Email updates

Keep up to date with the latest news and content from BMC Plant Biology and BioMed Central.

Open Access Highly Accessed Research article

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

Nadia Shakoor12, Ramesh Nair1, Oswald Crasta13, Geoffrey Morris2, Alex Feltus4 and Stephen Kresovich24*

Author Affiliations

1 Chromatin Inc, Chicago, Illinois, USA

2 Department of Biological Sciences, The University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA

3 Current address: Dow AgroSciences, Indianapolis, Indiana, USA

4 Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA

For all author emails, please log on.

BMC Plant Biology 2014, 14:35  doi:10.1186/1471-2229-14-35

Published: 23 January 2014

Abstract

Background

Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement.

Results

This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes.

Conclusions

Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.

Keywords:
Sorghum bicolor; Gene atlas; Transcriptome; Gene expression; Functional genomics; Microarray