The grass Brachypodium distachyon has been identified as a model system to study energy crops for the production of cellulosic ethanol. Brachypodium’s small genome has recently been fully sequenced to further understand its biology. By profiling the auxin, indole-3-acetic acid (IAA), in Brachypodium, we are trying to establish growth conditions in which we can detect quantifiable differences in IAA levels. Comparing IAA levels with transcript levels for putative Brachypodium orthologs (functionally similar genes from difference species) to predicted Arabidopsis thaliana IAA biosynthetic genes will then provide evidence for or against specific Brachypodium genes being involved in IAA synthesis. The Brachypodium genome database has been mined using the BLAST bioinformatics algorithm to identify potential orthologs to a number of Arabidopsis IAA biosynthetic genes. Brachypodium wildtype tissue has been grown under full and etiolated (dark) light conditions, and IAA levels determined at various stages of root and shoot development through the use of solid phase extraction (SPE) and gas chromatograph-mass spectrometry (GC-MS) methods. Preliminary results show differences in IAA levels between root and shoot tissue. Previous work on IAA biosynthetic pathways in Arabidopsis shows that IAA is derived from the amino acid tryptophan (Trp) during early stages of development. With these tentative differences in mind, the goals of this project will focus on two research objectives. First, pulse-labeling experiments using stable-isotope labeled Trp and anthranilate will be conducted to determine if a similar Trp-dependent pathway is observed in Brachypodium. Second, once significant differences between growth conditions and IAA levels are observed, RNA from Brachypodium will be extracted, converted to cDNA via reverse transcription and applied to a microarray chip containing the Brachypodium genome to quantify differences in transcript expression between the two growth conditions in order to identify genes potentially involved in IAA biosynthesis.