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Open Access Methodology article

Spotted cotton oligonucleotide microarrays for gene expression analysis

Joshua A Udall1*, Lex E Flagel2, Foo Cheung3, Andrew W Woodward4, Ran Hovav2, Ryan A Rapp2, Jordan M Swanson2, Jinsuk J Lee4, Alan R Gingle5, Dan Nettleton6, Christopher D Town3, Z Jeffrey Chen4 and Jonathan F Wendel2

Author Affiliations

1 Department of Plant and Animal Sciences, Brigham Young University, Provo, UT, 84062, USA

2 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA

3 The Institute for Genomic Research, A Division of the J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850 USA

4 Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA

5 Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USA

6 Department of Statistics, Iowa State University, Ames, IA, 50011, USA

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BMC Genomics 2007, 8:81  doi:10.1186/1471-2164-8-81

Published: 27 March 2007



Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species.


Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results.


The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through webcite.