title: Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity.
abstract: Molecular markers that enable monitoring of fungi in their natural environment or assist in the identification of specific strains would facilitate Trichoderma utilization, particularly as an agricultural biocontrol agent (BCA). In this study, sequence analysis of internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) of the ribosomal RNA (rRNA) gene cluster, a fragment of the translation elongation factor 1-alpha (tef1) gene, and random amplified polymorphic DNA (RAPD) markers were applied to determine the genetic diversity of Trichoderma atroviride strains collected in Poland, and also in order to identify loci and PCR-based molecular markers useful in genetic variation assessment of that fungus. Although tef1 and RAPD analysis showed limited genetic diversity among T. atroviride strains collected in Poland, it was possible to distinguish major groups that clustered most of the analyzed strains. Polymorphic RAPD amplicons were cloned and sequenced, yielding sequences representing 13 T. atroviride loci. Based on these sequences, a set of PCR-based markers specific to T. atroviride was developed and examined. Three cleaved amplified polymorphic sequence (CAPS) markers could assist in distinguishing T. atroviride strains. The genomic regions identified may be useful for further exploration and development of more precise markers suitable for T. atroviride identification and monitoring, especially in environmental samples.
authors: Department of Plant Genetics Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776, Warszawa, Poland.
authors: Dominik
authors: D
authors: Skoneczny
authors: Michał
authors: M
authors: Oskiera
authors: Magdalena
authors: M
authors: Szczech
authors: Grzegorz
authors: G
authors: Bartoszewski
mesh_terms: D016000:Cluster Analysis; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D056426:Genetic Loci; D005819:Genetic Markers; D014644:Genetic Variation; D008969:Molecular Sequence Data; D058889:Molecular Typing; D016533:Mycological Typing Techniques; D020648:Peptide Elongation Factor 1 / Q000235:genetics; D010802:Phylogeny; D011044:Poland; D019105:Random Amplified Polymorphic DNA Technique; D017422:Sequence Analysis, DNA; D014242:Trichoderma / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D005819:Genetic Markers; D020648:Peptide Elongation Factor 1