Research article

Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array

Sayan Das^{* 1,2} , Prasanna R Bhat^{* 1} , Chinta Sudhakar^1,3 , Jeffrey D Ehlers¹ , Steve Wanamaker¹ , Philip A Roberts² , Xinping Cui⁴ and Timothy J Close¹

¹Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA

²Department of Nematology, University of California, Riverside, CA 92521 USA

³Department of Botany and Biotechnology, Sri Krishnadevaraya University, Anantapur, 515 003 India

⁴Department of Statistics, University of California, Riverside, CA 92521 USA

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:107doi:10.1186/1471-2164-9-107

Published:	28 February 2008

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%.

Conclusion

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.