Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

doi:10.1186/1746-4811-4-13

Plant Methods

Volume 4

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Edwards JD
Janda J
Sweeney MT
Gaikwad AB
Liu B
Leung H
Galbraith DW

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Liu B
Leung H
Galbraith DW
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Methodology

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

Jeremy D Edwards¹ , Jaroslav Janda² , Megan T Sweeney² , Ambika B Gaikwad³ , Bin Liu⁴ , Hei Leung⁵ and David W Galbraith²

¹University of Florida, Gulf Coast Research & Education Center, Wimauma FL, 33598, USA

²University of Arizona, Department of Plant Sciences and Bio5 Institute for Collaborative Bioresearch, Tucson AZ, 85721, USA

³National Research Centre on DNA Fingerprinting, National Bureau of Plant Genetic Resources, New Delhi, India

⁴Guangdong Academy of Agricultural Sciences (GDAAS), Guangdong, Pr China

⁵International Rice Research Institute (IRRI), Los Banos, The Philippines

author email corresponding author email

Plant Methods 2008, 4:13doi:10.1186/1746-4811-4-13


Published:	29 May 2008

Additional files

Additional File 1:

Genomic locations of the 880 SFP oligonucleotide probes.

Format: XLS Size: 260KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 2:

SFP genotype scores for rice accessions. A score of "1" indicates presence of the allele that is complementary to the probe sequence and a score of "0" indicates absence. Missing data are indicated by a "?" character.

Format: XLS Size: 251KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 4:

Low Cost Labeling Method.

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Additional File 3:

Sources of the positive, negative, and multi-copy control oligonucleotide probes.

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Additional File 5:

SFP discovery scripts.

Format: TXT Size: 44KB Download file

Additional File 6:

Output of SFP discovery scripts.

Format: TXT Size: 165KB Download file

Additional File 7:

R-scripts for data analysis.

Format: TXT Size: 9KB Download file