Whole Genome Gene Expression Profiling of Multiple Tissue Types and Developmental Stages in Sorghum bicolor

Sorghum is an important staple cereal crop worldwide; it is unique in its advanced ability to grow in marginal, semi-arid environments.  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.

This study utilizes the first whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue-specific sorghum genes and novel regulatory sequences.  This genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genome.  The sequences used to construct the probesets included all identified Sorghum bicolor exons and UTRs. We also added sequences for putative non-coding RNAs that may play a role in gene regulation (e.g. microRNAs).  Confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design.

We are presenting a preliminary summary of the microarray dataset, including analysis of tissue-specific gene expression and identification of co-regulated gene modules and networks.  We generated expression profiles for 79 samples with a combination of four different tissue types (shoot, root, leaves and stem), two dissected stem tissues (pith and rind) across subsets of four developmental stages (10, 38, 60 and 70 days after planting) and six genotypes, which included five public sorghum lines (PI 455230, Atlas, PI 152611, AR2400, and Fremont) and one proprietary restorer line from Chromatin.