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Open Access Highly Accessed Research article

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

Diana V Dugas1, Marcela K Monaco2, Andrew Olson2, Robert R Klein3, Sunita Kumari2, Doreen Ware24 and Patricia E Klein1*

Author Affiliations

1 Department of Horticulture, Texas A&M University, College Station, TX 77843, USA

2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA

3 USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX 77843, USA

4 USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA

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BMC Genomics 2011, 12:514  doi:10.1186/1471-2164-12-514

Published: 18 October 2011

Abstract

Background

Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.

Results

RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed.

Conclusions

The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.