affinity differences and affinity shape powers formed by the neighboring probes in each probe set were computed into SFP weight scores. This method was validated by known sequence information and was comprehensively compared with previously-reported methods using the same datasets. A web application using this algorithm has been implemented for SFP detection. Using this method, we identified 364 SFPs in a barley near-isogenic line pair carrying either the wild type or the mutant uniculm2 (cul2) allele. Most of the SFP polymorphisms were identified on chromosome 6H in the vicinity of the Cul2 locus.
conclusionThis SFP discovery method exhibits better performance in specificity and sensitivity over previously-reported methods. It can be used for other organisms for which GeneChip technology is available. The web-based tool will facilitate SFP discovery. The 364 SFPs discovered in a barley near-isogenic line pair provide a set of genetic markers for fine mapping and future map-based cloning of the Cul2 locus.
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