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SNaPshot and CE-SSCP: two simple and cost-effective methods to reveal genetic variability within a virus species

Delaunay Agnès, Dallot Sylvie, Filloux Denis, Dupuy Virginie, Roumagnac Philippe, Jacquot Emmanuel. 2015. SNaPshot and CE-SSCP: two simple and cost-effective methods to reveal genetic variability within a virus species. In : Plant pathology: techniques and protocols. Lacomme Christophe (ed.). New York : Springer [Etats-Unis], pp. 187-206. (Methods in Molecular Biology, 1302) ISBN 978-1-4939-2619-0

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Abstract : The multiplex SNaPshot and the capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) procedures are here used for rapid and high-throughput description of the molecular variability of viral populations. Both approaches are based on (1) standard amplification of genomic sequence(s), (2) labeled primers or labeled single-stranded DNA, and (3) migration of fluorescent-labeled molecules in capillary electrophoresis system. The SNaPshot technology was used to describe the diversity of 20 targeted single nucleotide polymorphisms (SNPs) selected from alignment of viral genomic sequences retrieved from public database. The CE-SSCP procedure was applied to identify the polymorphisms of two small (<500 bases in length) genomic regions of viral genomes. The different steps of SNaPshot and CE-SSCP setup procedures are presented using Potato virus Y (PVY, Potyvirus) and Plum pox virus (PPV, Potyvirus) RNA viruses as molecular targets, respectively. (Résumé d'auteur)

Classification Agris : H20 - Plant diseases
U30 - Research methods

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

  • Delaunay Agnès, INRA (FRA)
  • Dallot Sylvie, INRA (FRA)
  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Dupuy Virginie, CIRAD-BIOS-UMR CMAEE (FRA)
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-5002-6039
  • Jacquot Emmanuel, INRA (FRA)

Autres liens de la publication

Source : Cirad-Agritrop (https://agritrop.cirad.fr/576062/)

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