Spotted cotton oligonucleotide microarrays for gene expression analysis.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.
Udall
Joshua A
JA
Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA. jaudall@byu.edu
Flagel
Lex E
LE
Cheung
Foo
F
Woodward
Andrew W
AW
Hovav
Ran
R
Rapp
Ryan A
RA
Swanson
Jordan M
JM
Lee
Jinsuk J
JJ
Gingle
Alan R
AR
Nettleton
Dan
D
Town
Christopher D
CD
Chen
Z Jeffrey
ZJ
Wendel
Jonathan F
JF
D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D017343:Genes, Plant; D003368:Gossypium / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis