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ARS Home » Southeast Area » Florence, South Carolina » Coastal Plain Soil, Water and Plant Conservation Research » Research » Publications at this Location » Publication #296562

Title: RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum) root tissue under water-deficit stress

item Bowman, Megan
item Park, Wonkeun
item Bauer, Philip
item UDALL, J. - Brigham Young University
item PAGE, J. - Brigham Young University
item RANEY, J. - Brigham Young University
item Scheffler, Brian
item JONES, D - Cotton, Inc
item Campbell, Benjamin - Todd

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2013
Publication Date: 12/6/2013
Citation: Bowman, M.J., Park, W., Bauer, P.J., Udall, J.A., Page, J.T., Raney, J., Scheffler, B.E., Jones, D.C., Campbell, B.T. 2013. RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum) root tissue under water-deficit stress. PLoS One. 8:e82634.

Interpretive Summary: This manuscript describes an RNA sequencing project to measure global gene expression patterns in the root tissues of field grown upland cotton under water deficit stress. Differential expression patterns of specific candidate genes associated with water deficit stress were confirmed using Real time quantitative polymerase chain reaction (RT-qPCR). Additionally, a computational pipeline was used to classify the putative genome localization of genes identified by the RNA sequencing evaluation.

Technical Abstract: An RNA-Seq experiment was performed using field grown cotton plants subjected to different water supplies (well-watered and naturally rain fed) to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns confirming the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts has detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.