ARS | Publication request: Genome-wide identification of differentially expressed genes under water deficit stress in Upland cotton (Gossypium hirsutum L.)

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 10, 2012
Publication Date: July 23, 2012
Citation: Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2012. Genome-wide identification of differentially expressed genes under water deficit stress in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Plant Biology. Available: http://www.biomedcentral.com/1471-2229/12/90.

Interpretive Summary: Cotton is the world’s primary fiber crop and is a major agricultural commodity in over 30 countries across the world. Like many other world commodities, sustainable cotton production is challenged by restricted natural resources. In response to the anticipated increase of agricultural water demand, a major research direction is to develop crops that use less water or that use water more efficiently. In this study, our objective was to understand the mechanisms underlying expression of genes in response to water deficit stress in cotton. A global gene expression analysis was conducted to compare expression profiles between non-irrigated (water deficit stressed) and irrigated field-grown in root and leaf tissues from a putative drought tolerant cultivar. In total, we detected 519 putative genes with diverse gene expression responses to water deficit stress in root and leaf tissues. For a subset of the 519 genes (147), we provide possible functional and biological roles in response to water deficit stress. The genes identified in this study provide potential targets to manipulate the water use characteristics of cotton at the molecular level.

Technical Abstract: Cotton is the world’s primary fiber crop and is a major agricultural commodity in over 30 countries across the world. Like many other world commodities, sustainable cotton production is challenged by restricted natural resources. In response to the anticipated increase of agricultural water demand, a major research direction is to develop crops that use less water or that use water more efficiently. In this study, our objective was to understand the mechanisms underlying expression of genes in response to water deficit stress in cotton. A global expression analysis using cDNA-Amplified Fragment Length Polymorphism was conducted to compare expression profiles between non-irrigated (water deficit stressed) and irrigated field-grown in root and leaf tissues from a putative drought tolerant cultivar. In total, we detected 519 differentially expressed transcript derived fragments from water deficit stressed root and leaf tissues in tetraploid cotton. For 147 of the 519, we provided gene ontology, functional/biological distribution, and possible roles of gene duplication. This discovery illustrates a comprehensive mechanism of cotton plants under water deficit stress that is complicated by the complex, tetraploid genome. The genes identified in this study provide potential targets to manipulate the water use characteristics of cotton at the molecular level.