Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array.
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.
Das
Sayan
S
Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA. sayan.das@email.ucr.edu
Bhat
Prasanna R
PR
Sudhakar
Chinta
C
Ehlers
Jeffrey D
JD
Wanamaker
Steve
S
Roberts
Philip A
PA
Cui
Xinping
X
Close
Timothy J
TJ
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*
D005819:Genetic Markers; D018075:RNA, Complementary; D004247:DNA