Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array.
BMC Genomics, 2008/2/28;9:107.
Das S[1], Bhat PR, Sudhakar C, Ehlers JD, Wanamaker S, Roberts PA, Cui X, Close TJ
Affiliations
PMID: 18307807DOI: 10.1186/1471-2164-9-107
Impact factor: 4.547
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.
MeSH terms
Animals; Crops, Agricultural; DNA; Electrophoresis, Agar Gel; Fabaceae; Genetic Markers; Genome, Plant; Humans; Mice; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Polymorphism, Genetic; RNA, Complementary; Reproducibility of Results; Sequence Alignment; Glycine max
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