Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Brachypodium Genome Tiling Array and Transcriptomics

2008 Awardee

Investigators: Todd C. Mockler and Todd P. Michael

Institutions: Oregon State University, Waksman Institute of Microbiology, Rutgers

Non-Technical Summary: Despite its obvious importance in plant development and stress responses, relatively little is known about how the global regulation of gene expression at the transcriptional level in plants is achieved. We will pursue a hypothesis-generating approach to better understand the gene regulation networks underlying traits of major importance for both the quality and quantity of biomass. The exceptional recent developments of genomics resources in Brachypodium distachyon enables a new approach to discovery and manipulation of transcriptional control mechanisms in grasses including bioenergy feedstock crops. The goals of this project are to design a Brachypodium genome array, make it available for commercial manufacture and distribution to any researcher, and then use these arrays to map major gene expression changes of relevance to important traits of grass crops. A readily available Brachypodium whole genome array will facilitate research leading to targets for manipulation to improve productivity, sustainability, and stress tolerance in plant feedstocks. This resource will leverage the DOE-JGI investment in generating the Brachypodium genome sequence.

Objectives: We will: 1) Design an Affymetrix whole-genome microarray for Brachypodium distachyon; 2) Use the microarrays we design to compare gene expression over major developmental stages, diurnal and circadian time-courses, and stress conditions; and 3) Conduct bioinformatic analysis and create a comprehensive public gene expression atlas.

Approach:1) In collaboration with Affymetrix we will design a custom whole genome microarray based on the final (8X) JGI genome assemblies, with gene predictions from a composite approach combining deep microread transcriptome sequencing with gene predictions, ESTs and cDNAs. A portion of the array space will be used to tile each predicted exon and intron with multiple probes with a predefined resolution. The remainder of the genome will be tiled to represent predicted non-coding/intergenic regions; 2) We will use the Brachypodium arrays to establish baseline expression profiles by comparing the transcriptomes of a number of different developmental stages, environmental conditions, and stress treatments. Planned comparisons include: (a) different tissues from plants of different developmental stages (roots, shoots, leaves, developing flower spikes, developing seeds, germinating seeds, etiolated seedlings); (b) diurnal and circadian sampling in light/dark/temperature cycles; and (c) plants exposed to abiotic stresses (heat, cold, salt, dehydration, nutrient limitation, and light stress) and biotic stresses; 3) We will create a comprehensive public gene expression atlas. We will analyze and compare the expression patterns of Brachypodium genes with respect to their inferred biological functions. We will cluster co-expressed genes and promoter analyses will be used to predict transcription factor binding sites in their upstream regions. Our results will be integrated into the gene annotations available through and other annotation databases, and we will develop bioinformatic tools for public access to these resources.

Project Contact
Name: Todd C. Mockler
Phone: 541-737-5207
Fax: 541-737-3573
Email: [email protected]