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

Abstract

BackgroundHigher 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.ResultsRNA-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.ConclusionsThe 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.

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO2 Source in Plants

“…4) is consistent with a reduction in the photosynthetic activity expected due to the CO 2 starvation. In addition, the significant increase in the concentration of Val agrees with previous observations in ABA-treated or water-stressed plants (Dugas et al, 2011). Finally, Glu plays a signaling role in the activated ionotropic receptors that act as amino acidgated Ca 2+ channels (Forde, 2014), and these receptors interact with ABA (Kang et al, 2004).…”

nana plant2 Encodes a Maize Ortholog of the Arabidopsis Brassinosteroid Biosynthesis Gene DWARF1, Identifying Developmental Interactions between Brassinosteroids and Gibberellins

“…FPKM values and histograms were obtained from qteller.com for selected maize and sorghum (Sorghum bicolor) genes (Wang et al, 2009;Li et al, 2010;Davidson et al, 2011Davidson et al, , 2012Dugas et al, 2011;Schnable and Freeling, 2011;Waters et al, 2011;Bolduc et al, 2012;Chang et al, 2012;Kakumanu et al, 2012;Mizuno et al, 2012). Recreation of these histograms could be obtained at http://www.qteller.com.…”

Plant Environmental Stress Responses for Survival and Biomass Enhancement

“…Recent transcriptome and proteome analyses have focused on responses to osmotic stress in various plant species. The results have indicated the involvement of general processes in altering the gene expression of plants, including crops and woody plants, such as Arabidopsis, rice, maize, wheat, barley, sorghum, soybean, tomato, chickpea, cotton, poplar, loblolly pine, grapevine, and cassava [84][85][86][87][88][89][90][91][92][93][94][95][96][97][98][99][100][101]. Most of these works have used macro-or microarrays and recently they identified the mass of transcriptomes using next-generation sequencing.…”