title: Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array.
abstract: BACKGROUND
  Cowpea (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.
  
  
  RESULTS
  Here 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%.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA. sayan.das@email.ucr.edu
authors.forename: Sayan
authors.initials: S
authors.lastname: Das
authors.forename: Prasanna R
authors.initials: PR
authors.lastname: Bhat
authors.forename: Chinta
authors.initials: C
authors.lastname: Sudhakar
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Ehlers
authors.forename: Steve
authors.initials: S
authors.lastname: Wanamaker
authors.forename: Philip A
authors.initials: PA
authors.lastname: Roberts
authors.forename: Xinping
authors.initials: X
authors.lastname: Cui
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Close
mesh_terms: D000818:Animals; D018556:Crops, Agricultural / Q000235:genetics; D004247:DNA / Q000235:genetics; D004587:Electrophoresis, Agar Gel; D007887:Fabaceae / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D006801:Humans; D051379:Mice; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D018075:RNA, Complementary / Q000235:genetics; D015203:Reproducibility of Results; D016415:Sequence Alignment; D013025:Glycine max / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D018075:RNA, Complementary; D004247:DNA