A Universally Primed-Polymerase Chain Reaction (UP-PCR) Marker to Discriminate Clonostachys rosea ACM941 from Related Strains

Demissie, Zerihun A.; Brown, William G.; Loewen, Michele C.

doi:10.3390/jof5020039

**A Universally Primed-Polymerase Chain Reaction (UP-PCR) Marker to Discriminate Clonostachys rosea ACM941 from Related Strains**

Journal Article · Tue May 14 00:00:00 EDT 2019 · Journal of Fungi

DOI:https://doi.org/10.3390/jof5020039· OSTI ID:1628394

Demissie, Zerihun A. ^[1]; Brown, William G. ^[2]; Loewen, Michele C. ^[3]

National Research Council of Canada, Ottawa, ON (Canada); DOE/OSTI
Adjuvants Plus Inc., Kingsville, ON (Canada)
National Research Council of Canada, Ottawa, ON (Canada); Queens University, Kingston, ON (Canada); University of Ottawa, ON (Canada)

Clonostachys rosea strain ACM941 is an effective biocontrol agent against several crop diseases including Fusarium head blight. In anticipation of its increased relevance going forward, the development of a reliable DNA-based molecular marker to track it is essential. Universally primed-PCR (UP-PCR) has been used successfully to differentiate other C. rosea strains. Herein, the development of a UP-PCR marker for ACM941 is described. A combination of two primers (AS15 and L45) produced a ~450 bp fragment that was unique to ACM941 compared to other commercial biocontrol agents. Primers subsequently designed based on the obtained fragment also produced a similarly unique band from ACM941 alone. BLAST analysis of the amplified sequence did not yield any homologous sequence in available online databases or within the closely related C. rosea IK726 and CBS125111 strains’ genomes. The specificity of this marker for ACM941 was validated against ten additional C. rosea strains isolated from Canada, with ACM941 producing the brightest band. Taken together, these results imply that the UP-PCR primers AS15 and L45 and the amplified fragment can be used to detect and monitor the ACM941 strain after its release into the environment.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1628394

Journal Information:: Journal of Fungi, Journal Name: Journal of Fungi Journal Issue: 2 Vol. 5; ISSN 2309-608X; ISSN JFOUCU

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

References (22)

Concentration and cultivar effects on efficacy of CLO-1 biofungicide in controlling Fusarium head blight of wheat Xue, Allen G.; Chen, Yuanhong; Voldeng, Harvey D. Biological Control, Vol. 73 https://doi.org/10.1016/j.biocontrol.2014.02.010	journal	June 2014
A new antibiotic kills pathogens without detectable resistance Ling, Losee L.; Schneider, Tanja; Peoples, Aaron J. Nature, Vol. 517, Issue 7535 https://doi.org/10.1038/nature14098	journal	January 2015
Nitrogen transformations in modern agriculture and the role of biological nitrification inhibition Coskun, Devrim; Britto, Dev T.; Shi, Weiming Nature Plants, Vol. 3, Issue 6 https://doi.org/10.1038/nplants.2017.74	journal	June 2017
The Taxonomic Position of Saccharomyces boulardii as Evaluated by Sequence Analysis of the D1/D2 Domain of 26S rDNA, the ITS1-5.8S rDNA-ITS2 Region and the Mitochondrial Cytochrome-c Oxidase II Gene van der Aa Kühle, Alis; Jespersen, Lene Systematic and Applied Microbiology, Vol. 26, Issue 4 https://doi.org/10.1078/072320203770865873	journal	January 2003
Biological control of fusarium head blight of wheat with Clonostachys rosea strain ACM941 Hue, A. G.; Voldeng, H. D.; Savard, M. E. Canadian Journal of Plant Pathology, Vol. 31, Issue 2 https://doi.org/10.1080/07060660909507590	journal	June 2009
Insights on the Evolution of Mycoparasitism from the Genome of Clonostachys rosea Karlsson, Magnus; Durling, Mikael Brandström; Choi, Jaeyoung Genome Biology and Evolution, Vol. 7, Issue 2 https://doi.org/10.1093/gbe/evu292	journal	January 2015
Genetic Relatedness Among Anastomosis Groups in Rhizoctonia as Measured by DNA/DNA Hybridization Vilgalys, Rytas Phytopathology, Vol. 78, Issue 6 https://doi.org/10.1094/phyto-78-698	journal	January 1988
Isolation of DNA Fragments from Polyacrylamide Gels by the Crush and Soak Method Sambrook, Joseph; Russell, David W. Cold Spring Harbor Protocols, Vol. 2006, Issue 1 https://doi.org/10.1101/pdb.prot2936	journal	June 2006
Improved template representation in cpn60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers Hill, Janet E.; Town, Jennifer R.; Hemmingsen, Sean M. Environmental Microbiology, Vol. 8, Issue 4 https://doi.org/10.1111/j.1462-2920.2005.00944.x	journal	April 2006
Food Security: The Challenge of Feeding 9 Billion People Godfray, H. C. J.; Beddington, J. R.; Crute, I. R. Science, Vol. 327, Issue 5967 https://doi.org/10.1126/science.1185383	journal	January 2010
Precise Detection and Tracing of Trichoderma hamatum 382 in Compost-Amended Potting Mixes by Using Molecular Markers Abbasi, Pervaiz A.; Miller, Sally A.; Meulia, Tea Applied and Environmental Microbiology, Vol. 65, Issue 12 https://doi.org/10.1128/aem.65.12.5421-5426.1999	journal	December 1999
Identification of a Universally Primed-PCR-Derived Sequence-Characterized Amplified Region Marker for an Antagonistic Strain of Clonostachys rosea and Development of a Strain-Specific PCR Detection Assay Bulat, S. A.; Lubeck, M.; Alekhina, I. A. Applied and Environmental Microbiology, Vol. 66, Issue 11 https://doi.org/10.1128/aem.66.11.4758-4763.2000	journal	November 2000
Fungal Molecular Systematics Bruns, T. D.; White, T. J.; Taylor, J. W. Annual Review of Ecology and Systematics, Vol. 22, Issue 1 https://doi.org/10.1146/annurev.es.22.110191.002521	journal	November 1991
Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi) Badotti, Fernanda; de Oliveira, Francislon Silva; Garcia, Cleverson Fernando BMC Microbiology, Vol. 17, Issue 1 https://doi.org/10.1186/s12866-017-0958-x	journal	February 2017
UP-PCR analysis and ITS1 ribotyping of strains of Trichoderma and Gliocladium Bulat, Sergey A.; Lübeck, Mette; Mironenko, Nina Mycological Research, Vol. 102, Issue 8 https://doi.org/10.1017/S0953756297005686	journal	August 1998
Delineation of Trichoderma harzianum into two different genotypic groups by a highly robust fingerprinting method, UP-PCR, and UP-PCR product cross-hybridization Lübeck, Mette; Alekhina, Irina A.; Lübeck, Peter Stephensen Mycological Research, Vol. 103, Issue 3 https://doi.org/10.1017/S0953756298007126	journal	March 1999
Fungal systematics: is a new age of enlightenment at hand? Hibbett, David S.; Taylor, John W. Nature Reviews Microbiology, Vol. 11, Issue 2 https://doi.org/10.1038/nrmicro2963	journal	January 2013
Genetic Relatedness Among Anastomosis Groups in Rhizoctonia as Measured by DNA/DNA Hybridization Vilgalys, Rytas Phytopathology, Vol. 78, Issue 6 https://doi.org/10.1094/Phyto-78-698	journal	January 1988
Precise Detection and Tracing of Trichoderma hamatum 382 in Compost-Amended Potting Mixes by Using Molecular Markers Abbasi, Pervaiz A.; Miller, Sally A.; Meulia, Tea Applied and Environmental Microbiology, Vol. 65, Issue 12 https://doi.org/10.1128/AEM.65.12.5421-5426.1999	journal	December 1999
Identification of a Universally Primed-PCR-Derived Sequence-Characterized Amplified Region Marker for an Antagonistic Strain of Clonostachys rosea and Development of a Strain-Specific PCR Detection Assay Bulat, S. A.; Lubeck, M.; Alekhina, I. A. Applied and Environmental Microbiology, Vol. 66, Issue 11 https://doi.org/10.1128/AEM.66.11.4758-4763.2000	journal	November 2000
Biological control of fusarium head blight of wheat with Clonostachys rosea strain ACM941 Xue, Allen; Chen, Yuanhong; Voldeng, Harvey Cereal Research Communications, Vol. 36, Issue Supplement 6 https://doi.org/10.1556/CRC.36.2008.Suppl.B.62	journal	September 2008
Profiling of the Transcriptomic Responses of Clonostachys rosea Upon Treatment With Fusarium graminearum Secretome Demissie, Zerihun A.; Foote, Simon J.; Tan, Yifang Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01061	journal	June 2018

Similar Records

Profiling of the Transcriptomic Responses of Clonostachys rosea Upon Treatment With Fusarium graminearum Secretome

Journal Article · Wed Jun 06 20:00:00 EDT 2018 · Frontiers in Microbiology · OSTI ID:1628167

Mitochondrial D-loop {open_quotes}signatures{close_quotes} produced by low-stringency single specific primer PCR constitute a simple comparative human identity test

Journal Article · Thu Feb 29 23:00:00 EST 1996 · American Journal of Human Genetics · OSTI ID:381809

[One-step PCR sequencing]. Final report, July 1, 1994--August 31, 1997

Technical Report · Tue Dec 30 23:00:00 EST 1997 · OSTI ID:353382

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
Clonostachys rosea
SCAR
UP-PCR
bio-fertilizer
biocontrol agent
genetic marker
sequence characterized amplified regions
universal primers

A Universally Primed-Polymerase Chain Reaction (UP-PCR) Marker to Discriminate Clonostachys rosea ACM941 from Related Strains

Citation Formats

References (22)

Similar Records

Related Subjects

**A Universally Primed-Polymerase Chain Reaction (UP-PCR) Marker to Discriminate Clonostachys rosea ACM941 from Related Strains**