title: Rapid nested PCR-based detection of Ramularia collo-cygni direct from barley.
abstract: Ramularia collo-cygni is a barley pathogen of increasing importance in Northern and Central Europe, New Zealand and South America. Accurate visual and microscopic identification of the pathogen from diseased tissue is difficult. A nested PCR-based diagnostic test has been developed as part of an initiative to map the distribution of the pathogen in Scotland. The entire nuclear ribosomal internal transcribed spacer and 5.8S rRNA gene regions from 14 isolates of diverse global origin exhibited complete homology following sequence characterization. Two pairs of species-specific primers, based on inter-specific sequence divergence with closely related species, were designed and empirically evaluated for diagnostic nested PCR. Nested primers Rcc3 and Rcc4 consistently amplified a single product of 256 bp from DNA of 24 R. collo-cygni isolates of diverse global provenance, but not from other Ramularia species, or other fungi commonly encountered in cereal pathosystems, as well as Hordeum or Secale DNA preparations. Using this approach, R. collo-cygni was successfully identified from naturally infected barley leaf, awn and grain samples of diverse geographical provenance, in particular from symptoms that lacked the presence of characteristic conidiophores. It is envisaged that this assay will become established as an important tool in continuing studies into the ecology, aetiology and epidemiology of this poorly understood yet economically damaging plant pathogen.
authors.affiliation: Crop and Soil Research Group, Scottish Agricultural College, West Mains Road, Edinburgh, UK. neil.havis@sac.ac.uk
authors.forename: Neil D
authors.initials: ND
authors.lastname: Havis
authors.forename: Simonj P
authors.initials: SP
authors.lastname: Oxley
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Piper
authors.forename: Stephen R H
authors.initials: SR
authors.lastname: Langrell
mesh_terms: D001203:Ascomycota / Q000235:genetics / Q000302:isolation & purification*; D017931:DNA Primers / Q000737:chemistry; D004271:DNA, Fungal / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D002523:Edible Grain / Q000382:microbiology; D004587:Electrophoresis, Agar Gel; D001467:Hordeum / Q000235:genetics / Q000382:microbiology*; D008969:Molecular Sequence Data; D018515:Plant Leaves / Q000382:microbiology; D016133:Polymerase Chain Reaction / Q000379:methods*; D012340:RNA, Ribosomal, 5.8S / Q000235:genetics; D012434:Secale / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D012340:RNA, Ribosomal, 5.8S