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Open Access Research article

Genome-wide identification of differentially expressed genes under water deficit stress in upland cotton (Gossypium hirsutum L.)

Wonkeun Park1, Brian E Scheffler2, Philip J Bauer1 and B Todd Campbell1*

Author Affiliations

1 USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, SC, USA

2 USDA-ARS, MSA Genomics Laboratory, Stoneville, MS, USA

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BMC Plant Biology 2012, 12:90  doi:10.1186/1471-2229-12-90

Published: 15 June 2012

Additional files

Additional file 1:

Annotation of 147 differntially expressed TDFs.

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Additional file 2:

Clustal W2 multiple sequence alignment of two TDF homologs and cotton aquaporins. Priming sites for two selective markers are shown above alignment panels. Three different nucleotide sequences are highlighted and predicted amino acid sequences are shown below the alignment. Only coding regions are used for comparisons and one Taq-GT selective marker site for the 06 C03 is not shown here. Numbers to the right represent nucleotide positions from ATG of ESTs and from the end of TDFs, respectively.

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Additional file 3:

cDNA-AFLP gel image with three primer sets for two technical replicates. Two independent reactions were performed and loaded side by side to show reproducible amplification. wL and dL denote samples from irrigated and water deficit stressed leaf, respectively. wR and dR denote samples from irrigated and water deficit stressed root, respectively. Asterisk means replicated reaction. TDFs with reproducible differences are shown in green arrows and a red arrow shows a non-reproducible TDF. Size markers are presented in right side.

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