Open Access Research article

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

Sayan Das12, Prasanna R Bhat1, Chinta Sudhakar13, Jeffrey D Ehlers1, Steve Wanamaker1, Philip A Roberts2, Xinping Cui4 and Timothy J Close1*

Author Affiliations

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

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

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

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

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BMC Genomics 2008, 9:107  doi: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.