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4 December 2014 Development and Characterization of Nuclear Microsatellite Markers in the Endophytic Fungus Epichloë festucae (Clavicipitaceae)
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Endophytic fungi are very common and important components in plant microbiomes. They are capable of infecting their host plant's tissues without causing obvious symptoms to the host (Hyde and Soytong, 2008). The Epichloë endophytes (Ascomycota: Clavicipitaceae) are one of the most studied systems of plant-endophyte associations because they form symbiotic relationships with several economically important turf and forage cool season grasses (Clay and Schardl, 2002). These endophytes are important agents influencing the growth and persistence of host grasses, and a genetically compatible endophyte infection has been demonstrated to provide a selective advantage to the host (Ahlholm et al., 2002; Saikkonen et al., 2006, 2010a, b). The Epichloë endophytes are a group of filamentous fungi that comprise sexual Epichloë species and their asexual derivatives, Neotyphodium species, which have been recently classified as Epichloë (Leuchtmann et al., 2014). Epichloë festucae Leuchtm., Schardl & Siegel is a fungal epichloid systemic endophyte, which systematically and intercellularly colonizes aboveground tissues and seeds of Festuca rubra L. by means of haploid hyphae. Festuca rubra is a perennial grass with rapid expansion world-wide in a wide range of ecosystems, and it is one of the most important turfgrasses in temperate regions (Inda et al., 2008). Previously, nuclear microsatellite markers have been developed for Epichloë species by Moon et al. (1999) and expressed sequence tag (EST)–derived simple sequence repeats (SSRs) for pasture grass endophytes by van Zijll de Jong et al. (2003), and among those markers, four polymorphic nuclear microsatellite markers have been used in a population genetic study on E. festucae (Wäli et al., 2007). Because highly polymorphic genomic microsatellites are effective tools for studying population genetic characteristics, in this study, we aim to develop additional polymorphic microsatellite primers for E. festucae.


The unplaced genomic scaffold sequences of E. festucae were downloaded (GenBank accession no. JH158803–JH158837) and searched for ≥10 mono- and dinucleotide repeats, and for ≥8 tri-, tetra-, penta-, and hexanucleotide repeats by using MSATCOMMANDER (Faircloth, 2008). The selected marker regions possessed the maximum length of the repeat motif, a minimum distance of 100,000 bp between the repeat motifs within the same accession, and the presence of appropriate flanking sequences for primer design with the following criteria: primer length of 18–27 bp, GC content 40–60%, annealing temperature 55–58°C, and expected amplicon size of 100–300 bp. Twenty-four primer pairs were designed with Primer3 software (Rozen and Skaletsky, 2000). The forward primers were labeled with fluorescent dyes for automated electrophoresis, and the primers were obtained from Oligomer Oy (Helsinki, Finland).

To isolate E. festucae from endophyte-infected (E+) plants of F. rubra, three leaves were collected from each selected tiller from pots containing replanted F. rubra in the greenhouse of Ruissalo Botanical Garden, Finland. The plant material was kept at 4°C for 24 h, followed by surface sterilization, including a treatment in 75% ethanol for 30 s, 4% sodium hypochlorite for 3 min, and 75% ethanol for 15 s. Then, a leaf was cut into five segments and planted on auto-claved Petri dishes containing 5% potato dextrose agar (PDA). Agar plates were stored at room temperature until mycelium emerged from the plated leaf fragments, after which a small sample of mycelium was transferred to a new PDA plate on a piece of sterile cellophane (9 cm in diameter). Epichloë festucae identity was determined based on the morphological characteristics observed in cultures, and based on the sequences of the ITS1, 5.8S rRNA, and ITS2 region of a set of isolates from different locations, compared with GenBank resources ( using BLAST searches. PCR amplification of the ITS1, 5.8S rRNA, and ITS2 region was performed using primers ITS1 and ITS5 ( Epichloë festucae is the only systemic fungus described for F. rubra, and the systemic endophyte has always been E. festucae when we have previously sequenced fungi from F. rubra (e.g., Wäli et al., 2007). The risk that the mycelium growing on PDA corresponds to another related fungal endophyte different from E. festucae is marginal, especially as grasses are commonly assumed to be infected by only one systemic fungus. Replanted agar plates were stored at room temperature until the growth of the mycelium was sufficient for DNA extraction. Mycelium growth was scraped from the cellophane into an Eppendorf tube for DNA extraction. DNA was extracted from pure cultures of E. festucae with the E.Z.N.A. Plant DNA Kit (Omega Bio-Tek, Norcross, Georgia, USA), and a NanoDrop Lite spectrophotometer (Thermo Fisher Scientific, Wilmington, Delaware, USA) was used to reveal the yield and purity of DNA. The PCR reactions were performed with a single microsatellite primer pair in a 10-µL reaction mixture containing 5–10 ng genomic DNA, 1× GoTaq Flexi Buffer, 1.0 mM MgCl2 solution, 0.2 mM of each dNTP, 0.2 µM of each primer, and 1.25 units GoTaq G2 HotStart Polymerase (Promega Corporation, Madison, Wisconsin, USA). PCR reactions were performed in a C1000 Thermal Cycler (Bio-Rad, Applied Biosystems, Foster City, California, USA) as follows: an initial denaturation at 95°C for 2 min; followed by 30 cycles at 95°C for 30 s, 57°C for 30 s, and 73°C for 30 s; and a final extension at 73°C for 5 min. Each PCR product was amplified singly. The amplification success was controlled with a set of PCR products using 2% agarose gels (SeaKem LE Agarose; Lonza, Rockland, Maine, USA). The products were run on an ABI 3130x1 Genetic Analyzer using the GeneScan 500 ROX Size Standard (Applied Biosystems) at the Institute of Biotechnology, University of Helsinki, Finland, and assigned to allelic sizes with Peak Scanner version 1 software (Applied Biosystems). The unbiased haploid diversity (h) and the number of alleles (A) per locus and population were calculated using GenAlEx version 6.5 (Peakall and Smouse, 2006, 2012).

Table 1.

Characteristics of the 15 nuclear microsatellite markers developed for the endophyte fungus Epichloë festucae.a

Table 2.

Characteristics of 14 nuclear polymorphic microsatellite loci in eight populations of Epichloë festucae.a

Initially, 24 individuals originating from populations in the Faroe Islands (N = 8), Finland (N = 8), and Spain (N = 8) were screened to reveal the competence of the 24 primer pairs. Nine primer pairs out of 24 were rejected from the further analysis because of unclear patterns with multiple bands and allelic dropouts, whereas 15 primer pairs amplified reliably and produced clearly interpretable single bands, and these were used in the further analyses (Table 1). Fifteen loci were screened for polymorphism using 70 individuals originating from four different populations in the Faroe Islands, one population from Finland, and three populations from Spain (Tables 1 and 2). One locus was monomorphic while 14 loci revealed polymorphism with altogether 123 alleles (Table 1). The number of alleles per locus varied from four to 16 at the species level and from one to seven at the population level (Table 2). The unbiased haploid diversity per locus varied from 0.435 to 0.874 at the species level, and from 0.000 to 0.933 at the population level (Table 2). The Spanish populations possessed a considerably higher number of alleles and haploid diversity (on average A = 5.1 and h = 0.591, respectively) compared to northern populations (on average A = 1.5 and h = 0.199, respectively).


Because endophytes have both scientific relevance and applied importance, these new polymorphic microsatellite markers will be useful for grass breeders, e.g., to improve commercial turfgrass cultivars of F. rubra, and for researchers to study different aspects of grass endophyte evolution. These markers presumably cross-amplify within the genus Epichloë, which includes host-specific endophytes of several important forage grasses (Leuchtmann et al., 2014).



J. U. Ahlholm , M. Helander , S. Lehtimäki , P. Wäli , and K. Saikkonen . 2002. Vertically transmitted endophytes: Effects of environmental conditions. Oikos 99: 173–183. Google Scholar


K. Clay , and K. Schardl . 2002. Evolutionary origins and ecological consequences of endophyte symbiosis with grasses. American Naturalist 160: S99–S127. Google Scholar


B. C. Faircloth 2008. MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8: 92–94. Google Scholar


K. D. Hyde , and K. Soytong . 2008. The fungal endophyte dilemma. Fungal Diversity 33: 163–173. Google Scholar


L. A. Inda , J. G. Segarra-Moragues , J. Muller , P. M. Peterson , and P. Catalan . 2008. Dated historical biogeography of the temperate Loliinae (Poaceae, Pooideae) grasses in the northern and southern hemispheres. Molecular Phylogenetics and Evolution 46: 932–957. Google Scholar


A. Leuchtmann , C. W. Bacon , C. L. Schardl , J. F. White Jr ., and M. Tadych . 2014. Nomenclatural realignment of Neotyphodium species with genus Epichloë. Mycologia 106: 202–215. Google Scholar


C. D. Moon , B. A. Tapper , and B. Scott . 1999. Identification of Epichloë endophytes in plants by microsatellite-based PCR fingerprinting assay with automated analysis. Applied and Environmental Microbiology 65: 1268–1279. Google Scholar


R. Peakall , and P. E. Smouse . 2006. GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295. Google Scholar


R. Peakall , and P. E. Smouse . 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics (Oxford, England) 28: 2537–2539. Google Scholar


S. Rozen , and H. J. Skaletsky . 2000. Primer3 on the WWW for general users and for biologist programmers. In S. Misener and S. A. Krawetz [eds.], Methods in molecular biology, vol. 132: Bioinformatics methods and protocols, 365–386. Humana Press, Totowa, New Jersey, USA. Google Scholar


K. Saikkonen , P. Lehtonen , M. Helander , J. Koricheva , and S. H. Faeth . 2006. Model systems in ecology: Dissecting the endophyte-grass literature. Trends in Plant Science 11: 428–433. Google Scholar


K. Saikkonen , S. Saari , and M. Helander . 2010a. Defensive mutualism between plants and endophytic fungi? Fungal Diversity 41: 101–113. Google Scholar


K. Saikkonen , P. R. Wäli , and M. Helander . 2010b. Genetic compatibility determines endophyte-grass combinations. PLoS ONE 5: e11395. Google Scholar


P. Wäli , J. U. Ahlholm , M. Helander , and K. Saikkonen . 2007. Occurrence and genetic structure of the systemic grass endophyte Epichloë festucae in fine fescue populations. Microbial Ecology 53: 20–29. Google Scholar


E. van Zijll de Jong , K. M. Guthridge , G. C. Spangenberg , and J. W. Foster . 2003. Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes. Genome 46: 277–290. Google Scholar


Appendix 1.

Voucher information for Epichloë festucae isolates used in this study.


[1] The research leading to these results has received funding from the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no. 262693 (INTERACT).

Maria von Cräutlein, Helena Korpelainen, Marjo Helander, Annika Öhberg, and Kari Saikkonen "Development and Characterization of Nuclear Microsatellite Markers in the Endophytic Fungus Epichloë festucae (Clavicipitaceae)," Applications in Plant Sciences 2(12), (4 December 2014).
Received: 26 September 2014; Accepted: 4 November 2014; Published: 4 December 2014

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