Discriminatory simplex and multiplex PCR for four species of the genus Sclerotinia

Ahmed Abd-Elmagid, Patricia A. Garrido, Robert Hunger, Justin L. Lyles, Michele A. Mansfield, Beth Krueger Gugino, Damon L. Smith, Hassan A. Melouk, Carla D. Garzon

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Sclerotinia sclerotiorum (Lib.) de Bary, S. minor Jagger, S. trifoliorum Eriks, and S. homoeocarpa F.T. Benn are the most relevant plant pathogenic species within the genus Sclerotinia because of their large range of economically important hosts, including tomato, peanut, alfalfa, and turfgrass, among others. Species identification based on morphological characteristics is challenging and time demanding, especially when one crop hosts multiple species. The objective of this study was to design specific primers compatible with multiplexing, for rapid, sensitive and accurate detection and discrimination among four Sclerotinia species. Specific primers were designed for the aspartyl protease gene of S. sclerotiorum, the calmodulin gene of S. trifoliorum, the elongation factor-1 alpha gene of S. homoeocarpa, and the laccase 2 gene of S. minor. The specificity and sensitivity of each primer set was tested individually and in multiplex against isolates of each species and validated using genomic DNA from infected plants. Each primer set consistently amplified DNA of its target gene only. DNA fragments of different sizes were amplified: a 264. bp PCR product for S. minor, a 218. bp product for S. homoeocarpa, a 171. bp product for S. sclerotiorum, and a 97. bp product for S. trifoliorum. These primer sets can be used individually or in multiplex for identification of Sclerotinia spp. in pure culture or from infected plants. The multiplex assay had a lower sensitivity limit than the simplex assays (0.0001. pg/μL DNA of each species). The multiplex assay developed is an accurate and rapid tool to differentiate between the most relevant plant pathogenic Sclerotinia species in a single PCR reaction.

Original languageEnglish (US)
Pages (from-to)293-300
Number of pages8
JournalJournal of Microbiological Methods
Volume92
Issue number3
DOIs
StatePublished - Mar 1 2013

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Ascomycota
Multiplex Polymerase Chain Reaction
Genes
DNA
Plant DNA
Peptide Elongation Factor 1
Aspartic Acid Proteases
Laccase
Polymerase Chain Reaction
Medicago sativa
Lycopersicon esculentum
Calmodulin
Sensitivity and Specificity

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)

Cite this

Abd-Elmagid, A., Garrido, P. A., Hunger, R., Lyles, J. L., Mansfield, M. A., Gugino, B. K., ... Garzon, C. D. (2013). Discriminatory simplex and multiplex PCR for four species of the genus Sclerotinia. Journal of Microbiological Methods, 92(3), 293-300. https://doi.org/10.1016/j.mimet.2012.12.020
Abd-Elmagid, Ahmed ; Garrido, Patricia A. ; Hunger, Robert ; Lyles, Justin L. ; Mansfield, Michele A. ; Gugino, Beth Krueger ; Smith, Damon L. ; Melouk, Hassan A. ; Garzon, Carla D. / Discriminatory simplex and multiplex PCR for four species of the genus Sclerotinia. In: Journal of Microbiological Methods. 2013 ; Vol. 92, No. 3. pp. 293-300.
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Abd-Elmagid, A, Garrido, PA, Hunger, R, Lyles, JL, Mansfield, MA, Gugino, BK, Smith, DL, Melouk, HA & Garzon, CD 2013, 'Discriminatory simplex and multiplex PCR for four species of the genus Sclerotinia' Journal of Microbiological Methods, vol. 92, no. 3, pp. 293-300. https://doi.org/10.1016/j.mimet.2012.12.020

Discriminatory simplex and multiplex PCR for four species of the genus Sclerotinia. / Abd-Elmagid, Ahmed; Garrido, Patricia A.; Hunger, Robert; Lyles, Justin L.; Mansfield, Michele A.; Gugino, Beth Krueger; Smith, Damon L.; Melouk, Hassan A.; Garzon, Carla D.

In: Journal of Microbiological Methods, Vol. 92, No. 3, 01.03.2013, p. 293-300.

Research output: Contribution to journalArticle

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T1 - Discriminatory simplex and multiplex PCR for four species of the genus Sclerotinia

AU - Abd-Elmagid, Ahmed

AU - Garrido, Patricia A.

AU - Hunger, Robert

AU - Lyles, Justin L.

AU - Mansfield, Michele A.

AU - Gugino, Beth Krueger

AU - Smith, Damon L.

AU - Melouk, Hassan A.

AU - Garzon, Carla D.

PY - 2013/3/1

Y1 - 2013/3/1

N2 - Sclerotinia sclerotiorum (Lib.) de Bary, S. minor Jagger, S. trifoliorum Eriks, and S. homoeocarpa F.T. Benn are the most relevant plant pathogenic species within the genus Sclerotinia because of their large range of economically important hosts, including tomato, peanut, alfalfa, and turfgrass, among others. Species identification based on morphological characteristics is challenging and time demanding, especially when one crop hosts multiple species. The objective of this study was to design specific primers compatible with multiplexing, for rapid, sensitive and accurate detection and discrimination among four Sclerotinia species. Specific primers were designed for the aspartyl protease gene of S. sclerotiorum, the calmodulin gene of S. trifoliorum, the elongation factor-1 alpha gene of S. homoeocarpa, and the laccase 2 gene of S. minor. The specificity and sensitivity of each primer set was tested individually and in multiplex against isolates of each species and validated using genomic DNA from infected plants. Each primer set consistently amplified DNA of its target gene only. DNA fragments of different sizes were amplified: a 264. bp PCR product for S. minor, a 218. bp product for S. homoeocarpa, a 171. bp product for S. sclerotiorum, and a 97. bp product for S. trifoliorum. These primer sets can be used individually or in multiplex for identification of Sclerotinia spp. in pure culture or from infected plants. The multiplex assay had a lower sensitivity limit than the simplex assays (0.0001. pg/μL DNA of each species). The multiplex assay developed is an accurate and rapid tool to differentiate between the most relevant plant pathogenic Sclerotinia species in a single PCR reaction.

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