Symbiotic relationship between some members of Poaceae family has been discovered and a group of fungi called endophyte. These symbionts belong to familly Clavicipitaceae which before were known as simple parasites of plant. These fungi grow intercellulary in leaf sheets of host plants then enter to the seed through the ovary and stay in aleuron layer. Presence of these fungi in plant leads to resistance to various biotic and abiotic stresses. Keeping these beneficial populations in host crops may lead to persistant productions during years and in different environments and will provide scientists with new resources of germplasm for selecting plants for resistance to various stresses. In this study, the endophyte fungi were isolated from leaf sheets of host plants : F. arundinacea, F. pratensis and L. prenne . Morphological characteristics of these fungi were examined on PDA media. To confirm Neotyphodium genus, IS1/IS3 primers were used. AFLP molecular marker with 11 primer combination for plant genotypes and 8 for fungi was applied. Most of the isolates were morphologically similar to general description of Neotyphodium . The primer set , IS1/IS3, amplifies a 444bp fragment with this genus. Based on morphological and molecular characters the genus Neotyphodium on F. arundinacea, F. pratensis and L. prenne was identified. The molecular results indicated that AFLP marker is able to discriminate between plant genotypes according to the species and geographic population. Endophyte isolates were clustered into three separated groups. Fungi species clustering was in consistent corresponding to plant species clustering. Except for two isolates, this was seen in the level of geographic populations. Reciprocal comparing between two dendrograms resulted from AFLP data demonstrate high host-specifity in the isolates used in our study. Since AFLP can not reveal genetic differences intra populations strongly, It is better to use SSR marker to confirm the accuracy of the results.
