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Detection and Validation of Single Feature Polymorphisms in Cowpea using a Soybean Genome Array
Sayan,,Das, University of California-Riverside, RIVERSIDE, CA (sdas001@ucr.edu)
Experiment design (8 hybridizations)
genotype
•CB46 •503-1
stress condition
•drought stressed •unstressed

This experiment has been imported by PLEXdb from NCBI GEO (GSE10284)

Series_summary:
Background: Cowpea (Vigna unguiculata L. Wal...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Detection and Validation of Single Feature Polymorphisms in Cowpea using a Soybean Genome Array
Accession No: GM19
Microarray: Soybean
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•CB46   •503-1
stress condition
•drought stressed   •unstressed
Quality Control: biological replicates
Treatment summary:
 genotype  stress condition  # replicates
 CB46  drought stressed  2
 CB46  unstressed  2
 503-1  drought stressed  2
 503-1  unstressed  2
Total hybridizations: 8
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE10284)

Series_summary:
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.
SUBMITTER_CITATION: Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array Sayan Das, Prasanna R. Bhat, Chinta Sudhakar, Jeffrey D. Ehlers, Steve Wanamaker, Philip A. Roberts, Xinping Cui, Timothy J. Close BMC Genomics 2008, 9:107

Keywords: Polymorphism discovery, array based genotyping

Series_overall_design:
Expression data were generated by hybridizing cowpea cRNA to the soybean genome array. A statistical method called robustified projection pursuit (RPP) was used for Single Feature Polymorphism(SFP) analysis. Only the values from the PM probes were utilized. The use of RNA as a surrogate for genomic DNA eliminated interference from highly repetitive DNA as a technical impediment to SFP detection. An important aspect of the RPP method is that it first utilizes a probe set level analysis to identify SFP-containing probe sets and then chooses individual probes from within each SFP-containing probe set. The net result is the identification of probes that directly overlay polymorphic sequences.

Separate comparisons were made between two genotypes (with two replicates each) for unstressed and drought stressed treatments, resulting in two SFP lists. In the context of SFPs, there is no necessity to have separate stress and control lists; in fact it would be simpler and less costly to have only one SFP list from highly complex RNA made by blending stressed and unstressed RNA. In our case, two separate lists were available as a consequence of another study not described here which compared gene expression patterns in stressed and control plants (data not shown). At 15% outlying score cut-off, we detected 488 SFP probes in stressed and 661 SFP probes in unstressed treatments. The union of these two lists contained 1058 SFP probes and the intersection contained 91. A total of 37 primer pairs targeting 37 putative SFP probe sets were initially tested, of which 25 yielded single amplicons of the expected sizes from both parents. These 25 amplicons targeted 14 probe sets selected from the intersection of the two SFP probe set lists and 11 from the remaining SFP probe sets. 9 of the 14 SFP probe sets (64%) from the intersection list were validated at the DNA sequence level and 8 of the other 11 (73%) were validated.
Publication: 'Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array', Das S, Bhat PR, Sudhakar C, Ehlers JD et al
BMC Genomics 2008 Feb 28;9:107
pubmed: 18307807
Created: 2009-06-04 14:16:17
Last Update: 2009-06-04 14:27:39
GEO Accession GSE10284
Submitter: PLEXdb Curator
Name: Sayan,,Das
Institution: University of California-Riverside, RIVERSIDE, CA
Head of Laboratory: --
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