ArticleBMC genomics2009
Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 40 citations in OpenAlex.
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- Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice.Scientific reports · 2015Article
- Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean.BMC genomics · 2015Article
- An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.G3 (Bethesda, Md.) · 2013Article
- Combining bulk segregation analysis and microarrays for mapping of the pH trait in melon.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 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
- 'maskBAD'--a package to detect and remove Affymetrix probes with binding affinity differences.BMC bioinformatics · 2012Article
- Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat.Genetica · 2011Article
- Expression level of a gibberellin 20-oxidase gene is associated with multiple agronomic and quality traits in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes.PloS one · 2010Article
- Article
- Homoeolog-specific transcriptional bias in allopolyploid wheat.BMC genomics · 2010Article
- Article
- High-throughput identification of genetic markers using representational oligonucleotide microarray analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- Genomics and bioinformatics resources for crop improvement.Plant & cell physiology · 2010Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (approximately 17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome.
resultsSix wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data.
conclusionThe Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.
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