ArticleBMC genomics2008
Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Cowpea speed breeding using regulated growth chamber conditions and seeds of oven-dried immature pods potentially accommodates eight generations per year.Plant methods · 2022Article
- A Cross-Species Gene Expression Marker-Based Genetic Map and QTL Analysis in Bambara Groundnut.Genes · 2017Article
- Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L.Journal of genetics · 2015Article
- Combining bulk segregation analysis and microarrays for mapping of the pH trait in melon.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Article
- 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
- Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.).Functional & integrative genomics · 2011Article
- Article
- Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array.BMC genomics · 2010Article
- High-throughput identification of genetic markers using representational oligonucleotide microarray analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.BMC 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
- Single feature polymorphisms between two rice cultivars detected using a median polish method.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCowpea (Vigna unguiculata L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping.
resultsHere we report detection and validation of SFPs in cowpea using a readily available soybean (Glycine max) genome array. Robustified projection pursuit (RPP) was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL) population segregating for several important traits including drought tolerance, Fusarium and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%.
conclusionWe conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources.
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