Differential Gene Expression of Endophyte-Infected and Endophyte-Free in Different Tissues of Lolium Arundinaceum.

Tall fescue (<i>Lolium arundinaceum</i>) plants symbiotic with the endophytic fungus, <i>Epichloe coenophiala</i> , (E+), have been shown to have better survivability and persistence than plants lacking the endophyte (E-).  To understand more about the grass-endophyte interactions and how endophyte affects the host plant physiology and gene expression, we have analyzed gene expression in different tissues (leaves, pseudostems, crowns and roots) of a genetically identical E+ and E- clone in greenhouse using RNA-Seq technology.  An in house tall fescue transcriptome assembly was generated using the RNA-Seq reads and mapping of the reads from the different tissue/endophyte replications (3) onto the assembly was done using CLC Genomics Workbench.  Analysis of differential gene expression was done using JMP Genomics and significant differences were calculated using a False Discovery Rate at α< 0.1 where differences were calculated using computed adjustments for each comparison separately.  The results indicated that no genes were differentially expressed across all tissues.  The highest number of differentially expressed genes was observed in the leaves.  This result was somewhat unexpected as the fungal endophyte is present only at low levels the leaves.  Genes and pathways of differentially expressed in the different tissues will be described.