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

BMC Genomics
Sayan DasTimothy J Close

Abstract

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. 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%. 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 s...Continue Reading

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Citations

Apr 17, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Weibo XieQifa Zhang
Apr 10, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Cornelia LangeHeinz Himmelbauer
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Datasets Mentioned

BETA
ET041523
ET041556
GSE
10284

Methods Mentioned

BETA
genotyping
PCR
amplicon sequencing
electrophoresis

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