ARS | Publication request: Microarray and Real-Time PCR Comparison of Endophyte-Infected and Endophyte-Free Tall Fescue Gene Expression

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract
Publication Acceptance Date: October 4, 2007
Publication Date: January 8, 2008
Citation: Dinkins, R.D., Barnes, A., Waters, W. 2008. Microarray and Real-Time PCR Comparison of Endophyte-Infected and Endophyte-Free Tall Fescue Gene Expression. Plant and Animal Genome Conference. Abstract #P704 . Plant & Animal Genomes XVI Conference, January 12-16, 2008, Town & Country Convention Center, San Diego, CA.

Technical Abstract: Many grasses have mutualistic symbioses with fungi of the family Clavicipitaceae. Tall fescue [Schedonorus arundinaceus (Schreb.) Dumont. = Festuca arundinacea (Schreb.)] can harbor the obligate endophyte, Neotyphodium coenophialum, that is asexually propagated and transmitted via host seeds. To dissect the host plant endophyte cross-talk, tall fescue global gene expression was analyzed using the Affymetrix Wheat Genome Array GeneChip® and Barley1 Genome Array GeneChip®. Total RNA was isolated from pseudostems of known endophyte-infected and endophyte-free plants and tested in triplicate. Analysis of the results was combined using four microarray analysis methods (MAS5, Plier, RMA and GCRMA) that were significantly (P<0.05) differentially expressed (greater than two-fold) over both the wheat and barley microarray chips. This combinatorial approach yielded 32 probe sets (genes) that were differentially expressed on both the wheat and barley microarray chips. Tall fescue ESTs were identified by BLASTn in GenBank for 20 of the probe sets. PCR and real-time PCR expression was evaluated on cDNA¿s of the original RNA samples evaluated by microarray, plus samples collected from plants in year two. Results revealed that primers for some of the tall fescue ESTs gave results similar to that observed in the microarray experiments suggesting that these genes are differentially expressed in response to the presence of the endophyte in tall fescue. In other cases no differences were observed between the endophyte-infected and endophyte-free suggesting the incorrect tall fescue EST was used for PCR primer design probably due to the limited tall fescue EST information presently in the databases.